Iron in PDB 8gn0: Crystal Structure of Dcbq-Bound Photosystem II Complex
Enzymatic activity of Crystal Structure of Dcbq-Bound Photosystem II Complex
All present enzymatic activity of Crystal Structure of Dcbq-Bound Photosystem II Complex:
1.10.3.9;
Protein crystallography data
The structure of Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0
was solved by
S.Kamada,
Y.Nakajima,
J.-R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.00 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.223,
228.205,
286.997,
90,
90,
90
|
R / Rfree (%)
|
15.2 /
18.5
|
Other elements in 8gn0:
The structure of Crystal Structure of Dcbq-Bound Photosystem II Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Dcbq-Bound Photosystem II Complex
(pdb code 8gn0). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 1 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:54.1
occ:1.00
|
NE2
|
A:HIS215
|
2.0
|
58.1
|
1.0
|
NE2
|
D:HIS214
|
2.1
|
53.7
|
1.0
|
O2
|
A:BCT421
|
2.2
|
60.6
|
1.0
|
NE2
|
D:HIS268
|
2.3
|
46.4
|
1.0
|
NE2
|
A:HIS272
|
2.3
|
53.7
|
1.0
|
O3
|
A:BCT421
|
2.3
|
59.6
|
1.0
|
C
|
A:BCT421
|
2.6
|
65.7
|
1.0
|
CE1
|
A:HIS215
|
2.9
|
53.2
|
1.0
|
CE1
|
D:HIS214
|
3.1
|
48.0
|
1.0
|
CD2
|
D:HIS214
|
3.1
|
47.4
|
1.0
|
CE1
|
D:HIS268
|
3.1
|
51.3
|
1.0
|
CD2
|
A:HIS215
|
3.1
|
44.7
|
1.0
|
CE1
|
A:HIS272
|
3.2
|
56.6
|
1.0
|
CD2
|
D:HIS268
|
3.4
|
48.2
|
1.0
|
CD2
|
A:HIS272
|
3.4
|
54.2
|
1.0
|
O1
|
A:BCT421
|
3.8
|
75.3
|
1.0
|
ND1
|
A:HIS215
|
4.1
|
51.5
|
1.0
|
ND1
|
D:HIS214
|
4.2
|
49.6
|
1.0
|
CG
|
A:HIS215
|
4.2
|
53.0
|
1.0
|
CG
|
D:HIS214
|
4.2
|
47.4
|
1.0
|
ND1
|
D:HIS268
|
4.3
|
51.1
|
1.0
|
ND1
|
A:HIS272
|
4.4
|
57.0
|
1.0
|
CG
|
D:HIS268
|
4.4
|
46.8
|
1.0
|
CG
|
A:HIS272
|
4.5
|
53.6
|
1.0
|
CG2
|
A:VAL219
|
4.6
|
51.1
|
1.0
|
CG2
|
D:VAL218
|
4.7
|
49.3
|
1.0
|
OH
|
A:TYR246
|
4.9
|
83.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 2 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe101
b:72.0
occ:1.00
|
FE
|
F:HEM101
|
0.0
|
72.0
|
1.0
|
NE2
|
E:HIS23
|
2.0
|
74.0
|
1.0
|
NB
|
F:HEM101
|
2.0
|
66.4
|
1.0
|
NC
|
F:HEM101
|
2.0
|
68.7
|
1.0
|
NA
|
F:HEM101
|
2.1
|
74.4
|
1.0
|
NE2
|
F:HIS24
|
2.1
|
73.5
|
1.0
|
ND
|
F:HEM101
|
2.1
|
70.3
|
1.0
|
CD2
|
F:HIS24
|
3.0
|
70.4
|
1.0
|
CE1
|
E:HIS23
|
3.0
|
75.7
|
1.0
|
CD2
|
E:HIS23
|
3.0
|
68.9
|
1.0
|
C1A
|
F:HEM101
|
3.0
|
72.4
|
1.0
|
C1C
|
F:HEM101
|
3.0
|
67.1
|
1.0
|
C4A
|
F:HEM101
|
3.1
|
76.2
|
1.0
|
C4D
|
F:HEM101
|
3.1
|
74.0
|
1.0
|
C4B
|
F:HEM101
|
3.1
|
66.0
|
1.0
|
C1B
|
F:HEM101
|
3.1
|
72.3
|
1.0
|
C4C
|
F:HEM101
|
3.1
|
71.4
|
1.0
|
C1D
|
F:HEM101
|
3.1
|
64.4
|
1.0
|
CE1
|
F:HIS24
|
3.1
|
71.7
|
1.0
|
CHA
|
F:HEM101
|
3.4
|
71.1
|
1.0
|
CHC
|
F:HEM101
|
3.4
|
61.1
|
1.0
|
CHB
|
F:HEM101
|
3.4
|
78.7
|
1.0
|
CHD
|
F:HEM101
|
3.5
|
70.8
|
1.0
|
ND1
|
E:HIS23
|
4.1
|
73.0
|
1.0
|
CG
|
F:HIS24
|
4.1
|
74.0
|
1.0
|
CG
|
E:HIS23
|
4.2
|
73.7
|
1.0
|
ND1
|
F:HIS24
|
4.2
|
72.4
|
1.0
|
C2A
|
F:HEM101
|
4.2
|
79.8
|
1.0
|
C3A
|
F:HEM101
|
4.2
|
78.7
|
1.0
|
C2C
|
F:HEM101
|
4.3
|
70.2
|
1.0
|
C3D
|
F:HEM101
|
4.3
|
65.0
|
1.0
|
C3B
|
F:HEM101
|
4.3
|
70.9
|
1.0
|
C2B
|
F:HEM101
|
4.3
|
71.9
|
1.0
|
C3C
|
F:HEM101
|
4.3
|
68.0
|
1.0
|
C2D
|
F:HEM101
|
4.3
|
66.2
|
1.0
|
CE1
|
E:TYR19
|
4.9
|
71.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 3 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe201
b:48.3
occ:1.00
|
FE
|
V:HEC201
|
0.0
|
48.3
|
1.0
|
NE2
|
V:HIS92
|
2.0
|
50.9
|
1.0
|
NE2
|
V:HIS41
|
2.0
|
43.6
|
1.0
|
NC
|
V:HEC201
|
2.0
|
45.1
|
1.0
|
NA
|
V:HEC201
|
2.1
|
48.7
|
1.0
|
NB
|
V:HEC201
|
2.1
|
47.7
|
1.0
|
ND
|
V:HEC201
|
2.1
|
46.3
|
1.0
|
CE1
|
V:HIS92
|
2.9
|
51.2
|
1.0
|
CE1
|
V:HIS41
|
2.9
|
46.2
|
1.0
|
CD2
|
V:HIS41
|
3.0
|
49.1
|
1.0
|
CD2
|
V:HIS92
|
3.0
|
51.9
|
1.0
|
C4C
|
V:HEC201
|
3.0
|
45.9
|
1.0
|
C1C
|
V:HEC201
|
3.1
|
46.9
|
1.0
|
C1D
|
V:HEC201
|
3.1
|
50.8
|
1.0
|
C4A
|
V:HEC201
|
3.1
|
50.7
|
1.0
|
C4D
|
V:HEC201
|
3.1
|
50.5
|
1.0
|
C1A
|
V:HEC201
|
3.1
|
45.8
|
1.0
|
C1B
|
V:HEC201
|
3.1
|
48.2
|
1.0
|
C4B
|
V:HEC201
|
3.1
|
46.9
|
1.0
|
CHD
|
V:HEC201
|
3.4
|
45.7
|
1.0
|
CHA
|
V:HEC201
|
3.4
|
45.9
|
1.0
|
CHB
|
V:HEC201
|
3.4
|
47.6
|
1.0
|
CHC
|
V:HEC201
|
3.5
|
45.6
|
1.0
|
ND1
|
V:HIS92
|
4.0
|
52.3
|
1.0
|
ND1
|
V:HIS41
|
4.1
|
44.0
|
1.0
|
CG
|
V:HIS92
|
4.1
|
54.1
|
1.0
|
CG
|
V:HIS41
|
4.2
|
48.8
|
1.0
|
C3C
|
V:HEC201
|
4.3
|
41.6
|
1.0
|
C2C
|
V:HEC201
|
4.3
|
45.6
|
1.0
|
C3A
|
V:HEC201
|
4.3
|
49.6
|
1.0
|
C2A
|
V:HEC201
|
4.3
|
49.0
|
1.0
|
C3D
|
V:HEC201
|
4.3
|
46.1
|
1.0
|
C2D
|
V:HEC201
|
4.3
|
46.9
|
1.0
|
C2B
|
V:HEC201
|
4.3
|
43.2
|
1.0
|
C3B
|
V:HEC201
|
4.3
|
50.2
|
1.0
|
CE1
|
V:TYR75
|
4.8
|
45.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 4 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe2605
b:52.3
occ:1.00
|
NE2
|
a:HIS215
|
2.1
|
50.9
|
1.0
|
O2
|
a:BCT2608
|
2.1
|
56.9
|
1.0
|
NE2
|
d:HIS214
|
2.1
|
49.9
|
1.0
|
NE2
|
a:HIS272
|
2.3
|
45.6
|
1.0
|
NE2
|
d:HIS268
|
2.3
|
44.8
|
1.0
|
O3
|
a:BCT2608
|
2.3
|
61.8
|
1.0
|
C
|
a:BCT2608
|
2.6
|
66.6
|
1.0
|
CE1
|
a:HIS215
|
3.0
|
49.6
|
1.0
|
CD2
|
a:HIS215
|
3.1
|
45.8
|
1.0
|
CE1
|
d:HIS214
|
3.1
|
45.9
|
1.0
|
CD2
|
d:HIS214
|
3.1
|
41.6
|
1.0
|
CE1
|
a:HIS272
|
3.2
|
50.9
|
1.0
|
CE1
|
d:HIS268
|
3.2
|
44.9
|
1.0
|
CD2
|
d:HIS268
|
3.3
|
42.2
|
1.0
|
CD2
|
a:HIS272
|
3.3
|
49.2
|
1.0
|
O1
|
a:BCT2608
|
3.8
|
74.5
|
1.0
|
ND1
|
a:HIS215
|
4.2
|
49.5
|
1.0
|
ND1
|
d:HIS214
|
4.2
|
45.8
|
1.0
|
CG
|
a:HIS215
|
4.2
|
45.9
|
1.0
|
CG
|
d:HIS214
|
4.3
|
45.5
|
1.0
|
ND1
|
a:HIS272
|
4.3
|
51.9
|
1.0
|
ND1
|
d:HIS268
|
4.4
|
44.1
|
1.0
|
CG
|
a:HIS272
|
4.4
|
50.1
|
1.0
|
CG
|
d:HIS268
|
4.4
|
43.2
|
1.0
|
CG2
|
a:VAL219
|
4.6
|
51.6
|
1.0
|
CG2
|
d:VAL218
|
4.9
|
45.2
|
1.0
|
OH
|
a:TYR246
|
5.0
|
77.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 5 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe103
b:69.3
occ:1.00
|
FE
|
e:HEM103
|
0.0
|
69.3
|
1.0
|
NC
|
e:HEM103
|
2.0
|
69.5
|
1.0
|
NE2
|
e:HIS23
|
2.1
|
72.3
|
1.0
|
NB
|
e:HEM103
|
2.1
|
65.0
|
1.0
|
NE2
|
f:HIS24
|
2.1
|
74.5
|
1.0
|
NA
|
e:HEM103
|
2.1
|
70.2
|
1.0
|
ND
|
e:HEM103
|
2.1
|
69.1
|
1.0
|
CD2
|
f:HIS24
|
3.0
|
66.5
|
1.0
|
C1C
|
e:HEM103
|
3.0
|
69.0
|
1.0
|
CE1
|
e:HIS23
|
3.0
|
72.6
|
1.0
|
C1A
|
e:HEM103
|
3.0
|
69.1
|
1.0
|
C4D
|
e:HEM103
|
3.0
|
69.1
|
1.0
|
C4C
|
e:HEM103
|
3.1
|
72.3
|
1.0
|
C4B
|
e:HEM103
|
3.1
|
71.8
|
1.0
|
CD2
|
e:HIS23
|
3.1
|
72.3
|
1.0
|
C1D
|
e:HEM103
|
3.1
|
76.2
|
1.0
|
CE1
|
f:HIS24
|
3.1
|
72.6
|
1.0
|
C4A
|
e:HEM103
|
3.1
|
75.7
|
1.0
|
C1B
|
e:HEM103
|
3.2
|
72.2
|
1.0
|
CHC
|
e:HEM103
|
3.4
|
69.4
|
1.0
|
CHA
|
e:HEM103
|
3.4
|
67.2
|
1.0
|
CHD
|
e:HEM103
|
3.5
|
75.4
|
1.0
|
CHB
|
e:HEM103
|
3.6
|
74.1
|
1.0
|
ND1
|
e:HIS23
|
4.1
|
74.1
|
1.0
|
CG
|
f:HIS24
|
4.2
|
66.5
|
1.0
|
CG
|
e:HIS23
|
4.2
|
76.1
|
1.0
|
ND1
|
f:HIS24
|
4.2
|
68.3
|
1.0
|
C2C
|
e:HEM103
|
4.2
|
76.1
|
1.0
|
C3C
|
e:HEM103
|
4.2
|
75.4
|
1.0
|
C2A
|
e:HEM103
|
4.3
|
79.6
|
1.0
|
C3D
|
e:HEM103
|
4.3
|
76.5
|
1.0
|
C2D
|
e:HEM103
|
4.3
|
77.0
|
1.0
|
C3A
|
e:HEM103
|
4.3
|
78.4
|
1.0
|
C3B
|
e:HEM103
|
4.3
|
80.8
|
1.0
|
C2B
|
e:HEM103
|
4.4
|
78.5
|
1.0
|
CE1
|
e:TYR19
|
4.9
|
77.0
|
1.0
|
NE1
|
f:TRP20
|
5.0
|
80.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 8gn0
Go back to
Iron Binding Sites List in 8gn0
Iron binding site 6 out
of 6 in the Crystal Structure of Dcbq-Bound Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe201
b:56.7
occ:1.00
|
FE
|
v:HEC201
|
0.0
|
56.7
|
1.0
|
NE2
|
v:HIS41
|
2.0
|
53.3
|
1.0
|
NC
|
v:HEC201
|
2.0
|
55.5
|
1.0
|
NB
|
v:HEC201
|
2.0
|
59.1
|
1.0
|
NE2
|
v:HIS92
|
2.0
|
52.8
|
1.0
|
NA
|
v:HEC201
|
2.1
|
59.0
|
1.0
|
ND
|
v:HEC201
|
2.1
|
54.7
|
1.0
|
CD2
|
v:HIS41
|
3.0
|
50.7
|
1.0
|
CD2
|
v:HIS92
|
3.0
|
52.7
|
1.0
|
CE1
|
v:HIS41
|
3.0
|
51.3
|
1.0
|
C1C
|
v:HEC201
|
3.0
|
58.6
|
1.0
|
C4B
|
v:HEC201
|
3.0
|
61.1
|
1.0
|
CE1
|
v:HIS92
|
3.0
|
54.8
|
1.0
|
C4D
|
v:HEC201
|
3.1
|
55.0
|
1.0
|
C4C
|
v:HEC201
|
3.1
|
57.9
|
1.0
|
C1A
|
v:HEC201
|
3.1
|
53.6
|
1.0
|
C1B
|
v:HEC201
|
3.1
|
58.5
|
1.0
|
C1D
|
v:HEC201
|
3.1
|
55.5
|
1.0
|
C4A
|
v:HEC201
|
3.1
|
61.9
|
1.0
|
CHC
|
v:HEC201
|
3.4
|
62.3
|
1.0
|
CHA
|
v:HEC201
|
3.4
|
50.2
|
1.0
|
CHD
|
v:HEC201
|
3.4
|
52.7
|
1.0
|
CHB
|
v:HEC201
|
3.5
|
54.0
|
1.0
|
ND1
|
v:HIS41
|
4.1
|
50.5
|
1.0
|
ND1
|
v:HIS92
|
4.1
|
57.1
|
1.0
|
CG
|
v:HIS41
|
4.1
|
55.1
|
1.0
|
CG
|
v:HIS92
|
4.1
|
56.1
|
1.0
|
C2C
|
v:HEC201
|
4.3
|
53.8
|
1.0
|
C3B
|
v:HEC201
|
4.3
|
60.1
|
1.0
|
C3D
|
v:HEC201
|
4.3
|
53.0
|
1.0
|
C3C
|
v:HEC201
|
4.3
|
53.8
|
1.0
|
C2B
|
v:HEC201
|
4.3
|
58.3
|
1.0
|
C2A
|
v:HEC201
|
4.3
|
56.4
|
1.0
|
C2D
|
v:HEC201
|
4.3
|
55.4
|
1.0
|
C3A
|
v:HEC201
|
4.3
|
59.7
|
1.0
|
CE1
|
v:TYR75
|
4.9
|
63.0
|
1.0
|
|
Reference:
S.Kamada,
Y.Nakajima,
J.R.Shen.
Structural Insights Into the Action Mechanisms of Artificial Electron Acceptors in Photosystem II. J.Biol.Chem. V. 299 04839 2023.
ISSN: ESSN 1083-351X
PubMed: 37209822
DOI: 10.1016/J.JBC.2023.104839
Page generated: Sat Aug 10 04:55:05 2024
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