Manganese in PDB 8ira: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay:
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay, PDB code: 8ira
was solved by
H.Li,
M.Suga,
J.R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.98 /
2.20
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.75,
231.6,
288.28,
90,
90,
90
|
|
R / Rfree (%)
|
14.9 /
18.3
|
Other elements in 8ira:
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay also contains other interesting chemical elements:
Manganese Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Manganese atom in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
(pdb code 8ira). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the
Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay, PDB code: 8ira:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 1 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:44.6
occ:0.40
|
MN1
|
A:OEX413
|
0.0
|
44.6
|
0.4
|
|
MN1
|
A:OEX413
|
0.0
|
46.1
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.9
|
0.4
|
|
OE2
|
A:GLU189
|
1.8
|
45.8
|
0.4
|
|
O1
|
A:OEX413
|
1.8
|
41.4
|
0.6
|
|
OE2
|
A:GLU189
|
1.8
|
46.1
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
54.9
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
63.5
|
0.6
|
|
OD2
|
A:ASP342
|
2.1
|
42.9
|
0.6
|
|
NE2
|
A:HIS332
|
2.1
|
47.0
|
0.6
|
|
NE2
|
A:HIS332
|
2.1
|
46.8
|
0.4
|
|
OD2
|
A:ASP342
|
2.2
|
42.2
|
0.4
|
|
O5
|
A:OEX413
|
2.6
|
63.0
|
0.4
|
|
O5
|
A:OEX413
|
2.7
|
73.0
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
48.6
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
46.5
|
0.6
|
|
CD
|
A:GLU189
|
2.9
|
50.2
|
0.4
|
|
CD
|
A:GLU189
|
3.0
|
50.8
|
0.6
|
|
CE1
|
A:HIS332
|
3.0
|
42.2
|
0.4
|
|
CG
|
A:ASP342
|
3.0
|
44.0
|
0.6
|
|
CE1
|
A:HIS332
|
3.1
|
42.1
|
0.6
|
|
CG
|
A:ASP342
|
3.1
|
43.3
|
0.4
|
|
CD2
|
A:HIS332
|
3.1
|
44.0
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
44.0
|
0.4
|
|
MN3
|
A:OEX413
|
3.2
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
3.2
|
46.5
|
0.4
|
|
OD1
|
A:ASP342
|
3.3
|
41.9
|
0.4
|
|
OD1
|
A:ASP342
|
3.4
|
41.5
|
0.6
|
|
O2
|
A:OEX413
|
3.4
|
47.0
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
47.4
|
0.4
|
|
OE1
|
A:GLU189
|
3.5
|
43.4
|
0.4
|
|
O2
|
A:OEX413
|
3.5
|
44.2
|
0.4
|
|
OE1
|
A:GLU189
|
3.6
|
57.5
|
0.6
|
|
OE1
|
A:GLU333
|
3.9
|
44.1
|
0.4
|
|
OE1
|
A:GLU333
|
3.9
|
43.7
|
0.6
|
|
NE2
|
A:HIS337
|
4.0
|
44.2
|
0.4
|
|
NE2
|
A:HIS337
|
4.0
|
44.3
|
0.6
|
|
CG
|
A:GLU189
|
4.1
|
46.1
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
46.0
|
0.6
|
|
O
|
A:HOH591
|
4.1
|
47.1
|
0.4
|
|
ND1
|
A:HIS332
|
4.1
|
41.0
|
0.4
|
|
ND1
|
A:HIS332
|
4.2
|
41.2
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
47.0
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.4
|
|
OXT
|
A:ALA344
|
4.2
|
45.5
|
0.6
|
|
OXT
|
A:ALA344
|
4.4
|
44.8
|
0.4
|
|
OE1
|
C:GLU354
|
4.4
|
53.5
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
45.5
|
0.6
|
|
O
|
A:HOH591
|
4.4
|
54.5
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
43.6
|
0.4
|
|
OE1
|
C:GLU354
|
4.5
|
52.8
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
50.4
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
50.9
|
0.6
|
|
CG1
|
A:VAL185
|
4.6
|
41.6
|
0.4
|
|
CE1
|
A:HIS337
|
4.6
|
45.9
|
0.4
|
|
CG1
|
A:VAL185
|
4.6
|
41.6
|
0.6
|
|
CE1
|
A:HIS337
|
4.6
|
45.8
|
0.6
|
|
O
|
A:HOH621
|
4.6
|
46.0
|
0.6
|
|
CD
|
A:GLU333
|
4.6
|
45.5
|
0.6
|
|
CD
|
A:GLU333
|
4.7
|
45.5
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
46.1
|
0.4
|
|
O
|
A:ALA344
|
4.7
|
52.1
|
0.4
|
|
O
|
A:ALA344
|
4.8
|
51.7
|
0.6
|
|
MN4
|
A:OEX413
|
4.9
|
48.8
|
0.4
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.6
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.4
|
|
O4
|
A:OEX413
|
4.9
|
44.5
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
53.0
|
0.4
|
|
CD
|
C:GLU354
|
4.9
|
53.8
|
0.6
|
|
O4
|
A:OEX413
|
5.0
|
44.3
|
0.4
|
|
OE2
|
A:GLU333
|
5.0
|
48.1
|
0.6
|
|
MN4
|
A:OEX413
|
5.0
|
52.2
|
0.6
|
|
OE2
|
A:GLU333
|
5.0
|
48.0
|
0.4
|
|
Manganese binding site 2 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 2 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.1
occ:0.60
|
MN1
|
A:OEX413
|
0.0
|
46.1
|
0.6
|
|
MN1
|
A:OEX413
|
0.0
|
44.6
|
0.4
|
|
O1
|
A:OEX413
|
1.7
|
41.9
|
0.4
|
|
O1
|
A:OEX413
|
1.8
|
41.4
|
0.6
|
|
OE2
|
A:GLU189
|
1.8
|
45.8
|
0.4
|
|
OE2
|
A:GLU189
|
1.9
|
46.1
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
54.9
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
63.5
|
0.6
|
|
OD2
|
A:ASP342
|
2.1
|
42.9
|
0.6
|
|
NE2
|
A:HIS332
|
2.1
|
47.0
|
0.6
|
|
NE2
|
A:HIS332
|
2.1
|
46.8
|
0.4
|
|
OD2
|
A:ASP342
|
2.2
|
42.2
|
0.4
|
|
O5
|
A:OEX413
|
2.6
|
63.0
|
0.4
|
|
O5
|
A:OEX413
|
2.7
|
73.0
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
48.6
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
46.5
|
0.6
|
|
CD
|
A:GLU189
|
2.9
|
50.2
|
0.4
|
|
CD
|
A:GLU189
|
3.0
|
50.8
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
44.0
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
43.3
|
0.4
|
|
CE1
|
A:HIS332
|
3.1
|
42.2
|
0.4
|
|
CE1
|
A:HIS332
|
3.1
|
42.1
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
44.0
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
44.0
|
0.4
|
|
MN3
|
A:OEX413
|
3.2
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
3.2
|
46.5
|
0.4
|
|
OD1
|
A:ASP342
|
3.3
|
41.9
|
0.4
|
|
OD1
|
A:ASP342
|
3.3
|
41.5
|
0.6
|
|
O2
|
A:OEX413
|
3.4
|
47.0
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
47.4
|
0.4
|
|
O2
|
A:OEX413
|
3.5
|
44.2
|
0.4
|
|
OE1
|
A:GLU189
|
3.5
|
43.4
|
0.4
|
|
OE1
|
A:GLU189
|
3.6
|
57.5
|
0.6
|
|
OE1
|
A:GLU333
|
3.9
|
44.1
|
0.4
|
|
OE1
|
A:GLU333
|
3.9
|
43.7
|
0.6
|
|
NE2
|
A:HIS337
|
3.9
|
44.2
|
0.4
|
|
NE2
|
A:HIS337
|
4.0
|
44.3
|
0.6
|
|
O
|
A:HOH591
|
4.1
|
47.1
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
46.1
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
46.0
|
0.6
|
|
ND1
|
A:HIS332
|
4.2
|
41.0
|
0.4
|
|
ND1
|
A:HIS332
|
4.2
|
41.2
|
0.6
|
|
OXT
|
A:ALA344
|
4.2
|
45.5
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
47.0
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
44.8
|
0.4
|
|
OE1
|
C:GLU354
|
4.4
|
53.5
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
45.5
|
0.6
|
|
OE1
|
C:GLU354
|
4.4
|
52.8
|
0.4
|
|
O
|
A:HOH591
|
4.4
|
54.5
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
43.6
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
50.4
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
50.9
|
0.6
|
|
CE1
|
A:HIS337
|
4.6
|
45.9
|
0.4
|
|
CG1
|
A:VAL185
|
4.6
|
41.6
|
0.4
|
|
CE1
|
A:HIS337
|
4.6
|
45.8
|
0.6
|
|
CG1
|
A:VAL185
|
4.6
|
41.6
|
0.6
|
|
CD
|
A:GLU333
|
4.6
|
45.5
|
0.6
|
|
O
|
A:HOH621
|
4.6
|
46.0
|
0.6
|
|
CD
|
A:GLU333
|
4.6
|
45.5
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
46.1
|
0.4
|
|
O
|
A:ALA344
|
4.7
|
52.1
|
0.4
|
|
O
|
A:ALA344
|
4.8
|
51.7
|
0.6
|
|
MN4
|
A:OEX413
|
4.8
|
48.8
|
0.4
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.6
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.4
|
|
O4
|
A:OEX413
|
4.9
|
44.5
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
53.8
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
53.0
|
0.4
|
|
O4
|
A:OEX413
|
4.9
|
44.3
|
0.4
|
|
MN4
|
A:OEX413
|
4.9
|
52.2
|
0.6
|
|
OE2
|
A:GLU333
|
4.9
|
48.1
|
0.6
|
|
OE2
|
A:GLU333
|
5.0
|
48.0
|
0.4
|
|
Manganese binding site 3 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 3 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:48.6
occ:0.40
|
MN2
|
A:OEX413
|
0.0
|
48.6
|
0.4
|
|
MN2
|
A:OEX413
|
0.1
|
46.5
|
0.6
|
|
OXT
|
A:ALA344
|
1.8
|
45.5
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.9
|
0.4
|
|
O2
|
A:OEX413
|
1.8
|
47.0
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.4
|
0.6
|
|
O2
|
A:OEX413
|
1.9
|
44.2
|
0.4
|
|
OXT
|
A:ALA344
|
1.9
|
44.8
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
63.5
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
54.9
|
0.4
|
|
OD1
|
A:ASP342
|
2.0
|
41.5
|
0.6
|
|
OE1
|
C:GLU354
|
2.1
|
53.5
|
0.6
|
|
OD1
|
A:ASP342
|
2.1
|
41.9
|
0.4
|
|
OE1
|
C:GLU354
|
2.1
|
52.8
|
0.4
|
|
MN1
|
A:OEX413
|
2.8
|
46.1
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.5
|
0.4
|
|
MN1
|
A:OEX413
|
2.8
|
44.6
|
0.4
|
|
C
|
A:ALA344
|
2.8
|
47.0
|
0.6
|
|
C
|
A:ALA344
|
2.8
|
47.0
|
0.4
|
|
CD
|
C:GLU354
|
2.9
|
53.8
|
0.6
|
|
CD
|
C:GLU354
|
2.9
|
53.0
|
0.4
|
|
CG
|
A:ASP342
|
2.9
|
44.0
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
43.3
|
0.4
|
|
OE2
|
C:GLU354
|
3.1
|
50.4
|
0.4
|
|
OE2
|
C:GLU354
|
3.1
|
50.9
|
0.6
|
|
OD2
|
A:ASP342
|
3.1
|
42.9
|
0.6
|
|
O
|
A:ALA344
|
3.1
|
52.1
|
0.4
|
|
O
|
A:ALA344
|
3.2
|
51.7
|
0.6
|
|
OD2
|
A:ASP342
|
3.3
|
42.2
|
0.4
|
|
CA1
|
A:OEX413
|
3.4
|
47.4
|
0.4
|
|
CA1
|
A:OEX413
|
3.4
|
50.4
|
0.6
|
|
O5
|
A:OEX413
|
3.5
|
63.0
|
0.4
|
|
O5
|
A:OEX413
|
3.6
|
73.0
|
0.6
|
|
NE2
|
A:HIS337
|
3.9
|
44.2
|
0.4
|
|
NE2
|
A:HIS337
|
3.9
|
44.3
|
0.6
|
|
O
|
C:HOH737
|
4.0
|
49.3
|
0.6
|
|
O
|
C:HOH737
|
4.0
|
49.2
|
0.4
|
|
O
|
A:HOH591
|
4.1
|
47.1
|
0.4
|
|
CA
|
A:ALA344
|
4.1
|
48.3
|
0.6
|
|
OE2
|
A:GLU189
|
4.2
|
46.1
|
0.6
|
|
OE2
|
A:GLU189
|
4.2
|
45.8
|
0.4
|
|
CA
|
A:ALA344
|
4.2
|
48.3
|
0.4
|
|
CG
|
C:GLU354
|
4.2
|
53.5
|
0.6
|
|
O4
|
A:OEX413
|
4.2
|
44.5
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
52.2
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.5
|
0.6
|
|
N
|
A:ALA344
|
4.3
|
53.4
|
0.4
|
|
O4
|
A:OEX413
|
4.3
|
44.3
|
0.4
|
|
CB
|
A:ASP342
|
4.3
|
45.5
|
0.6
|
|
O
|
A:HOH591
|
4.3
|
54.5
|
0.6
|
|
OE1
|
A:GLU333
|
4.3
|
43.7
|
0.6
|
|
OE1
|
A:GLU333
|
4.4
|
44.1
|
0.4
|
|
CD2
|
A:HIS337
|
4.4
|
47.1
|
0.6
|
|
CD2
|
A:HIS337
|
4.4
|
47.1
|
0.4
|
|
CB
|
A:ASP342
|
4.4
|
43.6
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
46.0
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
46.1
|
0.4
|
|
NE2
|
A:HIS332
|
4.6
|
46.8
|
0.4
|
|
NE2
|
A:HIS332
|
4.6
|
47.0
|
0.6
|
|
CA
|
A:ASP342
|
4.7
|
46.7
|
0.6
|
|
C
|
A:ASP342
|
4.7
|
47.3
|
0.6
|
|
OD1
|
A:ASP170
|
4.7
|
46.9
|
0.6
|
|
NH1
|
C:ARG357
|
4.8
|
43.6
|
0.4
|
|
CA
|
A:ASP342
|
4.8
|
46.4
|
0.4
|
|
CB
|
C:GLU354
|
4.8
|
40.2
|
0.6
|
|
NH1
|
C:ARG357
|
4.8
|
43.5
|
0.6
|
|
CB
|
C:GLU354
|
4.9
|
40.3
|
0.4
|
|
OD1
|
A:ASP170
|
4.9
|
45.0
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
50.8
|
0.6
|
|
C
|
A:ASP342
|
4.9
|
47.4
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
50.2
|
0.4
|
|
O
|
A:ASP342
|
4.9
|
51.2
|
0.6
|
|
OE1
|
A:GLU189
|
4.9
|
57.5
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
55.6
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
55.7
|
0.6
|
|
Manganese binding site 4 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 4 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.5
occ:0.60
|
MN2
|
A:OEX413
|
0.0
|
46.5
|
0.6
|
|
MN2
|
A:OEX413
|
0.1
|
48.6
|
0.4
|
|
OXT
|
A:ALA344
|
1.8
|
45.5
|
0.6
|
|
O2
|
A:OEX413
|
1.8
|
47.0
|
0.6
|
|
O1
|
A:OEX413
|
1.9
|
41.9
|
0.4
|
|
O1
|
A:OEX413
|
1.9
|
41.4
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
63.5
|
0.6
|
|
O2
|
A:OEX413
|
1.9
|
44.2
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
54.9
|
0.4
|
|
OXT
|
A:ALA344
|
1.9
|
44.8
|
0.4
|
|
OD1
|
A:ASP342
|
2.0
|
41.5
|
0.6
|
|
OE1
|
C:GLU354
|
2.0
|
53.5
|
0.6
|
|
OE1
|
C:GLU354
|
2.0
|
52.8
|
0.4
|
|
OD1
|
A:ASP342
|
2.1
|
41.9
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
47.8
|
0.6
|
|
MN1
|
A:OEX413
|
2.8
|
46.1
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.5
|
0.4
|
|
CD
|
C:GLU354
|
2.8
|
53.8
|
0.6
|
|
MN1
|
A:OEX413
|
2.8
|
44.6
|
0.4
|
|
CD
|
C:GLU354
|
2.8
|
53.0
|
0.4
|
|
CG
|
A:ASP342
|
2.9
|
44.0
|
0.6
|
|
C
|
A:ALA344
|
2.9
|
47.0
|
0.6
|
|
C
|
A:ALA344
|
2.9
|
47.0
|
0.4
|
|
CG
|
A:ASP342
|
3.0
|
43.3
|
0.4
|
|
OE2
|
C:GLU354
|
3.0
|
50.4
|
0.4
|
|
OE2
|
C:GLU354
|
3.1
|
50.9
|
0.6
|
|
OD2
|
A:ASP342
|
3.1
|
42.9
|
0.6
|
|
O
|
A:ALA344
|
3.2
|
52.1
|
0.4
|
|
O
|
A:ALA344
|
3.2
|
51.7
|
0.6
|
|
OD2
|
A:ASP342
|
3.3
|
42.2
|
0.4
|
|
CA1
|
A:OEX413
|
3.4
|
47.4
|
0.4
|
|
CA1
|
A:OEX413
|
3.4
|
50.4
|
0.6
|
|
O5
|
A:OEX413
|
3.6
|
63.0
|
0.4
|
|
O5
|
A:OEX413
|
3.6
|
73.0
|
0.6
|
|
NE2
|
A:HIS337
|
3.8
|
44.2
|
0.4
|
|
NE2
|
A:HIS337
|
3.8
|
44.3
|
0.6
|
|
O
|
C:HOH737
|
4.0
|
49.3
|
0.6
|
|
O
|
C:HOH737
|
4.0
|
49.2
|
0.4
|
|
O
|
A:HOH591
|
4.1
|
47.1
|
0.4
|
|
CG
|
C:GLU354
|
4.1
|
53.5
|
0.6
|
|
OE2
|
A:GLU189
|
4.2
|
46.1
|
0.6
|
|
CA
|
A:ALA344
|
4.2
|
48.3
|
0.6
|
|
OE2
|
A:GLU189
|
4.2
|
45.8
|
0.4
|
|
O4
|
A:OEX413
|
4.2
|
44.5
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
52.2
|
0.4
|
|
CA
|
A:ALA344
|
4.2
|
48.3
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.5
|
0.6
|
|
O4
|
A:OEX413
|
4.3
|
44.3
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.4
|
0.4
|
|
CB
|
A:ASP342
|
4.3
|
45.5
|
0.6
|
|
OE1
|
A:GLU333
|
4.3
|
43.7
|
0.6
|
|
CD2
|
A:HIS337
|
4.3
|
47.1
|
0.6
|
|
OE1
|
A:GLU333
|
4.3
|
44.1
|
0.4
|
|
CD2
|
A:HIS337
|
4.3
|
47.1
|
0.4
|
|
O
|
A:HOH591
|
4.4
|
54.5
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
43.6
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
46.0
|
0.6
|
|
NE2
|
A:HIS332
|
4.6
|
46.8
|
0.4
|
|
NE2
|
A:HIS332
|
4.6
|
47.0
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
46.1
|
0.4
|
|
CA
|
A:ASP342
|
4.7
|
46.7
|
0.6
|
|
C
|
A:ASP342
|
4.7
|
47.3
|
0.6
|
|
OD1
|
A:ASP170
|
4.8
|
46.9
|
0.6
|
|
CB
|
C:GLU354
|
4.8
|
40.2
|
0.6
|
|
CA
|
A:ASP342
|
4.8
|
46.4
|
0.4
|
|
NH1
|
C:ARG357
|
4.8
|
43.6
|
0.4
|
|
CB
|
C:GLU354
|
4.8
|
40.3
|
0.4
|
|
NH1
|
C:ARG357
|
4.9
|
43.5
|
0.6
|
|
OD1
|
A:ASP170
|
4.9
|
45.0
|
0.4
|
|
C
|
A:ASP342
|
4.9
|
47.4
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
50.8
|
0.6
|
|
O
|
A:ASP342
|
4.9
|
51.2
|
0.6
|
|
CD
|
A:GLU189
|
4.9
|
50.2
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
55.6
|
0.4
|
|
OE1
|
A:GLU189
|
5.0
|
57.5
|
0.6
|
|
CZ
|
C:ARG357
|
5.0
|
55.7
|
0.6
|
|
CE1
|
A:HIS337
|
5.0
|
45.9
|
0.4
|
|
Manganese binding site 5 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 5 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.5
occ:0.40
|
MN3
|
A:OEX413
|
0.0
|
46.5
|
0.4
|
|
MN3
|
A:OEX413
|
0.0
|
47.8
|
0.6
|
|
O2
|
A:OEX413
|
1.8
|
44.2
|
0.4
|
|
O2
|
A:OEX413
|
1.9
|
47.0
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.5
|
0.6
|
|
OE1
|
A:GLU333
|
1.9
|
43.7
|
0.6
|
|
OE2
|
C:GLU354
|
1.9
|
50.9
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.3
|
0.4
|
|
O5
|
A:OEX413
|
2.0
|
63.0
|
0.4
|
|
OE1
|
A:GLU333
|
2.0
|
44.1
|
0.4
|
|
O5
|
A:OEX413
|
2.0
|
73.0
|
0.6
|
|
O3
|
A:OEX413
|
2.0
|
63.5
|
0.6
|
|
OE2
|
C:GLU354
|
2.0
|
50.4
|
0.4
|
|
O3
|
A:OEX413
|
2.1
|
54.9
|
0.4
|
|
MN4
|
A:OEX413
|
2.8
|
48.8
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
46.5
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
48.6
|
0.4
|
|
MN4
|
A:OEX413
|
2.8
|
52.2
|
0.6
|
|
CD
|
A:GLU333
|
2.8
|
45.5
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.4
|
|
CD
|
C:GLU354
|
2.9
|
53.8
|
0.6
|
|
CD
|
C:GLU354
|
3.0
|
53.0
|
0.4
|
|
OE2
|
A:GLU333
|
3.1
|
48.1
|
0.6
|
|
OE2
|
A:GLU333
|
3.1
|
48.0
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
46.1
|
0.6
|
|
MN1
|
A:OEX413
|
3.2
|
44.6
|
0.4
|
|
OE1
|
C:GLU354
|
3.3
|
53.5
|
0.6
|
|
OE1
|
C:GLU354
|
3.3
|
52.8
|
0.4
|
|
O1
|
A:OEX413
|
3.4
|
41.9
|
0.4
|
|
O1
|
A:OEX413
|
3.5
|
41.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
47.4
|
0.4
|
|
CA1
|
A:OEX413
|
3.6
|
50.4
|
0.6
|
|
NH2
|
C:ARG357
|
3.9
|
46.0
|
0.6
|
|
NH2
|
C:ARG357
|
3.9
|
46.1
|
0.4
|
|
OD1
|
A:ASP170
|
4.0
|
46.9
|
0.6
|
|
OD2
|
A:ASP170
|
4.1
|
41.9
|
0.6
|
|
NE2
|
A:HIS337
|
4.1
|
44.3
|
0.6
|
|
NE2
|
A:HIS337
|
4.1
|
44.2
|
0.4
|
|
OD2
|
A:ASP170
|
4.1
|
42.2
|
0.4
|
|
O
|
C:HOH689
|
4.1
|
41.4
|
0.4
|
|
NE2
|
A:HIS332
|
4.2
|
46.8
|
0.4
|
|
OD1
|
A:ASP170
|
4.2
|
45.0
|
0.4
|
|
NE2
|
A:HIS332
|
4.2
|
47.0
|
0.6
|
|
O
|
A:HOH515
|
4.2
|
49.3
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
53.5
|
0.6
|
|
CG
|
A:GLU333
|
4.2
|
45.6
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
52.2
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
45.5
|
0.6
|
|
O
|
A:HOH515
|
4.3
|
44.0
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
45.6
|
0.4
|
|
OXT
|
A:ALA344
|
4.4
|
44.8
|
0.4
|
|
O
|
A:HOH544
|
4.4
|
42.8
|
0.6
|
|
O
|
A:HOH544
|
4.4
|
40.3
|
0.4
|
|
OD1
|
A:ASP342
|
4.4
|
41.5
|
0.6
|
|
CD2
|
A:HIS332
|
4.5
|
44.0
|
0.4
|
|
CG
|
A:ASP170
|
4.5
|
42.7
|
0.6
|
|
CD2
|
A:HIS332
|
4.5
|
44.0
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
41.9
|
0.4
|
|
O
|
A:HOH548
|
4.6
|
42.7
|
0.4
|
|
OD2
|
A:ASP342
|
4.6
|
42.9
|
0.6
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.4
|
|
OE2
|
A:GLU189
|
4.6
|
46.1
|
0.6
|
|
O
|
A:ALA344
|
4.6
|
52.1
|
0.4
|
|
O
|
A:HOH548
|
4.6
|
42.8
|
0.6
|
|
CB
|
A:GLU333
|
4.6
|
45.3
|
0.6
|
|
OE2
|
A:GLU189
|
4.6
|
45.8
|
0.4
|
|
CB
|
A:GLU333
|
4.7
|
45.0
|
0.4
|
|
O
|
A:ALA344
|
4.7
|
51.7
|
0.6
|
|
OD2
|
A:ASP342
|
4.8
|
42.2
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
45.9
|
0.4
|
|
O
|
A:HOH621
|
4.8
|
46.1
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
45.8
|
0.6
|
|
O
|
A:HOH621
|
4.8
|
46.0
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
55.6
|
0.4
|
|
C
|
A:ALA344
|
5.0
|
47.0
|
0.6
|
|
CG
|
A:ASP342
|
5.0
|
44.0
|
0.6
|
|
C
|
A:ALA344
|
5.0
|
47.0
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
55.7
|
0.6
|
|
Manganese binding site 6 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 6 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:47.8
occ:0.60
|
MN3
|
A:OEX413
|
0.0
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
0.0
|
46.5
|
0.4
|
|
O2
|
A:OEX413
|
1.8
|
44.2
|
0.4
|
|
O2
|
A:OEX413
|
1.8
|
47.0
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.5
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.3
|
0.4
|
|
O5
|
A:OEX413
|
1.9
|
63.0
|
0.4
|
|
OE2
|
C:GLU354
|
2.0
|
50.9
|
0.6
|
|
OE1
|
A:GLU333
|
2.0
|
43.7
|
0.6
|
|
O5
|
A:OEX413
|
2.0
|
73.0
|
0.6
|
|
OE1
|
A:GLU333
|
2.0
|
44.1
|
0.4
|
|
O3
|
A:OEX413
|
2.0
|
63.5
|
0.6
|
|
OE2
|
C:GLU354
|
2.0
|
50.4
|
0.4
|
|
O3
|
A:OEX413
|
2.1
|
54.9
|
0.4
|
|
MN4
|
A:OEX413
|
2.8
|
48.8
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
46.5
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
48.6
|
0.4
|
|
MN4
|
A:OEX413
|
2.8
|
52.2
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.6
|
|
CD
|
C:GLU354
|
2.9
|
53.8
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.4
|
|
CD
|
C:GLU354
|
3.0
|
53.0
|
0.4
|
|
OE2
|
A:GLU333
|
3.1
|
48.1
|
0.6
|
|
OE2
|
A:GLU333
|
3.2
|
48.0
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
46.1
|
0.6
|
|
MN1
|
A:OEX413
|
3.2
|
44.6
|
0.4
|
|
OE1
|
C:GLU354
|
3.3
|
53.5
|
0.6
|
|
OE1
|
C:GLU354
|
3.3
|
52.8
|
0.4
|
|
O1
|
A:OEX413
|
3.4
|
41.9
|
0.4
|
|
O1
|
A:OEX413
|
3.5
|
41.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
47.4
|
0.4
|
|
CA1
|
A:OEX413
|
3.6
|
50.4
|
0.6
|
|
NH2
|
C:ARG357
|
3.9
|
46.0
|
0.6
|
|
NH2
|
C:ARG357
|
3.9
|
46.1
|
0.4
|
|
OD1
|
A:ASP170
|
3.9
|
46.9
|
0.6
|
|
OD2
|
A:ASP170
|
4.1
|
41.9
|
0.6
|
|
OD2
|
A:ASP170
|
4.1
|
42.2
|
0.4
|
|
NE2
|
A:HIS337
|
4.1
|
44.3
|
0.6
|
|
NE2
|
A:HIS337
|
4.1
|
44.2
|
0.4
|
|
O
|
C:HOH689
|
4.2
|
41.4
|
0.4
|
|
OD1
|
A:ASP170
|
4.2
|
45.0
|
0.4
|
|
NE2
|
A:HIS332
|
4.2
|
46.8
|
0.4
|
|
O
|
A:HOH515
|
4.2
|
49.3
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
53.5
|
0.6
|
|
NE2
|
A:HIS332
|
4.2
|
47.0
|
0.6
|
|
OXT
|
A:ALA344
|
4.2
|
45.5
|
0.6
|
|
CG
|
C:GLU354
|
4.3
|
52.2
|
0.4
|
|
O
|
A:HOH515
|
4.3
|
44.0
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
45.6
|
0.6
|
|
CG
|
A:GLU333
|
4.3
|
45.6
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
44.8
|
0.4
|
|
O
|
A:HOH544
|
4.4
|
42.8
|
0.6
|
|
CG
|
A:ASP170
|
4.4
|
42.7
|
0.6
|
|
O
|
A:HOH544
|
4.4
|
40.3
|
0.4
|
|
OD1
|
A:ASP342
|
4.4
|
41.5
|
0.6
|
|
CD2
|
A:HIS332
|
4.5
|
44.0
|
0.4
|
|
CD2
|
A:HIS332
|
4.5
|
44.0
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
41.9
|
0.4
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.4
|
|
O
|
A:ALA344
|
4.6
|
52.1
|
0.4
|
|
O
|
A:HOH548
|
4.6
|
42.7
|
0.4
|
|
OD2
|
A:ASP342
|
4.6
|
42.9
|
0.6
|
|
OE2
|
A:GLU189
|
4.6
|
46.1
|
0.6
|
|
O
|
A:HOH548
|
4.6
|
42.8
|
0.6
|
|
OE2
|
A:GLU189
|
4.6
|
45.8
|
0.4
|
|
CB
|
A:GLU333
|
4.7
|
45.3
|
0.6
|
|
O
|
A:ALA344
|
4.7
|
51.7
|
0.6
|
|
CB
|
A:GLU333
|
4.7
|
45.0
|
0.4
|
|
OD2
|
A:ASP342
|
4.8
|
42.2
|
0.4
|
|
O
|
A:HOH621
|
4.8
|
46.1
|
0.4
|
|
O
|
A:HOH621
|
4.8
|
46.0
|
0.6
|
|
CE1
|
A:HIS337
|
4.8
|
45.9
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
45.8
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
55.6
|
0.4
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.6
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
55.7
|
0.6
|
|
CG
|
A:ASP342
|
5.0
|
44.0
|
0.6
|
|
Manganese binding site 7 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 7 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:48.8
occ:0.40
|
MN4
|
A:OEX413
|
0.0
|
48.8
|
0.4
|
|
MN4
|
A:OEX413
|
0.2
|
52.2
|
0.6
|
|
OD2
|
A:ASP170
|
1.8
|
41.9
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.3
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
44.5
|
0.6
|
|
OE2
|
A:GLU333
|
1.9
|
48.1
|
0.6
|
|
O
|
A:HOH544
|
2.0
|
42.8
|
0.6
|
|
OD2
|
A:ASP170
|
2.0
|
42.2
|
0.4
|
|
OE2
|
A:GLU333
|
2.1
|
48.0
|
0.4
|
|
O
|
A:HOH544
|
2.1
|
40.3
|
0.4
|
|
O5
|
A:OEX413
|
2.2
|
73.0
|
0.6
|
|
O
|
A:HOH548
|
2.3
|
42.7
|
0.4
|
|
O5
|
A:OEX413
|
2.3
|
63.0
|
0.4
|
|
O
|
A:HOH548
|
2.3
|
42.8
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.5
|
0.4
|
|
CG
|
A:ASP170
|
2.9
|
42.7
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.6
|
|
CD
|
A:GLU333
|
3.0
|
45.5
|
0.4
|
|
CG
|
A:ASP170
|
3.1
|
42.6
|
0.4
|
|
OE1
|
A:GLU333
|
3.2
|
43.7
|
0.6
|
|
OE1
|
A:GLU333
|
3.2
|
44.1
|
0.4
|
|
OD1
|
A:ASP170
|
3.2
|
46.9
|
0.6
|
|
OD1
|
A:ASP170
|
3.5
|
45.0
|
0.4
|
|
O
|
A:HOH621
|
3.7
|
46.1
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.2
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
47.0
|
0.6
|
|
O
|
A:HOH621
|
3.7
|
46.0
|
0.6
|
|
O
|
A:HOH515
|
3.8
|
44.0
|
0.4
|
|
CA1
|
A:OEX413
|
3.8
|
47.4
|
0.4
|
|
O
|
A:HOH515
|
3.9
|
49.3
|
0.6
|
|
CA1
|
A:OEX413
|
4.0
|
50.4
|
0.6
|
|
OD1
|
A:ASP61
|
4.1
|
45.3
|
0.6
|
|
O
|
A:HOH561
|
4.1
|
43.8
|
0.4
|
|
O
|
A:HOH628
|
4.1
|
53.5
|
0.6
|
|
CB
|
A:ASP170
|
4.2
|
43.6
|
0.6
|
|
O
|
A:HOH561
|
4.2
|
44.8
|
0.6
|
|
O
|
A:HOH628
|
4.2
|
51.8
|
0.4
|
|
OD1
|
A:ASP61
|
4.2
|
45.0
|
0.4
|
|
CG
|
A:GLU333
|
4.2
|
45.6
|
0.6
|
|
OE2
|
C:GLU354
|
4.3
|
50.9
|
0.6
|
|
O
|
A:SER169
|
4.3
|
48.0
|
0.6
|
|
CG
|
A:GLU333
|
4.4
|
45.6
|
0.4
|
|
CB
|
A:ASP170
|
4.4
|
43.4
|
0.4
|
|
OE2
|
C:GLU354
|
4.4
|
50.4
|
0.4
|
|
NH2
|
C:ARG357
|
4.4
|
46.1
|
0.4
|
|
CA
|
A:ASP170
|
4.4
|
48.9
|
0.6
|
|
NH2
|
C:ARG357
|
4.5
|
46.0
|
0.6
|
|
O
|
A:SER169
|
4.5
|
47.5
|
0.4
|
|
O3
|
A:OEX413
|
4.5
|
63.5
|
0.6
|
|
CA
|
A:ASP170
|
4.6
|
48.6
|
0.4
|
|
O3
|
A:OEX413
|
4.6
|
54.9
|
0.4
|
|
MN1
|
A:OEX413
|
4.8
|
46.1
|
0.6
|
|
C
|
A:SER169
|
4.9
|
49.8
|
0.6
|
|
MN1
|
A:OEX413
|
4.9
|
44.6
|
0.4
|
|
N
|
A:ASP170
|
4.9
|
44.9
|
0.6
|
|
O
|
D:HOH510
|
4.9
|
45.5
|
0.4
|
|
O
|
D:HOH510
|
4.9
|
45.3
|
0.6
|
|
C
|
A:SER169
|
5.0
|
49.7
|
0.4
|
|
CG
|
A:ASP61
|
5.0
|
47.9
|
0.6
|
|
Manganese binding site 8 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 8 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:52.2
occ:0.60
|
MN4
|
A:OEX413
|
0.0
|
52.2
|
0.6
|
|
MN4
|
A:OEX413
|
0.2
|
48.8
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
44.3
|
0.4
|
|
OE2
|
A:GLU333
|
1.9
|
48.1
|
0.6
|
|
OD2
|
A:ASP170
|
1.9
|
41.9
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
44.5
|
0.6
|
|
OE2
|
A:GLU333
|
2.0
|
48.0
|
0.4
|
|
O
|
A:HOH544
|
2.0
|
42.8
|
0.6
|
|
OD2
|
A:ASP170
|
2.1
|
42.2
|
0.4
|
|
O
|
A:HOH544
|
2.1
|
40.3
|
0.4
|
|
O
|
A:HOH548
|
2.1
|
42.7
|
0.4
|
|
O
|
A:HOH548
|
2.2
|
42.8
|
0.6
|
|
O5
|
A:OEX413
|
2.3
|
73.0
|
0.6
|
|
O5
|
A:OEX413
|
2.4
|
63.0
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
47.8
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.5
|
0.4
|
|
CD
|
A:GLU333
|
2.8
|
45.5
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.4
|
|
CG
|
A:ASP170
|
2.9
|
42.7
|
0.6
|
|
OE1
|
A:GLU333
|
3.1
|
43.7
|
0.6
|
|
CG
|
A:ASP170
|
3.2
|
42.6
|
0.4
|
|
OE1
|
A:GLU333
|
3.2
|
44.1
|
0.4
|
|
OD1
|
A:ASP170
|
3.3
|
46.9
|
0.6
|
|
OD1
|
A:ASP170
|
3.6
|
45.0
|
0.4
|
|
O
|
A:HOH515
|
3.7
|
44.0
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.2
|
0.4
|
|
O2
|
A:OEX413
|
3.8
|
47.0
|
0.6
|
|
O
|
A:HOH621
|
3.8
|
46.1
|
0.4
|
|
O
|
A:HOH515
|
3.8
|
49.3
|
0.6
|
|
O
|
A:HOH621
|
3.9
|
46.0
|
0.6
|
|
OD1
|
A:ASP61
|
3.9
|
45.3
|
0.6
|
|
CA1
|
A:OEX413
|
4.0
|
47.4
|
0.4
|
|
OD1
|
A:ASP61
|
4.1
|
45.0
|
0.4
|
|
O
|
A:HOH561
|
4.1
|
43.8
|
0.4
|
|
CA1
|
A:OEX413
|
4.1
|
50.4
|
0.6
|
|
O
|
A:HOH561
|
4.1
|
44.8
|
0.6
|
|
CG
|
A:GLU333
|
4.2
|
45.6
|
0.6
|
|
O
|
A:HOH628
|
4.2
|
53.5
|
0.6
|
|
CB
|
A:ASP170
|
4.3
|
43.6
|
0.6
|
|
OE2
|
C:GLU354
|
4.3
|
50.9
|
0.6
|
|
O
|
A:HOH628
|
4.3
|
51.8
|
0.4
|
|
O
|
A:SER169
|
4.3
|
48.0
|
0.6
|
|
CG
|
A:GLU333
|
4.3
|
45.6
|
0.4
|
|
OE2
|
C:GLU354
|
4.4
|
50.4
|
0.4
|
|
O
|
A:SER169
|
4.4
|
47.5
|
0.4
|
|
NH2
|
C:ARG357
|
4.4
|
46.1
|
0.4
|
|
CB
|
A:ASP170
|
4.5
|
43.4
|
0.4
|
|
CA
|
A:ASP170
|
4.5
|
48.9
|
0.6
|
|
NH2
|
C:ARG357
|
4.5
|
46.0
|
0.6
|
|
O3
|
A:OEX413
|
4.6
|
63.5
|
0.6
|
|
CA
|
A:ASP170
|
4.6
|
48.6
|
0.4
|
|
O3
|
A:OEX413
|
4.6
|
54.9
|
0.4
|
|
O
|
D:HOH510
|
4.8
|
45.5
|
0.4
|
|
O
|
D:HOH510
|
4.8
|
45.3
|
0.6
|
|
C
|
A:SER169
|
4.8
|
49.8
|
0.6
|
|
CG
|
A:ASP61
|
4.9
|
47.9
|
0.6
|
|
N
|
A:ASP170
|
4.9
|
44.9
|
0.6
|
|
MN1
|
A:OEX413
|
4.9
|
46.1
|
0.6
|
|
C
|
A:SER169
|
4.9
|
49.7
|
0.4
|
|
MN1
|
A:OEX413
|
5.0
|
44.6
|
0.4
|
|
CG
|
A:ASP61
|
5.0
|
47.8
|
0.4
|
|
Manganese binding site 9 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 9 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn411
b:48.2
occ:0.40
|
MN1
|
a:OEX411
|
0.0
|
48.2
|
0.4
|
|
MN1
|
a:OEX411
|
0.0
|
48.4
|
0.6
|
|
O1
|
a:OEX411
|
1.8
|
50.3
|
0.6
|
|
OE2
|
a:GLU189
|
1.8
|
52.9
|
0.4
|
|
O1
|
a:OEX411
|
1.8
|
49.7
|
0.4
|
|
OE2
|
a:GLU189
|
1.8
|
54.0
|
0.6
|
|
O3
|
a:OEX411
|
1.9
|
46.1
|
0.6
|
|
O3
|
a:OEX411
|
1.9
|
46.1
|
0.4
|
|
NE2
|
a:HIS332
|
2.1
|
51.1
|
0.6
|
|
NE2
|
a:HIS332
|
2.1
|
50.8
|
0.4
|
|
OD2
|
a:ASP342
|
2.1
|
48.5
|
0.6
|
|
OD2
|
a:ASP342
|
2.1
|
48.3
|
0.4
|
|
O5
|
a:OEX411
|
2.6
|
52.1
|
0.4
|
|
O5
|
a:OEX411
|
2.6
|
52.5
|
0.6
|
|
MN2
|
a:OEX411
|
2.8
|
50.8
|
0.4
|
|
MN2
|
a:OEX411
|
2.8
|
51.1
|
0.6
|
|
CD
|
a:GLU189
|
2.9
|
49.4
|
0.4
|
|
CE1
|
a:HIS332
|
2.9
|
52.3
|
0.4
|
|
CE1
|
a:HIS332
|
2.9
|
53.0
|
0.6
|
|
CD
|
a:GLU189
|
2.9
|
49.4
|
0.6
|
|
CG
|
a:ASP342
|
3.0
|
51.1
|
0.6
|
|
CG
|
a:ASP342
|
3.1
|
51.2
|
0.4
|
|
CD2
|
a:HIS332
|
3.1
|
53.6
|
0.6
|
|
CD2
|
a:HIS332
|
3.2
|
53.5
|
0.4
|
|
OD1
|
a:ASP342
|
3.2
|
51.2
|
0.6
|
|
MN3
|
a:OEX411
|
3.2
|
52.0
|
0.6
|
|
OD1
|
a:ASP342
|
3.3
|
51.4
|
0.4
|
|
MN3
|
a:OEX411
|
3.3
|
49.0
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
49.6
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
52.5
|
0.6
|
|
CA1
|
a:OEX411
|
3.5
|
56.8
|
0.6
|
|
O2
|
a:OEX411
|
3.5
|
48.1
|
0.6
|
|
CA1
|
a:OEX411
|
3.5
|
52.9
|
0.4
|
|
O2
|
a:OEX411
|
3.6
|
47.5
|
0.4
|
|
OE1
|
a:GLU333
|
3.7
|
50.9
|
0.6
|
|
OE1
|
a:GLU333
|
3.9
|
50.5
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
53.8
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
53.8
|
0.6
|
|
ND1
|
a:HIS332
|
4.1
|
48.8
|
0.4
|
|
ND1
|
a:HIS332
|
4.1
|
48.9
|
0.6
|
|
CG
|
a:GLU189
|
4.1
|
54.6
|
0.4
|
|
O
|
a:HOH591
|
4.1
|
55.2
|
0.4
|
|
CG
|
a:GLU189
|
4.2
|
54.5
|
0.6
|
|
CG
|
a:HIS332
|
4.2
|
49.8
|
0.6
|
|
CG
|
a:HIS332
|
4.2
|
49.7
|
0.4
|
|
O
|
a:HOH591
|
4.3
|
56.5
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
54.5
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
53.6
|
0.4
|
|
CB
|
a:ASP342
|
4.4
|
45.1
|
0.6
|
|
CB
|
a:ASP342
|
4.4
|
45.4
|
0.4
|
|
OE1
|
c:GLU354
|
4.5
|
50.0
|
0.4
|
|
OE1
|
c:GLU354
|
4.5
|
50.3
|
0.6
|
|
CD
|
a:GLU333
|
4.5
|
53.0
|
0.6
|
|
CG1
|
a:VAL185
|
4.6
|
44.6
|
0.4
|
|
OE2
|
c:GLU354
|
4.6
|
50.0
|
0.6
|
|
CG1
|
a:VAL185
|
4.6
|
44.5
|
0.6
|
|
O
|
a:ALA344
|
4.6
|
52.6
|
0.6
|
|
OE2
|
c:GLU354
|
4.6
|
48.2
|
0.4
|
|
CD
|
a:GLU333
|
4.7
|
52.4
|
0.4
|
|
CE1
|
a:HIS337
|
4.7
|
49.5
|
0.4
|
|
O
|
a:ALA344
|
4.7
|
51.9
|
0.4
|
|
O
|
a:HOH620
|
4.8
|
54.1
|
0.6
|
|
CE1
|
a:HIS337
|
4.8
|
49.5
|
0.6
|
|
O
|
a:HOH620
|
4.8
|
54.0
|
0.4
|
|
MN4
|
a:OEX411
|
4.8
|
48.4
|
0.4
|
|
C
|
a:ALA344
|
4.8
|
52.5
|
0.6
|
|
C
|
a:ALA344
|
4.9
|
52.5
|
0.4
|
|
OE2
|
a:GLU333
|
4.9
|
50.7
|
0.6
|
|
MN4
|
a:OEX411
|
4.9
|
53.1
|
0.6
|
|
CD
|
c:GLU354
|
5.0
|
51.8
|
0.4
|
|
Manganese binding site 10 out
of 16 in 8ira
Go back to
Manganese Binding Sites List in 8ira
Manganese binding site 10 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 200-Microsecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn411
b:48.4
occ:0.60
|
MN1
|
a:OEX411
|
0.0
|
48.4
|
0.6
|
|
MN1
|
a:OEX411
|
0.0
|
48.2
|
0.4
|
|
O1
|
a:OEX411
|
1.8
|
50.3
|
0.6
|
|
O1
|
a:OEX411
|
1.8
|
49.7
|
0.4
|
|
OE2
|
a:GLU189
|
1.8
|
52.9
|
0.4
|
|
O3
|
a:OEX411
|
1.8
|
46.1
|
0.6
|
|
O3
|
a:OEX411
|
1.8
|
46.1
|
0.4
|
|
OE2
|
a:GLU189
|
1.8
|
54.0
|
0.6
|
|
NE2
|
a:HIS332
|
2.1
|
51.1
|
0.6
|
|
OD2
|
a:ASP342
|
2.1
|
48.5
|
0.6
|
|
NE2
|
a:HIS332
|
2.1
|
50.8
|
0.4
|
|
OD2
|
a:ASP342
|
2.1
|
48.3
|
0.4
|
|
O5
|
a:OEX411
|
2.6
|
52.1
|
0.4
|
|
O5
|
a:OEX411
|
2.7
|
52.5
|
0.6
|
|
MN2
|
a:OEX411
|
2.8
|
50.8
|
0.4
|
|
MN2
|
a:OEX411
|
2.8
|
51.1
|
0.6
|
|
CE1
|
a:HIS332
|
2.9
|
52.3
|
0.4
|
|
CE1
|
a:HIS332
|
2.9
|
53.0
|
0.6
|
|
CD
|
a:GLU189
|
2.9
|
49.4
|
0.4
|
|
CD
|
a:GLU189
|
3.0
|
49.4
|
0.6
|
|
CG
|
a:ASP342
|
3.0
|
51.1
|
0.6
|
|
CG
|
a:ASP342
|
3.0
|
51.2
|
0.4
|
|
CD2
|
a:HIS332
|
3.1
|
53.6
|
0.6
|
|
OD1
|
a:ASP342
|
3.2
|
51.2
|
0.6
|
|
CD2
|
a:HIS332
|
3.2
|
53.5
|
0.4
|
|
OD1
|
a:ASP342
|
3.2
|
51.4
|
0.4
|
|
MN3
|
a:OEX411
|
3.2
|
52.0
|
0.6
|
|
MN3
|
a:OEX411
|
3.3
|
49.0
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
49.6
|
0.4
|
|
OE1
|
a:GLU189
|
3.5
|
52.5
|
0.6
|
|
O2
|
a:OEX411
|
3.5
|
48.1
|
0.6
|
|
CA1
|
a:OEX411
|
3.5
|
56.8
|
0.6
|
|
CA1
|
a:OEX411
|
3.5
|
52.9
|
0.4
|
|
O2
|
a:OEX411
|
3.6
|
47.5
|
0.4
|
|
OE1
|
a:GLU333
|
3.7
|
50.9
|
0.6
|
|
OE1
|
a:GLU333
|
3.9
|
50.5
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
53.8
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
53.8
|
0.6
|
|
ND1
|
a:HIS332
|
4.1
|
48.8
|
0.4
|
|
ND1
|
a:HIS332
|
4.1
|
48.9
|
0.6
|
|
CG
|
a:GLU189
|
4.1
|
54.6
|
0.4
|
|
O
|
a:HOH591
|
4.2
|
55.2
|
0.4
|
|
CG
|
a:HIS332
|
4.2
|
49.8
|
0.6
|
|
CG
|
a:HIS332
|
4.2
|
49.7
|
0.4
|
|
CG
|
a:GLU189
|
4.2
|
54.5
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
54.5
|
0.6
|
|
O
|
a:HOH591
|
4.3
|
56.5
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
53.6
|
0.4
|
|
CB
|
a:ASP342
|
4.4
|
45.1
|
0.6
|
|
CB
|
a:ASP342
|
4.4
|
45.4
|
0.4
|
|
OE1
|
c:GLU354
|
4.4
|
50.0
|
0.4
|
|
OE1
|
c:GLU354
|
4.5
|
50.3
|
0.6
|
|
CD
|
a:GLU333
|
4.5
|
53.0
|
0.6
|
|
OE2
|
c:GLU354
|
4.6
|
50.0
|
0.6
|
|
OE2
|
c:GLU354
|
4.6
|
48.2
|
0.4
|
|
O
|
a:ALA344
|
4.6
|
52.6
|
0.6
|
|
CG1
|
a:VAL185
|
4.6
|
44.6
|
0.4
|
|
CE1
|
a:HIS337
|
4.7
|
49.5
|
0.4
|
|
CG1
|
a:VAL185
|
4.7
|
44.5
|
0.6
|
|
CD
|
a:GLU333
|
4.7
|
52.4
|
0.4
|
|
CE1
|
a:HIS337
|
4.7
|
49.5
|
0.6
|
|
O
|
a:ALA344
|
4.7
|
51.9
|
0.4
|
|
O
|
a:HOH620
|
4.8
|
54.1
|
0.6
|
|
O
|
a:HOH620
|
4.8
|
54.0
|
0.4
|
|
C
|
a:ALA344
|
4.8
|
52.5
|
0.6
|
|
MN4
|
a:OEX411
|
4.9
|
48.4
|
0.4
|
|
C
|
a:ALA344
|
4.9
|
52.5
|
0.4
|
|
OE2
|
a:GLU333
|
4.9
|
50.7
|
0.6
|
|
CD
|
c:GLU354
|
5.0
|
51.8
|
0.4
|
|
CD2
|
a:HIS337
|
5.0
|
48.3
|
0.6
|
|
MN4
|
a:OEX411
|
5.0
|
53.1
|
0.6
|
|
CD
|
c:GLU354
|
5.0
|
52.6
|
0.6
|
|
Reference:
H.Li,
Y.Nakajima,
E.Nango,
S.Owada,
D.Yamada,
K.Hashimoto,
F.Luo,
R.Tanaka,
F.Akita,
K.Kato,
J.M.Kang,
Y.Saitoh,
S.Kishi,
H.Yu,
N.Matsubara,
H.Fujii,
M.Sugahara,
M.Suzuki,
T.Masuda,
T.Kimura,
T.N.Thao,
S.Yonekura,
L.J.Yu,
T.Tosha,
K.Tono,
Y.Joti,
T.Hatsui,
M.Yabashi,
M.Kubo,
S.Iwata,
H.Isobe,
K.Yamaguchi,
M.Suga,
J.R.Shen.
Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sun Oct 6 12:36:43 2024
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