Manganese in PDB 8wb4: Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Enzymatic activity of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
All present enzymatic activity of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae:
1.10.3.9;
Other elements in 8wb4:
The structure of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
(pdb code 8wb4). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Structure of Psii-Acpii Supercomplex From Cryptophyte Algae, PDB code: 8wb4:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 1 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn601
b:181.9
occ:1.00
|
MN1
|
A:OEX601
|
0.0
|
181.9
|
1.0
|
O1
|
A:OEX601
|
1.8
|
168.3
|
1.0
|
O3
|
A:OEX601
|
1.8
|
167.6
|
1.0
|
O5
|
A:OEX601
|
2.6
|
162.7
|
1.0
|
MN2
|
A:OEX601
|
2.7
|
181.7
|
1.0
|
MN3
|
A:OEX601
|
3.3
|
178.6
|
1.0
|
OE2
|
A:GLU189
|
3.4
|
88.0
|
1.0
|
OD2
|
A:ASP342
|
3.4
|
148.5
|
1.0
|
O
|
A:ASP342
|
3.4
|
153.3
|
1.0
|
CA1
|
A:OEX601
|
3.5
|
168.3
|
1.0
|
CG
|
A:ASP342
|
3.5
|
150.9
|
1.0
|
O2
|
A:OEX601
|
3.7
|
168.0
|
1.0
|
CD
|
A:GLU189
|
3.7
|
92.0
|
1.0
|
OD1
|
A:ASP342
|
3.7
|
151.3
|
1.0
|
OE1
|
A:GLU189
|
4.1
|
96.4
|
1.0
|
CB
|
A:ASP342
|
4.3
|
151.4
|
1.0
|
CG
|
A:GLU189
|
4.3
|
82.7
|
1.0
|
OE1
|
A:GLN165
|
4.3
|
74.1
|
1.0
|
C
|
A:ASP342
|
4.5
|
153.4
|
1.0
|
O
|
A:LEU343
|
4.8
|
148.2
|
1.0
|
CB
|
A:GLU189
|
4.8
|
73.7
|
1.0
|
MN4
|
A:OEX601
|
4.9
|
171.7
|
1.0
|
CA
|
A:ASP342
|
4.9
|
152.6
|
1.0
|
|
Manganese binding site 2 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 2 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn601
b:181.7
occ:1.00
|
MN2
|
A:OEX601
|
0.0
|
181.7
|
1.0
|
O1
|
A:OEX601
|
2.0
|
168.3
|
1.0
|
O2
|
A:OEX601
|
2.1
|
168.0
|
1.0
|
O3
|
A:OEX601
|
2.1
|
167.6
|
1.0
|
MN1
|
A:OEX601
|
2.7
|
181.9
|
1.0
|
MN3
|
A:OEX601
|
2.9
|
178.6
|
1.0
|
OE1
|
C:GLU342
|
3.1
|
115.9
|
1.0
|
OD1
|
A:ASP342
|
3.1
|
151.3
|
1.0
|
CA1
|
A:OEX601
|
3.3
|
168.3
|
1.0
|
CD
|
C:GLU342
|
3.3
|
116.9
|
1.0
|
OE2
|
C:GLU342
|
3.3
|
113.2
|
1.0
|
O
|
A:ASP342
|
3.7
|
153.3
|
1.0
|
CG
|
A:ASP342
|
3.9
|
150.9
|
1.0
|
O5
|
A:OEX601
|
3.9
|
162.7
|
1.0
|
O
|
A:LEU343
|
4.0
|
148.2
|
1.0
|
C
|
A:ASP342
|
4.3
|
153.4
|
1.0
|
OD2
|
A:ASP342
|
4.3
|
148.5
|
1.0
|
CG
|
C:GLU342
|
4.4
|
114.6
|
1.0
|
O4
|
A:OEX601
|
4.6
|
164.4
|
1.0
|
C
|
A:LEU343
|
4.6
|
147.8
|
1.0
|
CA
|
A:ASP342
|
4.8
|
152.6
|
1.0
|
CB
|
A:ASP342
|
4.8
|
151.4
|
1.0
|
|
Manganese binding site 3 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 3 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn601
b:178.6
occ:1.00
|
MN3
|
A:OEX601
|
0.0
|
178.6
|
1.0
|
O2
|
A:OEX601
|
1.9
|
168.0
|
1.0
|
O3
|
A:OEX601
|
2.0
|
167.6
|
1.0
|
O4
|
A:OEX601
|
2.1
|
164.4
|
1.0
|
O5
|
A:OEX601
|
2.4
|
162.7
|
1.0
|
MN4
|
A:OEX601
|
2.9
|
171.7
|
1.0
|
MN2
|
A:OEX601
|
2.9
|
181.7
|
1.0
|
OE1
|
A:GLU333
|
2.9
|
128.2
|
1.0
|
OE2
|
C:GLU342
|
3.1
|
113.2
|
1.0
|
MN1
|
A:OEX601
|
3.3
|
181.9
|
1.0
|
CA1
|
A:OEX601
|
3.4
|
168.3
|
1.0
|
OE2
|
A:GLU189
|
3.4
|
88.0
|
1.0
|
OE2
|
A:GLU333
|
3.6
|
128.9
|
1.0
|
O1
|
A:OEX601
|
3.6
|
168.3
|
1.0
|
CD
|
A:GLU333
|
3.6
|
129.4
|
1.0
|
CD
|
C:GLU342
|
4.0
|
116.9
|
1.0
|
NE2
|
A:HIS332
|
4.3
|
104.7
|
1.0
|
CD
|
A:GLU189
|
4.4
|
92.0
|
1.0
|
OE1
|
C:GLU342
|
4.4
|
115.9
|
1.0
|
OD1
|
A:ASP342
|
4.4
|
151.3
|
1.0
|
NH2
|
C:ARG345
|
4.4
|
88.6
|
1.0
|
CE1
|
A:HIS337
|
4.6
|
137.5
|
1.0
|
OE1
|
A:GLU189
|
4.6
|
96.4
|
1.0
|
OD2
|
A:ASP342
|
4.6
|
148.5
|
1.0
|
OD1
|
A:ASP170
|
4.7
|
86.3
|
1.0
|
NH1
|
C:ARG345
|
4.7
|
88.5
|
1.0
|
CD2
|
A:HIS332
|
4.8
|
104.2
|
1.0
|
CG
|
A:ASP342
|
4.9
|
150.9
|
1.0
|
CZ
|
C:ARG345
|
4.9
|
89.9
|
1.0
|
OD2
|
A:ASP170
|
5.0
|
88.7
|
1.0
|
|
Manganese binding site 4 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 4 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn601
b:171.7
occ:1.00
|
MN4
|
A:OEX601
|
0.0
|
171.7
|
1.0
|
O4
|
A:OEX601
|
2.1
|
164.4
|
1.0
|
O5
|
A:OEX601
|
2.4
|
162.7
|
1.0
|
OD1
|
A:ASP170
|
2.8
|
86.3
|
1.0
|
MN3
|
A:OEX601
|
2.9
|
178.6
|
1.0
|
CG
|
A:ASP170
|
3.1
|
83.4
|
1.0
|
OE2
|
A:GLU333
|
3.2
|
128.9
|
1.0
|
OD2
|
A:ASP170
|
3.5
|
88.7
|
1.0
|
CB
|
A:ASP170
|
3.8
|
68.8
|
1.0
|
CA1
|
A:OEX601
|
3.8
|
168.3
|
1.0
|
O2
|
A:OEX601
|
3.9
|
168.0
|
1.0
|
OE1
|
A:GLU189
|
3.9
|
96.4
|
1.0
|
CD
|
A:GLU333
|
4.1
|
129.4
|
1.0
|
OE2
|
A:GLU189
|
4.1
|
88.0
|
1.0
|
OE1
|
A:GLU333
|
4.3
|
128.2
|
1.0
|
CD
|
A:GLU189
|
4.5
|
92.0
|
1.0
|
O3
|
A:OEX601
|
4.5
|
167.6
|
1.0
|
CA
|
A:ASP170
|
4.5
|
70.5
|
1.0
|
NH1
|
C:ARG345
|
4.7
|
88.5
|
1.0
|
CG1
|
A:VAL185
|
4.7
|
69.4
|
1.0
|
OH
|
A:TYR161
|
4.8
|
68.3
|
1.0
|
MN1
|
A:OEX601
|
4.9
|
181.9
|
1.0
|
NH2
|
C:ARG345
|
5.0
|
88.6
|
1.0
|
CE2
|
A:TYR161
|
5.0
|
59.1
|
1.0
|
|
Manganese binding site 5 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 5 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn404
b:240.8
occ:1.00
|
MN1
|
a:OEX404
|
0.0
|
240.8
|
1.0
|
O1
|
a:OEX404
|
1.8
|
235.8
|
1.0
|
O3
|
a:OEX404
|
1.8
|
233.4
|
1.0
|
O5
|
a:OEX404
|
2.6
|
232.7
|
1.0
|
MN2
|
a:OEX404
|
2.7
|
242.9
|
1.0
|
OE2
|
a:GLU189
|
3.1
|
81.6
|
1.0
|
OD2
|
a:ASP342
|
3.2
|
144.4
|
1.0
|
MN3
|
a:OEX404
|
3.3
|
237.5
|
1.0
|
CG
|
a:ASP342
|
3.4
|
146.5
|
1.0
|
CD
|
a:GLU189
|
3.4
|
86.3
|
1.0
|
OD1
|
a:ASP342
|
3.5
|
146.3
|
1.0
|
CA1
|
a:OEX404
|
3.5
|
237.2
|
1.0
|
O2
|
a:OEX404
|
3.7
|
236.1
|
1.0
|
O
|
a:ASP342
|
3.8
|
147.0
|
1.0
|
OE1
|
a:GLU189
|
3.9
|
91.2
|
1.0
|
CG
|
a:GLU189
|
4.1
|
75.9
|
1.0
|
CB
|
a:ASP342
|
4.4
|
146.6
|
1.0
|
OE1
|
a:GLN165
|
4.4
|
68.6
|
1.0
|
CB
|
a:GLU189
|
4.8
|
65.0
|
1.0
|
C
|
a:ASP342
|
4.8
|
148.8
|
1.0
|
MN4
|
a:OEX404
|
4.9
|
231.2
|
1.0
|
NE2
|
a:HIS332
|
5.0
|
104.7
|
1.0
|
|
Manganese binding site 6 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 6 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn404
b:242.9
occ:1.00
|
MN2
|
a:OEX404
|
0.0
|
242.9
|
1.0
|
O1
|
a:OEX404
|
2.0
|
235.8
|
1.0
|
O2
|
a:OEX404
|
2.1
|
236.1
|
1.0
|
O3
|
a:OEX404
|
2.1
|
233.4
|
1.0
|
MN1
|
a:OEX404
|
2.7
|
240.8
|
1.0
|
OD1
|
a:ASP342
|
2.9
|
146.3
|
1.0
|
MN3
|
a:OEX404
|
2.9
|
237.5
|
1.0
|
OE1
|
c:GLU342
|
3.1
|
133.8
|
1.0
|
OE2
|
c:GLU342
|
3.1
|
133.7
|
1.0
|
CD
|
c:GLU342
|
3.2
|
133.3
|
1.0
|
CA1
|
a:OEX404
|
3.3
|
237.2
|
1.0
|
CG
|
a:ASP342
|
3.8
|
146.5
|
1.0
|
O5
|
a:OEX404
|
3.9
|
232.7
|
1.0
|
O
|
a:ASP342
|
4.1
|
147.0
|
1.0
|
OD2
|
a:ASP342
|
4.2
|
144.4
|
1.0
|
CG
|
c:GLU342
|
4.2
|
130.4
|
1.0
|
O
|
a:LEU343
|
4.3
|
142.8
|
1.0
|
O4
|
a:OEX404
|
4.6
|
230.4
|
1.0
|
C
|
a:ASP342
|
4.6
|
148.8
|
1.0
|
CB
|
a:ASP342
|
4.9
|
146.6
|
1.0
|
NH1
|
c:ARG345
|
4.9
|
106.3
|
1.0
|
OE1
|
a:GLU333
|
4.9
|
120.1
|
1.0
|
CZ
|
c:ARG345
|
4.9
|
103.9
|
1.0
|
NH2
|
c:ARG345
|
4.9
|
106.0
|
1.0
|
OE2
|
a:GLU189
|
5.0
|
81.6
|
1.0
|
CA
|
a:ASP342
|
5.0
|
147.5
|
1.0
|
|
Manganese binding site 7 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 7 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn404
b:237.5
occ:1.00
|
MN3
|
a:OEX404
|
0.0
|
237.5
|
1.0
|
O2
|
a:OEX404
|
1.9
|
236.1
|
1.0
|
O3
|
a:OEX404
|
2.0
|
233.4
|
1.0
|
O4
|
a:OEX404
|
2.1
|
230.4
|
1.0
|
O5
|
a:OEX404
|
2.4
|
232.7
|
1.0
|
OE1
|
a:GLU333
|
2.8
|
120.1
|
1.0
|
MN4
|
a:OEX404
|
2.9
|
231.2
|
1.0
|
MN2
|
a:OEX404
|
2.9
|
242.9
|
1.0
|
OE2
|
a:GLU333
|
2.9
|
122.6
|
1.0
|
OE2
|
c:GLU342
|
3.1
|
133.7
|
1.0
|
CD
|
a:GLU333
|
3.2
|
123.5
|
1.0
|
MN1
|
a:OEX404
|
3.3
|
240.8
|
1.0
|
CA1
|
a:OEX404
|
3.4
|
237.2
|
1.0
|
OE2
|
a:GLU189
|
3.5
|
81.6
|
1.0
|
O1
|
a:OEX404
|
3.6
|
235.8
|
1.0
|
CD
|
c:GLU342
|
4.1
|
133.3
|
1.0
|
NH2
|
c:ARG345
|
4.3
|
106.0
|
1.0
|
OD1
|
a:ASP170
|
4.4
|
75.9
|
1.0
|
CD
|
a:GLU189
|
4.4
|
86.3
|
1.0
|
NE2
|
a:HIS332
|
4.5
|
104.7
|
1.0
|
OD1
|
a:ASP342
|
4.6
|
146.3
|
1.0
|
NH1
|
c:ARG345
|
4.6
|
106.3
|
1.0
|
OE1
|
a:GLU189
|
4.6
|
91.2
|
1.0
|
OE1
|
c:GLU342
|
4.6
|
133.8
|
1.0
|
CG
|
a:GLU333
|
4.7
|
122.0
|
1.0
|
OD2
|
a:ASP342
|
4.7
|
144.4
|
1.0
|
CE1
|
a:HIS337
|
4.8
|
135.2
|
1.0
|
CD2
|
a:HIS332
|
4.8
|
103.0
|
1.0
|
CZ
|
c:ARG345
|
4.8
|
103.9
|
1.0
|
|
Manganese binding site 8 out
of 8 in 8wb4
Go back to
Manganese Binding Sites List in 8wb4
Manganese binding site 8 out
of 8 in the Structure of Psii-Acpii Supercomplex From Cryptophyte Algae
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Structure of Psii-Acpii Supercomplex From Cryptophyte Algae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mn404
b:231.2
occ:1.00
|
MN4
|
a:OEX404
|
0.0
|
231.2
|
1.0
|
O4
|
a:OEX404
|
2.1
|
230.4
|
1.0
|
O5
|
a:OEX404
|
2.4
|
232.7
|
1.0
|
OD1
|
a:ASP170
|
2.8
|
75.9
|
1.0
|
MN3
|
a:OEX404
|
2.9
|
237.5
|
1.0
|
OE2
|
a:GLU333
|
3.1
|
122.6
|
1.0
|
CG
|
a:ASP170
|
3.5
|
84.0
|
1.0
|
CB
|
a:ASP170
|
3.8
|
72.0
|
1.0
|
CA1
|
a:OEX404
|
3.8
|
237.2
|
1.0
|
O2
|
a:OEX404
|
3.9
|
236.1
|
1.0
|
CD
|
a:GLU333
|
4.1
|
123.5
|
1.0
|
OE1
|
a:GLU189
|
4.1
|
91.2
|
1.0
|
CA
|
a:ASP170
|
4.1
|
66.3
|
1.0
|
OE1
|
a:GLU333
|
4.3
|
120.1
|
1.0
|
OE2
|
a:GLU189
|
4.4
|
81.6
|
1.0
|
OD2
|
a:ASP170
|
4.4
|
94.7
|
1.0
|
O3
|
a:OEX404
|
4.5
|
233.4
|
1.0
|
CD
|
a:GLU189
|
4.7
|
86.3
|
1.0
|
CG1
|
a:VAL185
|
4.7
|
64.7
|
1.0
|
OH
|
a:TYR161
|
4.7
|
67.5
|
1.0
|
NH1
|
c:ARG345
|
4.7
|
106.3
|
1.0
|
CE2
|
a:TYR161
|
4.8
|
61.0
|
1.0
|
MN1
|
a:OEX404
|
4.9
|
240.8
|
1.0
|
N
|
a:ASP170
|
5.0
|
65.2
|
1.0
|
|
Reference:
Z.Mao,
X.Li,
Z.Li,
L.Shen,
X.Li,
Y.Yang,
W.Wang,
T.Kuang,
J.R.Shen,
G.Han.
Structure and Distinct Supramolecular Organization of A Psii-Acpii Dimer From A Cryptophyte Alga Chroomonas Placoidea. Nat Commun V. 15 4535 2024.
ISSN: ESSN 2041-1723
PubMed: 38806516
DOI: 10.1038/S41467-024-48878-X
Page generated: Sun Oct 6 14:10:01 2024
|