Manganese in PDB 8ir6: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond Delay
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond Delay
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond Delay:
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond Delay, PDB code: 8ir6
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 (%)
|
14.2 /
17.8
|
Other elements in 8ir6:
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay
(pdb code 8ir6). 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 20-Nanosecond Delay, PDB code: 8ir6:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 1 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.0
occ:0.40
|
MN1
|
A:OEX413
|
0.0
|
46.0
|
0.4
|
|
MN1
|
A:OEX413
|
0.1
|
45.2
|
0.6
|
|
O1
|
A:OEX413
|
1.7
|
42.1
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.8
|
0.4
|
|
OE2
|
A:GLU189
|
1.8
|
46.3
|
0.4
|
|
OE2
|
A:GLU189
|
1.8
|
46.1
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
55.9
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
50.5
|
0.4
|
|
NE2
|
A:HIS332
|
2.1
|
46.0
|
0.4
|
|
NE2
|
A:HIS332
|
2.1
|
46.1
|
0.6
|
|
OD2
|
A:ASP342
|
2.1
|
42.9
|
0.6
|
|
OD2
|
A:ASP342
|
2.2
|
42.8
|
0.4
|
|
O5
|
A:OEX413
|
2.6
|
64.2
|
0.6
|
|
O5
|
A:OEX413
|
2.6
|
57.3
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
47.2
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
46.2
|
0.4
|
|
CD
|
A:GLU189
|
2.9
|
46.0
|
0.4
|
|
CD
|
A:GLU189
|
3.0
|
46.0
|
0.6
|
|
CE1
|
A:HIS332
|
3.0
|
40.9
|
0.4
|
|
CG
|
A:ASP342
|
3.0
|
47.8
|
0.6
|
|
CG
|
A:ASP342
|
3.1
|
47.5
|
0.4
|
|
CE1
|
A:HIS332
|
3.1
|
40.6
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
42.3
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
42.3
|
0.4
|
|
MN3
|
A:OEX413
|
3.2
|
46.2
|
0.6
|
|
MN3
|
A:OEX413
|
3.2
|
46.3
|
0.4
|
|
OD1
|
A:ASP342
|
3.3
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
3.3
|
39.9
|
0.4
|
|
O2
|
A:OEX413
|
3.4
|
44.6
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
49.9
|
0.4
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
OE1
|
A:GLU189
|
3.5
|
51.5
|
0.4
|
|
O2
|
A:OEX413
|
3.5
|
44.4
|
0.4
|
|
OE1
|
A:GLU189
|
3.6
|
51.9
|
0.6
|
|
OE1
|
A:GLU333
|
3.8
|
42.4
|
0.6
|
|
OE1
|
A:GLU333
|
3.9
|
42.7
|
0.4
|
|
NE2
|
A:HIS337
|
4.0
|
44.5
|
0.6
|
|
NE2
|
A:HIS337
|
4.0
|
44.5
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
43.0
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.1
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.7
|
0.6
|
|
CG
|
A:GLU189
|
4.1
|
43.0
|
0.6
|
|
ND1
|
A:HIS332
|
4.1
|
42.3
|
0.4
|
|
ND1
|
A:HIS332
|
4.2
|
42.2
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
46.9
|
0.6
|
|
OXT
|
A:ALA344
|
4.4
|
46.8
|
0.4
|
|
OE2
|
C:GLU354
|
4.4
|
48.4
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
45.3
|
0.6
|
|
OE1
|
C:GLU354
|
4.4
|
51.4
|
0.6
|
|
CB
|
A:ASP342
|
4.4
|
45.4
|
0.4
|
|
OE1
|
C:GLU354
|
4.5
|
51.0
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
47.1
|
0.4
|
|
CE1
|
A:HIS337
|
4.5
|
44.4
|
0.6
|
|
CG1
|
A:VAL185
|
4.6
|
42.6
|
0.4
|
|
CE1
|
A:HIS337
|
4.6
|
44.5
|
0.4
|
|
CD
|
A:GLU333
|
4.6
|
45.4
|
0.6
|
|
CG1
|
A:VAL185
|
4.6
|
42.6
|
0.6
|
|
CD
|
A:GLU333
|
4.7
|
45.5
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
48.4
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
48.1
|
0.6
|
|
O
|
A:ALA344
|
4.7
|
51.3
|
0.4
|
|
O
|
A:ALA344
|
4.8
|
51.7
|
0.6
|
|
MN4
|
A:OEX413
|
4.8
|
49.1
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
51.5
|
0.6
|
|
MN4
|
A:OEX413
|
4.9
|
49.0
|
0.4
|
|
C
|
A:ALA344
|
4.9
|
47.1
|
0.6
|
|
OE2
|
A:GLU333
|
4.9
|
45.8
|
0.6
|
|
C
|
A:ALA344
|
4.9
|
47.0
|
0.4
|
|
O4
|
A:OEX413
|
4.9
|
46.0
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
51.2
|
0.4
|
|
O4
|
A:OEX413
|
5.0
|
46.1
|
0.4
|
|
OE2
|
A:GLU333
|
5.0
|
45.7
|
0.4
|
|
Manganese binding site 2 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 2 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:45.2
occ:0.60
|
MN1
|
A:OEX413
|
0.0
|
45.2
|
0.6
|
|
MN1
|
A:OEX413
|
0.1
|
46.0
|
0.4
|
|
OE2
|
A:GLU189
|
1.7
|
46.3
|
0.4
|
|
O1
|
A:OEX413
|
1.8
|
42.1
|
0.6
|
|
OE2
|
A:GLU189
|
1.8
|
46.1
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.8
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
55.9
|
0.6
|
|
O3
|
A:OEX413
|
2.0
|
50.5
|
0.4
|
|
NE2
|
A:HIS332
|
2.1
|
46.0
|
0.4
|
|
NE2
|
A:HIS332
|
2.1
|
46.1
|
0.6
|
|
OD2
|
A:ASP342
|
2.1
|
42.9
|
0.6
|
|
OD2
|
A:ASP342
|
2.2
|
42.8
|
0.4
|
|
O5
|
A:OEX413
|
2.6
|
64.2
|
0.6
|
|
O5
|
A:OEX413
|
2.6
|
57.3
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
47.2
|
0.6
|
|
MN2
|
A:OEX413
|
2.9
|
46.2
|
0.4
|
|
CD
|
A:GLU189
|
2.9
|
46.0
|
0.4
|
|
CE1
|
A:HIS332
|
3.0
|
40.9
|
0.4
|
|
CD
|
A:GLU189
|
3.0
|
46.0
|
0.6
|
|
CD2
|
A:HIS332
|
3.0
|
42.3
|
0.6
|
|
CE1
|
A:HIS332
|
3.0
|
40.6
|
0.6
|
|
CD2
|
A:HIS332
|
3.1
|
42.3
|
0.4
|
|
CG
|
A:ASP342
|
3.1
|
47.8
|
0.6
|
|
CG
|
A:ASP342
|
3.1
|
47.5
|
0.4
|
|
MN3
|
A:OEX413
|
3.2
|
46.2
|
0.6
|
|
MN3
|
A:OEX413
|
3.2
|
46.3
|
0.4
|
|
OD1
|
A:ASP342
|
3.3
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
3.3
|
39.9
|
0.4
|
|
O2
|
A:OEX413
|
3.5
|
44.6
|
0.6
|
|
OE1
|
A:GLU189
|
3.5
|
51.5
|
0.4
|
|
CA1
|
A:OEX413
|
3.5
|
49.9
|
0.4
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
O2
|
A:OEX413
|
3.6
|
44.4
|
0.4
|
|
OE1
|
A:GLU189
|
3.6
|
51.9
|
0.6
|
|
OE1
|
A:GLU333
|
3.8
|
42.4
|
0.6
|
|
OE1
|
A:GLU333
|
3.9
|
42.7
|
0.4
|
|
NE2
|
A:HIS337
|
4.0
|
44.5
|
0.6
|
|
NE2
|
A:HIS337
|
4.0
|
44.5
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
43.0
|
0.4
|
|
ND1
|
A:HIS332
|
4.1
|
42.3
|
0.4
|
|
CG
|
A:GLU189
|
4.1
|
43.0
|
0.6
|
|
O
|
A:HOH588
|
4.1
|
53.1
|
0.4
|
|
ND1
|
A:HIS332
|
4.1
|
42.2
|
0.6
|
|
O
|
A:HOH588
|
4.1
|
53.7
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.6
|
|
CG
|
A:HIS332
|
4.2
|
46.9
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
46.9
|
0.6
|
|
OE2
|
C:GLU354
|
4.4
|
48.4
|
0.6
|
|
OXT
|
A:ALA344
|
4.4
|
46.8
|
0.4
|
|
CB
|
A:ASP342
|
4.4
|
45.3
|
0.6
|
|
CB
|
A:ASP342
|
4.5
|
45.4
|
0.4
|
|
OE1
|
C:GLU354
|
4.5
|
51.4
|
0.6
|
|
OE1
|
C:GLU354
|
4.5
|
51.0
|
0.4
|
|
CE1
|
A:HIS337
|
4.5
|
44.4
|
0.6
|
|
CG1
|
A:VAL185
|
4.5
|
42.6
|
0.4
|
|
OE2
|
C:GLU354
|
4.5
|
47.1
|
0.4
|
|
CE1
|
A:HIS337
|
4.6
|
44.5
|
0.4
|
|
CG1
|
A:VAL185
|
4.6
|
42.6
|
0.6
|
|
CD
|
A:GLU333
|
4.6
|
45.4
|
0.6
|
|
CD
|
A:GLU333
|
4.6
|
45.5
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
48.4
|
0.4
|
|
O
|
A:HOH621
|
4.7
|
48.1
|
0.6
|
|
O
|
A:ALA344
|
4.8
|
51.3
|
0.4
|
|
O
|
A:ALA344
|
4.8
|
51.7
|
0.6
|
|
MN4
|
A:OEX413
|
4.8
|
49.1
|
0.6
|
|
MN4
|
A:OEX413
|
4.9
|
49.0
|
0.4
|
|
OE2
|
A:GLU333
|
4.9
|
45.8
|
0.6
|
|
CD
|
C:GLU354
|
4.9
|
51.5
|
0.6
|
|
O4
|
A:OEX413
|
4.9
|
46.0
|
0.6
|
|
C
|
A:ALA344
|
4.9
|
47.1
|
0.6
|
|
C
|
A:ALA344
|
5.0
|
47.0
|
0.4
|
|
CD
|
C:GLU354
|
5.0
|
51.2
|
0.4
|
|
O4
|
A:OEX413
|
5.0
|
46.1
|
0.4
|
|
OE2
|
A:GLU333
|
5.0
|
45.7
|
0.4
|
|
Manganese binding site 3 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 3 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.2
occ:0.40
|
MN2
|
A:OEX413
|
0.0
|
46.2
|
0.4
|
|
MN2
|
A:OEX413
|
0.1
|
47.2
|
0.6
|
|
O2
|
A:OEX413
|
1.8
|
44.6
|
0.6
|
|
O1
|
A:OEX413
|
1.8
|
41.8
|
0.4
|
|
OXT
|
A:ALA344
|
1.8
|
46.9
|
0.6
|
|
O2
|
A:OEX413
|
1.9
|
44.4
|
0.4
|
|
O1
|
A:OEX413
|
1.9
|
42.1
|
0.6
|
|
OXT
|
A:ALA344
|
1.9
|
46.8
|
0.4
|
|
O3
|
A:OEX413
|
1.9
|
50.5
|
0.4
|
|
O3
|
A:OEX413
|
2.0
|
55.9
|
0.6
|
|
OE1
|
C:GLU354
|
2.0
|
51.4
|
0.6
|
|
OD1
|
A:ASP342
|
2.1
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
2.1
|
39.9
|
0.4
|
|
OE1
|
C:GLU354
|
2.1
|
51.0
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
46.3
|
0.4
|
|
CD
|
C:GLU354
|
2.8
|
51.5
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.2
|
0.6
|
|
MN1
|
A:OEX413
|
2.8
|
46.0
|
0.4
|
|
C
|
A:ALA344
|
2.8
|
47.1
|
0.6
|
|
C
|
A:ALA344
|
2.8
|
47.0
|
0.4
|
|
MN1
|
A:OEX413
|
2.9
|
45.2
|
0.6
|
|
CD
|
C:GLU354
|
2.9
|
51.2
|
0.4
|
|
OE2
|
C:GLU354
|
3.0
|
48.4
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
47.8
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
47.5
|
0.4
|
|
OE2
|
C:GLU354
|
3.1
|
47.1
|
0.4
|
|
O
|
A:ALA344
|
3.1
|
51.3
|
0.4
|
|
O
|
A:ALA344
|
3.2
|
51.7
|
0.6
|
|
OD2
|
A:ASP342
|
3.2
|
42.9
|
0.6
|
|
OD2
|
A:ASP342
|
3.3
|
42.8
|
0.4
|
|
CA1
|
A:OEX413
|
3.4
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.4
|
49.9
|
0.4
|
|
O5
|
A:OEX413
|
3.5
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
3.6
|
64.2
|
0.6
|
|
NE2
|
A:HIS337
|
3.8
|
44.5
|
0.6
|
|
NE2
|
A:HIS337
|
3.9
|
44.5
|
0.4
|
|
O
|
C:HOH734
|
3.9
|
50.1
|
0.6
|
|
O
|
C:HOH734
|
4.0
|
49.3
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.1
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.7
|
0.6
|
|
OE2
|
A:GLU189
|
4.1
|
46.1
|
0.6
|
|
CA
|
A:ALA344
|
4.2
|
49.4
|
0.6
|
|
OE2
|
A:GLU189
|
4.2
|
46.3
|
0.4
|
|
CA
|
A:ALA344
|
4.2
|
49.4
|
0.4
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.4
|
|
O4
|
A:OEX413
|
4.2
|
46.0
|
0.6
|
|
N
|
A:ALA344
|
4.3
|
53.0
|
0.4
|
|
O4
|
A:OEX413
|
4.3
|
46.1
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.2
|
0.6
|
|
OE1
|
A:GLU333
|
4.3
|
42.4
|
0.6
|
|
OE1
|
A:GLU333
|
4.4
|
42.7
|
0.4
|
|
CB
|
A:ASP342
|
4.4
|
45.3
|
0.6
|
|
CD2
|
A:HIS337
|
4.4
|
45.0
|
0.6
|
|
CD2
|
A:HIS337
|
4.4
|
45.0
|
0.4
|
|
CB
|
A:ASP342
|
4.4
|
45.4
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
45.5
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
45.7
|
0.4
|
|
NE2
|
A:HIS332
|
4.6
|
46.0
|
0.4
|
|
NE2
|
A:HIS332
|
4.6
|
46.1
|
0.6
|
|
CA
|
A:ASP342
|
4.8
|
44.9
|
0.6
|
|
NH1
|
C:ARG357
|
4.8
|
43.0
|
0.4
|
|
CB
|
C:GLU354
|
4.8
|
41.6
|
0.6
|
|
C
|
A:ASP342
|
4.8
|
48.5
|
0.6
|
|
CA
|
A:ASP342
|
4.8
|
45.0
|
0.4
|
|
NH1
|
C:ARG357
|
4.8
|
43.0
|
0.6
|
|
OD1
|
A:ASP170
|
4.9
|
46.3
|
0.6
|
|
CB
|
C:GLU354
|
4.9
|
41.7
|
0.4
|
|
OD1
|
A:ASP170
|
4.9
|
46.5
|
0.4
|
|
C
|
A:ASP342
|
4.9
|
48.5
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
46.0
|
0.4
|
|
CZ
|
C:ARG357
|
4.9
|
54.7
|
0.4
|
|
CZ
|
C:ARG357
|
4.9
|
54.9
|
0.6
|
|
CD
|
A:GLU189
|
4.9
|
46.0
|
0.6
|
|
Manganese binding site 4 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 4 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:47.2
occ:0.60
|
MN2
|
A:OEX413
|
0.0
|
47.2
|
0.6
|
|
MN2
|
A:OEX413
|
0.1
|
46.2
|
0.4
|
|
O1
|
A:OEX413
|
1.8
|
41.8
|
0.4
|
|
O2
|
A:OEX413
|
1.8
|
44.6
|
0.6
|
|
O1
|
A:OEX413
|
1.9
|
42.1
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
50.5
|
0.4
|
|
OXT
|
A:ALA344
|
1.9
|
46.9
|
0.6
|
|
O3
|
A:OEX413
|
1.9
|
55.9
|
0.6
|
|
O2
|
A:OEX413
|
1.9
|
44.4
|
0.4
|
|
OXT
|
A:ALA344
|
1.9
|
46.8
|
0.4
|
|
OD1
|
A:ASP342
|
2.0
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
2.0
|
39.9
|
0.4
|
|
OE1
|
C:GLU354
|
2.1
|
51.4
|
0.6
|
|
OE1
|
C:GLU354
|
2.1
|
51.0
|
0.4
|
|
MN1
|
A:OEX413
|
2.8
|
46.0
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
46.3
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
46.2
|
0.6
|
|
MN1
|
A:OEX413
|
2.8
|
45.2
|
0.6
|
|
CD
|
C:GLU354
|
2.8
|
51.5
|
0.6
|
|
C
|
A:ALA344
|
2.9
|
47.1
|
0.6
|
|
C
|
A:ALA344
|
2.9
|
47.0
|
0.4
|
|
CD
|
C:GLU354
|
2.9
|
51.2
|
0.4
|
|
CG
|
A:ASP342
|
2.9
|
47.8
|
0.6
|
|
CG
|
A:ASP342
|
3.0
|
47.5
|
0.4
|
|
OE2
|
C:GLU354
|
3.0
|
48.4
|
0.6
|
|
OE2
|
C:GLU354
|
3.1
|
47.1
|
0.4
|
|
OD2
|
A:ASP342
|
3.2
|
42.9
|
0.6
|
|
O
|
A:ALA344
|
3.2
|
51.3
|
0.4
|
|
OD2
|
A:ASP342
|
3.2
|
42.8
|
0.4
|
|
O
|
A:ALA344
|
3.2
|
51.7
|
0.6
|
|
CA1
|
A:OEX413
|
3.4
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.4
|
49.9
|
0.4
|
|
O5
|
A:OEX413
|
3.5
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
3.5
|
64.2
|
0.6
|
|
NE2
|
A:HIS337
|
3.8
|
44.5
|
0.6
|
|
NE2
|
A:HIS337
|
3.8
|
44.5
|
0.4
|
|
O
|
C:HOH734
|
3.9
|
50.1
|
0.6
|
|
O
|
C:HOH734
|
4.0
|
49.3
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.1
|
0.4
|
|
OE2
|
A:GLU189
|
4.1
|
46.1
|
0.6
|
|
OE2
|
A:GLU189
|
4.1
|
46.3
|
0.4
|
|
O
|
A:HOH588
|
4.1
|
53.7
|
0.6
|
|
CA
|
A:ALA344
|
4.2
|
49.4
|
0.6
|
|
CA
|
A:ALA344
|
4.2
|
49.4
|
0.4
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.6
|
|
O4
|
A:OEX413
|
4.3
|
46.0
|
0.6
|
|
CG
|
C:GLU354
|
4.3
|
51.5
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.0
|
0.4
|
|
OE1
|
A:GLU333
|
4.3
|
42.4
|
0.6
|
|
O4
|
A:OEX413
|
4.3
|
46.1
|
0.4
|
|
OE1
|
A:GLU333
|
4.3
|
42.7
|
0.4
|
|
N
|
A:ALA344
|
4.3
|
53.2
|
0.6
|
|
CB
|
A:ASP342
|
4.3
|
45.3
|
0.6
|
|
CD2
|
A:HIS337
|
4.4
|
45.0
|
0.6
|
|
CD2
|
A:HIS337
|
4.4
|
45.0
|
0.4
|
|
CB
|
A:ASP342
|
4.4
|
45.4
|
0.4
|
|
NE2
|
A:HIS332
|
4.5
|
46.0
|
0.4
|
|
NE2
|
A:HIS332
|
4.5
|
46.1
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
45.5
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
45.7
|
0.4
|
|
CA
|
A:ASP342
|
4.7
|
44.9
|
0.6
|
|
CA
|
A:ASP342
|
4.8
|
45.0
|
0.4
|
|
C
|
A:ASP342
|
4.8
|
48.5
|
0.6
|
|
CB
|
C:GLU354
|
4.8
|
41.6
|
0.6
|
|
NH1
|
C:ARG357
|
4.9
|
43.0
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
46.0
|
0.4
|
|
C
|
A:ASP342
|
4.9
|
48.5
|
0.4
|
|
CB
|
C:GLU354
|
4.9
|
41.7
|
0.4
|
|
OD1
|
A:ASP170
|
4.9
|
46.3
|
0.6
|
|
NH1
|
C:ARG357
|
4.9
|
43.0
|
0.6
|
|
OD1
|
A:ASP170
|
4.9
|
46.5
|
0.4
|
|
CD
|
A:GLU189
|
4.9
|
46.0
|
0.6
|
|
CE1
|
A:HIS337
|
4.9
|
44.4
|
0.6
|
|
OE1
|
A:GLU189
|
5.0
|
51.5
|
0.4
|
|
CE1
|
A:HIS337
|
5.0
|
44.5
|
0.4
|
|
Manganese binding site 5 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 5 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.3
occ:0.40
|
MN3
|
A:OEX413
|
0.0
|
46.3
|
0.4
|
|
MN3
|
A:OEX413
|
0.0
|
46.2
|
0.6
|
|
O2
|
A:OEX413
|
1.8
|
44.6
|
0.6
|
|
O2
|
A:OEX413
|
1.8
|
44.4
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
46.0
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
46.1
|
0.4
|
|
OE2
|
C:GLU354
|
1.9
|
48.4
|
0.6
|
|
O5
|
A:OEX413
|
2.0
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
2.0
|
64.2
|
0.6
|
|
OE1
|
A:GLU333
|
2.0
|
42.4
|
0.6
|
|
OE1
|
A:GLU333
|
2.0
|
42.7
|
0.4
|
|
OE2
|
C:GLU354
|
2.0
|
47.1
|
0.4
|
|
O3
|
A:OEX413
|
2.1
|
50.5
|
0.4
|
|
O3
|
A:OEX413
|
2.1
|
55.9
|
0.6
|
|
MN4
|
A:OEX413
|
2.8
|
49.1
|
0.6
|
|
MN4
|
A:OEX413
|
2.8
|
49.0
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
47.2
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
46.2
|
0.4
|
|
CD
|
A:GLU333
|
2.8
|
45.4
|
0.6
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.4
|
|
CD
|
C:GLU354
|
3.0
|
51.5
|
0.6
|
|
CD
|
C:GLU354
|
3.0
|
51.2
|
0.4
|
|
OE2
|
A:GLU333
|
3.1
|
45.8
|
0.6
|
|
OE2
|
A:GLU333
|
3.1
|
45.7
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
46.0
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
45.2
|
0.6
|
|
OE1
|
C:GLU354
|
3.3
|
51.0
|
0.4
|
|
OE1
|
C:GLU354
|
3.4
|
51.4
|
0.6
|
|
O1
|
A:OEX413
|
3.4
|
41.8
|
0.4
|
|
O1
|
A:OEX413
|
3.4
|
42.1
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
49.9
|
0.4
|
|
NH2
|
C:ARG357
|
3.9
|
45.5
|
0.6
|
|
NH2
|
C:ARG357
|
3.9
|
45.7
|
0.4
|
|
OD2
|
A:ASP170
|
4.1
|
42.4
|
0.6
|
|
NE2
|
A:HIS337
|
4.1
|
44.5
|
0.4
|
|
NE2
|
A:HIS337
|
4.1
|
44.5
|
0.6
|
|
OD2
|
A:ASP170
|
4.1
|
42.6
|
0.4
|
|
O
|
C:HOH684
|
4.1
|
45.8
|
0.4
|
|
NE2
|
A:HIS332
|
4.2
|
46.0
|
0.4
|
|
OD1
|
A:ASP170
|
4.2
|
46.5
|
0.4
|
|
OD1
|
A:ASP170
|
4.2
|
46.3
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.6
|
|
NE2
|
A:HIS332
|
4.2
|
46.1
|
0.6
|
|
O
|
A:HOH517
|
4.2
|
47.4
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
43.8
|
0.6
|
|
O
|
A:HOH517
|
4.3
|
47.5
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
43.8
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
46.9
|
0.6
|
|
OXT
|
A:ALA344
|
4.4
|
46.8
|
0.4
|
|
O
|
A:HOH544
|
4.4
|
41.3
|
0.6
|
|
O
|
A:HOH544
|
4.4
|
41.2
|
0.4
|
|
CD2
|
A:HIS332
|
4.5
|
42.3
|
0.4
|
|
CD2
|
A:HIS332
|
4.5
|
42.3
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
39.9
|
0.4
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.6
|
|
O
|
A:HOH549
|
4.6
|
45.9
|
0.4
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.4
|
|
O
|
A:ALA344
|
4.6
|
51.3
|
0.4
|
|
O
|
A:HOH549
|
4.6
|
45.9
|
0.6
|
|
OE2
|
A:GLU189
|
4.6
|
46.3
|
0.4
|
|
CB
|
A:GLU333
|
4.7
|
45.2
|
0.6
|
|
OE2
|
A:GLU189
|
4.7
|
46.1
|
0.6
|
|
CB
|
A:GLU333
|
4.7
|
45.2
|
0.4
|
|
OD2
|
A:ASP342
|
4.7
|
42.9
|
0.6
|
|
O
|
A:ALA344
|
4.7
|
51.7
|
0.6
|
|
OD2
|
A:ASP342
|
4.8
|
42.8
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
44.5
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
44.4
|
0.6
|
|
O
|
A:HOH621
|
4.8
|
48.4
|
0.4
|
|
O
|
A:HOH621
|
4.9
|
48.1
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
54.7
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
54.9
|
0.6
|
|
C
|
A:ALA344
|
5.0
|
47.0
|
0.4
|
|
C
|
A:ALA344
|
5.0
|
47.1
|
0.6
|
|
Manganese binding site 6 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 6 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:46.2
occ:0.60
|
MN3
|
A:OEX413
|
0.0
|
46.2
|
0.6
|
|
MN3
|
A:OEX413
|
0.0
|
46.3
|
0.4
|
|
O2
|
A:OEX413
|
1.8
|
44.6
|
0.6
|
|
O2
|
A:OEX413
|
1.9
|
44.4
|
0.4
|
|
OE1
|
A:GLU333
|
1.9
|
42.4
|
0.6
|
|
OE1
|
A:GLU333
|
1.9
|
42.7
|
0.4
|
|
O5
|
A:OEX413
|
1.9
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
1.9
|
64.2
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
46.0
|
0.6
|
|
OE2
|
C:GLU354
|
2.0
|
48.4
|
0.6
|
|
O4
|
A:OEX413
|
2.0
|
46.1
|
0.4
|
|
O3
|
A:OEX413
|
2.0
|
50.5
|
0.4
|
|
OE2
|
C:GLU354
|
2.0
|
47.1
|
0.4
|
|
O3
|
A:OEX413
|
2.0
|
55.9
|
0.6
|
|
MN4
|
A:OEX413
|
2.8
|
49.1
|
0.6
|
|
MN4
|
A:OEX413
|
2.8
|
49.0
|
0.4
|
|
MN2
|
A:OEX413
|
2.8
|
47.2
|
0.6
|
|
CD
|
A:GLU333
|
2.8
|
45.4
|
0.6
|
|
MN2
|
A:OEX413
|
2.8
|
46.2
|
0.4
|
|
CD
|
A:GLU333
|
2.9
|
45.5
|
0.4
|
|
CD
|
C:GLU354
|
3.0
|
51.5
|
0.6
|
|
CD
|
C:GLU354
|
3.0
|
51.2
|
0.4
|
|
OE2
|
A:GLU333
|
3.0
|
45.8
|
0.6
|
|
OE2
|
A:GLU333
|
3.1
|
45.7
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
46.0
|
0.4
|
|
MN1
|
A:OEX413
|
3.2
|
45.2
|
0.6
|
|
OE1
|
C:GLU354
|
3.4
|
51.0
|
0.4
|
|
OE1
|
C:GLU354
|
3.4
|
51.4
|
0.6
|
|
O1
|
A:OEX413
|
3.4
|
41.8
|
0.4
|
|
O1
|
A:OEX413
|
3.4
|
42.1
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
50.4
|
0.6
|
|
CA1
|
A:OEX413
|
3.5
|
49.9
|
0.4
|
|
NH2
|
C:ARG357
|
3.9
|
45.5
|
0.6
|
|
NH2
|
C:ARG357
|
4.0
|
45.7
|
0.4
|
|
NE2
|
A:HIS337
|
4.1
|
44.5
|
0.4
|
|
OD2
|
A:ASP170
|
4.1
|
42.4
|
0.6
|
|
NE2
|
A:HIS337
|
4.1
|
44.5
|
0.6
|
|
NE2
|
A:HIS332
|
4.1
|
46.0
|
0.4
|
|
OD2
|
A:ASP170
|
4.2
|
42.6
|
0.4
|
|
O
|
C:HOH684
|
4.2
|
45.8
|
0.4
|
|
NE2
|
A:HIS332
|
4.2
|
46.1
|
0.6
|
|
CG
|
A:GLU333
|
4.2
|
43.8
|
0.6
|
|
CG
|
C:GLU354
|
4.2
|
51.5
|
0.6
|
|
OD1
|
A:ASP170
|
4.2
|
46.5
|
0.4
|
|
OD1
|
A:ASP170
|
4.2
|
46.3
|
0.6
|
|
CG
|
A:GLU333
|
4.3
|
43.8
|
0.4
|
|
O
|
A:HOH517
|
4.3
|
47.4
|
0.6
|
|
CG
|
C:GLU354
|
4.3
|
51.5
|
0.4
|
|
O
|
A:HOH517
|
4.3
|
47.5
|
0.4
|
|
OXT
|
A:ALA344
|
4.3
|
46.9
|
0.6
|
|
O
|
A:HOH544
|
4.4
|
41.3
|
0.6
|
|
OXT
|
A:ALA344
|
4.4
|
46.8
|
0.4
|
|
CD2
|
A:HIS332
|
4.4
|
42.3
|
0.4
|
|
O
|
A:HOH544
|
4.4
|
41.2
|
0.4
|
|
CD2
|
A:HIS332
|
4.4
|
42.3
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
40.6
|
0.6
|
|
OD1
|
A:ASP342
|
4.5
|
39.9
|
0.4
|
|
O
|
A:HOH549
|
4.6
|
45.9
|
0.4
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.6
|
|
OE2
|
A:GLU189
|
4.6
|
46.3
|
0.4
|
|
O
|
A:HOH549
|
4.6
|
45.9
|
0.6
|
|
CB
|
A:GLU333
|
4.6
|
45.2
|
0.6
|
|
CG
|
A:ASP170
|
4.6
|
42.6
|
0.4
|
|
O
|
A:ALA344
|
4.7
|
51.3
|
0.4
|
|
OE2
|
A:GLU189
|
4.7
|
46.1
|
0.6
|
|
CB
|
A:GLU333
|
4.7
|
45.2
|
0.4
|
|
OD2
|
A:ASP342
|
4.7
|
42.9
|
0.6
|
|
OD2
|
A:ASP342
|
4.7
|
42.8
|
0.4
|
|
CE1
|
A:HIS337
|
4.8
|
44.5
|
0.4
|
|
O
|
A:ALA344
|
4.8
|
51.7
|
0.6
|
|
CE1
|
A:HIS337
|
4.8
|
44.4
|
0.6
|
|
O
|
A:HOH621
|
4.8
|
48.4
|
0.4
|
|
O
|
A:HOH621
|
4.9
|
48.1
|
0.6
|
|
CZ
|
C:ARG357
|
5.0
|
54.7
|
0.4
|
|
Manganese binding site 7 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 7 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:49.0
occ:0.40
|
MN4
|
A:OEX413
|
0.0
|
49.0
|
0.4
|
|
MN4
|
A:OEX413
|
0.0
|
49.1
|
0.6
|
|
O4
|
A:OEX413
|
1.9
|
46.1
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
46.0
|
0.6
|
|
OD2
|
A:ASP170
|
2.0
|
42.4
|
0.6
|
|
OD2
|
A:ASP170
|
2.0
|
42.6
|
0.4
|
|
OE2
|
A:GLU333
|
2.0
|
45.8
|
0.6
|
|
OE2
|
A:GLU333
|
2.1
|
45.7
|
0.4
|
|
O
|
A:HOH544
|
2.1
|
41.3
|
0.6
|
|
O
|
A:HOH544
|
2.1
|
41.2
|
0.4
|
|
O
|
A:HOH549
|
2.3
|
45.9
|
0.6
|
|
O
|
A:HOH549
|
2.3
|
45.9
|
0.4
|
|
O5
|
A:OEX413
|
2.3
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
2.3
|
64.2
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.2
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.3
|
0.4
|
|
CD
|
A:GLU333
|
3.0
|
45.4
|
0.6
|
|
CD
|
A:GLU333
|
3.0
|
45.5
|
0.4
|
|
CG
|
A:ASP170
|
3.1
|
42.6
|
0.6
|
|
CG
|
A:ASP170
|
3.1
|
42.6
|
0.4
|
|
OE1
|
A:GLU333
|
3.2
|
42.7
|
0.4
|
|
OE1
|
A:GLU333
|
3.3
|
42.4
|
0.6
|
|
OD1
|
A:ASP170
|
3.5
|
46.5
|
0.4
|
|
OD1
|
A:ASP170
|
3.5
|
46.3
|
0.6
|
|
O
|
A:HOH621
|
3.7
|
48.4
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.4
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.6
|
0.6
|
|
O
|
A:HOH621
|
3.8
|
48.1
|
0.6
|
|
O
|
A:HOH517
|
3.8
|
47.4
|
0.6
|
|
O
|
A:HOH517
|
3.8
|
47.5
|
0.4
|
|
CA1
|
A:OEX413
|
3.8
|
49.9
|
0.4
|
|
CA1
|
A:OEX413
|
3.8
|
50.4
|
0.6
|
|
O
|
A:HOH568
|
4.1
|
45.3
|
0.4
|
|
O
|
A:HOH568
|
4.1
|
45.2
|
0.6
|
|
OD1
|
A:ASP61
|
4.2
|
44.1
|
0.6
|
|
O
|
A:HOH625
|
4.2
|
50.5
|
0.6
|
|
O
|
A:HOH625
|
4.2
|
49.8
|
0.4
|
|
OD1
|
A:ASP61
|
4.2
|
44.3
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
43.8
|
0.6
|
|
CB
|
A:ASP170
|
4.3
|
42.2
|
0.6
|
|
CG
|
A:GLU333
|
4.4
|
43.8
|
0.4
|
|
CB
|
A:ASP170
|
4.4
|
42.7
|
0.4
|
|
OE2
|
C:GLU354
|
4.4
|
48.4
|
0.6
|
|
OE2
|
C:GLU354
|
4.4
|
47.1
|
0.4
|
|
NH2
|
C:ARG357
|
4.4
|
45.7
|
0.4
|
|
O
|
A:SER169
|
4.4
|
45.9
|
0.6
|
|
O
|
A:SER169
|
4.5
|
46.0
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
45.5
|
0.6
|
|
CA
|
A:ASP170
|
4.5
|
47.6
|
0.6
|
|
CA
|
A:ASP170
|
4.6
|
47.6
|
0.4
|
|
O3
|
A:OEX413
|
4.6
|
55.9
|
0.6
|
|
O3
|
A:OEX413
|
4.6
|
50.5
|
0.4
|
|
MN1
|
A:OEX413
|
4.9
|
46.0
|
0.4
|
|
MN1
|
A:OEX413
|
4.9
|
45.2
|
0.6
|
|
O
|
D:HOH511
|
4.9
|
45.5
|
0.6
|
|
N
|
A:ASP170
|
4.9
|
45.0
|
0.6
|
|
O
|
D:HOH511
|
4.9
|
45.7
|
0.4
|
|
C
|
A:SER169
|
4.9
|
49.3
|
0.6
|
|
C
|
A:SER169
|
5.0
|
49.3
|
0.4
|
|
Manganese binding site 8 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 8 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn413
b:49.1
occ:0.60
|
MN4
|
A:OEX413
|
0.0
|
49.1
|
0.6
|
|
MN4
|
A:OEX413
|
0.0
|
49.0
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
46.1
|
0.4
|
|
O4
|
A:OEX413
|
1.9
|
46.0
|
0.6
|
|
OD2
|
A:ASP170
|
2.0
|
42.4
|
0.6
|
|
OE2
|
A:GLU333
|
2.0
|
45.8
|
0.6
|
|
OD2
|
A:ASP170
|
2.0
|
42.6
|
0.4
|
|
OE2
|
A:GLU333
|
2.1
|
45.7
|
0.4
|
|
O
|
A:HOH544
|
2.1
|
41.3
|
0.6
|
|
O
|
A:HOH544
|
2.1
|
41.2
|
0.4
|
|
O5
|
A:OEX413
|
2.3
|
57.3
|
0.4
|
|
O5
|
A:OEX413
|
2.3
|
64.2
|
0.6
|
|
O
|
A:HOH549
|
2.3
|
45.9
|
0.6
|
|
O
|
A:HOH549
|
2.3
|
45.9
|
0.4
|
|
MN3
|
A:OEX413
|
2.8
|
46.2
|
0.6
|
|
MN3
|
A:OEX413
|
2.8
|
46.3
|
0.4
|
|
CD
|
A:GLU333
|
3.0
|
45.4
|
0.6
|
|
CD
|
A:GLU333
|
3.0
|
45.5
|
0.4
|
|
CG
|
A:ASP170
|
3.1
|
42.6
|
0.6
|
|
CG
|
A:ASP170
|
3.1
|
42.6
|
0.4
|
|
OE1
|
A:GLU333
|
3.2
|
42.7
|
0.4
|
|
OE1
|
A:GLU333
|
3.3
|
42.4
|
0.6
|
|
OD1
|
A:ASP170
|
3.5
|
46.5
|
0.4
|
|
OD1
|
A:ASP170
|
3.5
|
46.3
|
0.6
|
|
O
|
A:HOH621
|
3.6
|
48.4
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.4
|
0.4
|
|
O2
|
A:OEX413
|
3.7
|
44.6
|
0.6
|
|
O
|
A:HOH621
|
3.8
|
48.1
|
0.6
|
|
O
|
A:HOH517
|
3.8
|
47.4
|
0.6
|
|
O
|
A:HOH517
|
3.8
|
47.5
|
0.4
|
|
CA1
|
A:OEX413
|
3.8
|
49.9
|
0.4
|
|
CA1
|
A:OEX413
|
3.8
|
50.4
|
0.6
|
|
O
|
A:HOH568
|
4.1
|
45.3
|
0.4
|
|
O
|
A:HOH568
|
4.2
|
45.2
|
0.6
|
|
OD1
|
A:ASP61
|
4.2
|
44.1
|
0.6
|
|
O
|
A:HOH625
|
4.2
|
50.5
|
0.6
|
|
O
|
A:HOH625
|
4.2
|
49.8
|
0.4
|
|
OD1
|
A:ASP61
|
4.2
|
44.3
|
0.4
|
|
CG
|
A:GLU333
|
4.3
|
43.8
|
0.6
|
|
CB
|
A:ASP170
|
4.4
|
42.2
|
0.6
|
|
CG
|
A:GLU333
|
4.4
|
43.8
|
0.4
|
|
CB
|
A:ASP170
|
4.4
|
42.7
|
0.4
|
|
OE2
|
C:GLU354
|
4.4
|
48.4
|
0.6
|
|
OE2
|
C:GLU354
|
4.4
|
47.1
|
0.4
|
|
NH2
|
C:ARG357
|
4.4
|
45.7
|
0.4
|
|
O
|
A:SER169
|
4.5
|
45.9
|
0.6
|
|
O
|
A:SER169
|
4.5
|
46.0
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
45.5
|
0.6
|
|
CA
|
A:ASP170
|
4.5
|
47.6
|
0.6
|
|
O3
|
A:OEX413
|
4.5
|
55.9
|
0.6
|
|
O3
|
A:OEX413
|
4.6
|
50.5
|
0.4
|
|
CA
|
A:ASP170
|
4.6
|
47.6
|
0.4
|
|
MN1
|
A:OEX413
|
4.8
|
46.0
|
0.4
|
|
MN1
|
A:OEX413
|
4.8
|
45.2
|
0.6
|
|
O
|
D:HOH511
|
4.9
|
45.5
|
0.6
|
|
N
|
A:ASP170
|
4.9
|
45.0
|
0.6
|
|
O
|
D:HOH511
|
4.9
|
45.7
|
0.4
|
|
C
|
A:SER169
|
4.9
|
49.3
|
0.6
|
|
Manganese binding site 9 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 9 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn413
b:50.3
occ:0.40
|
MN1
|
a:OEX413
|
0.0
|
50.3
|
0.4
|
|
MN1
|
a:OEX413
|
0.2
|
49.3
|
0.6
|
|
O1
|
a:OEX413
|
1.6
|
47.8
|
0.6
|
|
O3
|
a:OEX413
|
1.8
|
46.6
|
0.6
|
|
OE2
|
a:GLU189
|
1.8
|
52.5
|
0.4
|
|
O1
|
a:OEX413
|
1.8
|
48.9
|
0.4
|
|
OE2
|
a:GLU189
|
1.9
|
52.4
|
0.6
|
|
O3
|
a:OEX413
|
1.9
|
46.9
|
0.4
|
|
NE2
|
a:HIS332
|
2.1
|
49.1
|
0.4
|
|
OD2
|
a:ASP342
|
2.1
|
52.0
|
0.4
|
|
OD2
|
a:ASP342
|
2.2
|
52.6
|
0.6
|
|
NE2
|
a:HIS332
|
2.2
|
49.2
|
0.6
|
|
O5
|
a:OEX413
|
2.6
|
49.1
|
0.4
|
|
O5
|
a:OEX413
|
2.6
|
48.8
|
0.6
|
|
MN2
|
a:OEX413
|
2.7
|
52.4
|
0.6
|
|
MN2
|
a:OEX413
|
2.8
|
50.4
|
0.4
|
|
CD
|
a:GLU189
|
2.9
|
47.3
|
0.4
|
|
CE1
|
a:HIS332
|
2.9
|
47.9
|
0.4
|
|
CD
|
a:GLU189
|
2.9
|
47.2
|
0.6
|
|
CG
|
a:ASP342
|
3.0
|
53.1
|
0.6
|
|
CG
|
a:ASP342
|
3.1
|
53.1
|
0.4
|
|
CE1
|
a:HIS332
|
3.1
|
48.2
|
0.6
|
|
OD1
|
a:ASP342
|
3.1
|
51.3
|
0.6
|
|
CD2
|
a:HIS332
|
3.2
|
48.5
|
0.4
|
|
OD1
|
a:ASP342
|
3.3
|
52.6
|
0.4
|
|
MN3
|
a:OEX413
|
3.3
|
52.4
|
0.6
|
|
MN3
|
a:OEX413
|
3.3
|
51.5
|
0.4
|
|
CD2
|
a:HIS332
|
3.3
|
48.5
|
0.6
|
|
OE1
|
a:GLU189
|
3.4
|
49.4
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
49.1
|
0.6
|
|
CA1
|
a:OEX413
|
3.5
|
54.9
|
0.6
|
|
O2
|
a:OEX413
|
3.5
|
47.1
|
0.6
|
|
CA1
|
a:OEX413
|
3.5
|
54.8
|
0.4
|
|
O2
|
a:OEX413
|
3.6
|
47.4
|
0.4
|
|
OE1
|
a:GLU333
|
3.9
|
49.8
|
0.4
|
|
OE1
|
a:GLU333
|
3.9
|
49.9
|
0.6
|
|
NE2
|
a:HIS337
|
4.0
|
51.5
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
51.6
|
0.6
|
|
ND1
|
a:HIS332
|
4.1
|
50.1
|
0.4
|
|
CG
|
a:GLU189
|
4.1
|
52.0
|
0.4
|
|
O
|
a:HOH597
|
4.1
|
59.0
|
0.4
|
|
O
|
a:HOH597
|
4.2
|
59.3
|
0.6
|
|
OXT
|
a:ALA344
|
4.2
|
52.1
|
0.6
|
|
CG
|
a:GLU189
|
4.2
|
53.1
|
0.6
|
|
CG
|
a:HIS332
|
4.2
|
51.0
|
0.4
|
|
ND1
|
a:HIS332
|
4.2
|
50.2
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
51.7
|
0.4
|
|
CG
|
a:HIS332
|
4.4
|
51.0
|
0.6
|
|
OE1
|
c:GLU354
|
4.4
|
51.4
|
0.6
|
|
CB
|
a:ASP342
|
4.4
|
46.4
|
0.6
|
|
CB
|
a:ASP342
|
4.4
|
46.7
|
0.4
|
|
OE1
|
c:GLU354
|
4.5
|
51.2
|
0.4
|
|
CG1
|
a:VAL185
|
4.6
|
45.2
|
0.4
|
|
O
|
a:HOH622
|
4.6
|
55.6
|
0.6
|
|
OE2
|
c:GLU354
|
4.6
|
47.2
|
0.4
|
|
OE2
|
c:GLU354
|
4.7
|
46.8
|
0.6
|
|
CD
|
a:GLU333
|
4.7
|
52.7
|
0.4
|
|
O
|
a:ALA344
|
4.7
|
52.2
|
0.6
|
|
CE1
|
a:HIS337
|
4.7
|
50.9
|
0.4
|
|
O
|
a:ALA344
|
4.7
|
52.2
|
0.4
|
|
CG1
|
a:VAL185
|
4.7
|
45.1
|
0.6
|
|
CD
|
a:GLU333
|
4.7
|
52.8
|
0.6
|
|
CE1
|
a:HIS337
|
4.7
|
50.9
|
0.6
|
|
O
|
a:HOH622
|
4.8
|
55.2
|
0.4
|
|
C
|
a:ALA344
|
4.8
|
53.9
|
0.6
|
|
MN4
|
a:OEX413
|
4.8
|
50.9
|
0.4
|
|
C
|
a:ALA344
|
4.9
|
53.8
|
0.4
|
|
MN4
|
a:OEX413
|
4.9
|
50.5
|
0.6
|
|
CD
|
c:GLU354
|
4.9
|
49.2
|
0.6
|
|
CD
|
c:GLU354
|
5.0
|
49.2
|
0.4
|
|
Manganese binding site 10 out
of 16 in 8ir6
Go back to
Manganese Binding Sites List in 8ir6
Manganese binding site 10 out
of 16 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 20-Nanosecond 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 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn413
b:49.3
occ:0.60
|
MN1
|
a:OEX413
|
0.0
|
49.3
|
0.6
|
|
MN1
|
a:OEX413
|
0.2
|
50.3
|
0.4
|
|
O1
|
a:OEX413
|
1.7
|
47.8
|
0.6
|
|
OE2
|
a:GLU189
|
1.7
|
52.5
|
0.4
|
|
OE2
|
a:GLU189
|
1.8
|
52.4
|
0.6
|
|
O3
|
a:OEX413
|
1.8
|
46.6
|
0.6
|
|
O3
|
a:OEX413
|
1.9
|
46.9
|
0.4
|
|
O1
|
a:OEX413
|
2.0
|
48.9
|
0.4
|
|
NE2
|
a:HIS332
|
2.0
|
49.1
|
0.4
|
|
NE2
|
a:HIS332
|
2.1
|
49.2
|
0.6
|
|
OD2
|
a:ASP342
|
2.1
|
52.0
|
0.4
|
|
OD2
|
a:ASP342
|
2.2
|
52.6
|
0.6
|
|
O5
|
a:OEX413
|
2.6
|
49.1
|
0.4
|
|
O5
|
a:OEX413
|
2.6
|
48.8
|
0.6
|
|
CE1
|
a:HIS332
|
2.8
|
47.9
|
0.4
|
|
MN2
|
a:OEX413
|
2.9
|
52.4
|
0.6
|
|
CD
|
a:GLU189
|
2.9
|
47.3
|
0.4
|
|
CE1
|
a:HIS332
|
2.9
|
48.2
|
0.6
|
|
CD
|
a:GLU189
|
2.9
|
47.2
|
0.6
|
|
MN2
|
a:OEX413
|
2.9
|
50.4
|
0.4
|
|
CG
|
a:ASP342
|
3.0
|
53.1
|
0.6
|
|
CD2
|
a:HIS332
|
3.0
|
48.5
|
0.4
|
|
CG
|
a:ASP342
|
3.1
|
53.1
|
0.4
|
|
CD2
|
a:HIS332
|
3.2
|
48.5
|
0.6
|
|
OD1
|
a:ASP342
|
3.2
|
51.3
|
0.6
|
|
MN3
|
a:OEX413
|
3.4
|
52.4
|
0.6
|
|
MN3
|
a:OEX413
|
3.4
|
51.5
|
0.4
|
|
OD1
|
a:ASP342
|
3.4
|
52.6
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
49.4
|
0.4
|
|
OE1
|
a:GLU189
|
3.4
|
49.1
|
0.6
|
|
CA1
|
a:OEX413
|
3.6
|
54.9
|
0.6
|
|
O2
|
a:OEX413
|
3.6
|
47.1
|
0.6
|
|
CA1
|
a:OEX413
|
3.6
|
54.8
|
0.4
|
|
O2
|
a:OEX413
|
3.7
|
47.4
|
0.4
|
|
OE1
|
a:GLU333
|
3.9
|
49.8
|
0.4
|
|
OE1
|
a:GLU333
|
3.9
|
49.9
|
0.6
|
|
ND1
|
a:HIS332
|
3.9
|
50.1
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
51.5
|
0.4
|
|
NE2
|
a:HIS337
|
4.0
|
51.6
|
0.6
|
|
CG
|
a:HIS332
|
4.1
|
51.0
|
0.4
|
|
ND1
|
a:HIS332
|
4.1
|
50.2
|
0.6
|
|
CG
|
a:GLU189
|
4.1
|
52.0
|
0.4
|
|
CG
|
a:GLU189
|
4.2
|
53.1
|
0.6
|
|
CG
|
a:HIS332
|
4.2
|
51.0
|
0.6
|
|
O
|
a:HOH597
|
4.2
|
59.0
|
0.4
|
|
O
|
a:HOH597
|
4.3
|
59.3
|
0.6
|
|
OXT
|
a:ALA344
|
4.3
|
52.1
|
0.6
|
|
CB
|
a:ASP342
|
4.4
|
46.4
|
0.6
|
|
CB
|
a:ASP342
|
4.5
|
46.7
|
0.4
|
|
OXT
|
a:ALA344
|
4.5
|
51.7
|
0.4
|
|
OE1
|
c:GLU354
|
4.5
|
51.4
|
0.6
|
|
CG1
|
a:VAL185
|
4.5
|
45.2
|
0.4
|
|
OE1
|
c:GLU354
|
4.6
|
51.2
|
0.4
|
|
CG1
|
a:VAL185
|
4.6
|
45.1
|
0.6
|
|
CE1
|
a:HIS337
|
4.7
|
50.9
|
0.4
|
|
CD
|
a:GLU333
|
4.7
|
52.7
|
0.4
|
|
O
|
a:HOH622
|
4.7
|
55.6
|
0.6
|
|
CD
|
a:GLU333
|
4.7
|
52.8
|
0.6
|
|
CE1
|
a:HIS337
|
4.7
|
50.9
|
0.6
|
|
OE2
|
c:GLU354
|
4.7
|
47.2
|
0.4
|
|
OE2
|
c:GLU354
|
4.8
|
46.8
|
0.6
|
|
O
|
a:HOH622
|
4.8
|
55.2
|
0.4
|
|
O
|
a:ALA344
|
4.9
|
52.2
|
0.6
|
|
MN4
|
a:OEX413
|
4.9
|
50.9
|
0.4
|
|
O
|
a:ALA344
|
4.9
|
52.2
|
0.4
|
|
MN4
|
a:OEX413
|
4.9
|
50.5
|
0.6
|
|
C
|
a:ALA344
|
5.0
|
53.9
|
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 12:35:00 2024
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