Iron in PDB 7cou: Structure of Cyanobacterial Photosystem II in the Dark S1 State

Enzymatic activity of Structure of Cyanobacterial Photosystem II in the Dark S1 State

All present enzymatic activity of Structure of Cyanobacterial Photosystem II in the Dark S1 State:
1.10.3.9;

Protein crystallography data

The structure of Structure of Cyanobacterial Photosystem II in the Dark S1 State, PDB code: 7cou was solved by H.Li, J.-R.Shen, M.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.15, 232.7, 288.25, 90, 90, 90
R / Rfree (%) 16.9 / 21.1

Other elements in 7cou:

The structure of Structure of Cyanobacterial Photosystem II in the Dark S1 State also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms
Calcium (Ca) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cyanobacterial Photosystem II in the Dark S1 State (pdb code 7cou). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Cyanobacterial Photosystem II in the Dark S1 State, PDB code: 7cou:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7cou

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Iron binding site 1 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:53.4
occ:1.00
NE2 A:HIS215 2.0 48.0 1.0
O2 D:BCT401 2.1 51.8 1.0
NE2 D:HIS214 2.1 45.8 1.0
O1 D:BCT401 2.1 57.9 1.0
NE2 D:HIS268 2.3 46.8 1.0
NE2 A:HIS272 2.3 45.5 1.0
C D:BCT401 2.4 62.3 1.0
CE1 A:HIS215 2.8 41.0 1.0
CE1 D:HIS214 3.0 43.4 1.0
CD2 D:HIS214 3.1 39.0 1.0
CD2 A:HIS215 3.2 40.8 1.0
CE1 A:HIS272 3.2 46.3 1.0
CD2 D:HIS268 3.2 39.2 1.0
CE1 D:HIS268 3.3 39.7 1.0
CD2 A:HIS272 3.4 45.7 1.0
O3 D:BCT401 3.7 61.8 1.0
ND1 A:HIS215 4.0 43.5 1.0
ND1 D:HIS214 4.2 39.0 1.0
CG A:HIS215 4.2 42.5 1.0
CG D:HIS214 4.2 41.0 1.0
ND1 A:HIS272 4.4 46.7 1.0
CG D:HIS268 4.4 46.7 1.0
ND1 D:HIS268 4.4 47.6 1.0
CG A:HIS272 4.5 48.6 1.0
CG2 A:VAL219 4.6 47.8 1.0
CG2 D:VAL218 4.8 40.9 1.0

Iron binding site 2 out of 6 in 7cou

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Iron binding site 2 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:69.0
occ:1.00
FE E:HEC103 0.0 69.0 1.0
ND E:HEC103 2.0 66.0 1.0
NA E:HEC103 2.0 69.0 1.0
NC E:HEC103 2.1 63.0 1.0
NE2 F:HIS24 2.1 66.1 1.0
NE2 E:HIS23 2.1 72.0 1.0
NB E:HEC103 2.1 65.2 1.0
C4D E:HEC103 2.9 64.8 1.0
C1A E:HEC103 3.0 68.6 1.0
C1D E:HEC103 3.0 64.2 1.0
CE1 F:HIS24 3.0 67.6 1.0
C4C E:HEC103 3.1 63.6 1.0
C4A E:HEC103 3.1 70.0 1.0
CD2 E:HIS23 3.1 73.2 1.0
C4B E:HEC103 3.1 59.4 1.0
C1B E:HEC103 3.1 65.3 1.0
CD2 F:HIS24 3.1 67.4 1.0
CE1 E:HIS23 3.1 72.7 1.0
C1C E:HEC103 3.1 60.9 1.0
CHA E:HEC103 3.3 64.6 1.0
CHD E:HEC103 3.4 65.9 1.0
CHB E:HEC103 3.5 65.9 1.0
CHC E:HEC103 3.5 57.5 1.0
C2A E:HEC103 4.2 75.0 1.0
C3D E:HEC103 4.2 65.9 1.0
ND1 F:HIS24 4.2 68.0 1.0
C2D E:HEC103 4.2 63.8 1.0
ND1 E:HIS23 4.2 71.0 1.0
C3A E:HEC103 4.2 78.1 1.0
CG F:HIS24 4.2 67.6 1.0
CG E:HIS23 4.2 70.8 1.0
C3C E:HEC103 4.3 61.0 1.0
C2C E:HEC103 4.3 63.5 1.0
C2B E:HEC103 4.3 64.1 1.0
C3B E:HEC103 4.3 65.4 1.0
CE2 E:TYR19 4.9 69.0 1.0
NE1 F:TRP20 5.0 72.4 1.0

Iron binding site 3 out of 6 in 7cou

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Iron binding site 3 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:50.6
occ:1.00
FE V:HEC201 0.0 50.6 1.0
NA V:HEC201 2.0 48.2 1.0
NB V:HEC201 2.1 46.8 1.0
NC V:HEC201 2.1 47.7 1.0
NE2 V:HIS41 2.1 44.2 1.0
NE2 V:HIS92 2.1 46.0 1.0
ND V:HEC201 2.1 46.1 1.0
CD2 V:HIS92 3.0 51.4 1.0
CD2 V:HIS41 3.0 44.1 1.0
C4A V:HEC201 3.0 45.9 1.0
C1B V:HEC201 3.1 46.0 1.0
C1D V:HEC201 3.1 44.2 1.0
C1A V:HEC201 3.1 49.7 1.0
C4C V:HEC201 3.1 47.1 1.0
C4D V:HEC201 3.1 44.9 1.0
CE1 V:HIS41 3.1 48.5 1.0
C1C V:HEC201 3.1 51.0 1.0
C4B V:HEC201 3.1 47.5 1.0
CE1 V:HIS92 3.1 46.7 1.0
CHB V:HEC201 3.4 47.8 1.0
CHD V:HEC201 3.4 45.5 1.0
CHC V:HEC201 3.5 45.5 1.0
CHA V:HEC201 3.5 45.1 1.0
CG V:HIS92 4.2 55.8 1.0
ND1 V:HIS41 4.2 48.7 1.0
CG V:HIS41 4.2 43.5 1.0
ND1 V:HIS92 4.2 47.1 1.0
C3A V:HEC201 4.3 51.9 1.0
C2B V:HEC201 4.3 46.3 1.0
C2A V:HEC201 4.3 46.5 1.0
C3D V:HEC201 4.3 44.9 1.0
C2D V:HEC201 4.3 44.1 1.0
C3B V:HEC201 4.3 46.1 1.0
C2C V:HEC201 4.3 52.4 1.0
C3C V:HEC201 4.3 48.2 1.0
CE1 V:TYR75 4.8 47.4 1.0
OH V:TYR75 4.9 54.8 1.0

Iron binding site 4 out of 6 in 7cou

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Iron binding site 4 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:57.7
occ:1.00
O2 d:BCT401 2.1 54.1 1.0
NE2 d:HIS214 2.1 46.9 1.0
NE2 a:HIS215 2.2 49.8 1.0
NE2 a:HIS272 2.3 49.1 1.0
O1 d:BCT401 2.4 52.2 1.0
NE2 d:HIS268 2.4 49.9 1.0
C d:BCT401 2.5 62.1 1.0
CE1 a:HIS215 3.0 50.7 1.0
CE1 d:HIS214 3.0 44.5 1.0
CD2 d:HIS214 3.2 45.3 1.0
CE1 a:HIS272 3.2 49.7 1.0
CE1 d:HIS268 3.3 49.7 1.0
CD2 a:HIS215 3.3 44.9 1.0
CD2 a:HIS272 3.4 43.7 1.0
CD2 d:HIS268 3.4 47.9 1.0
O3 d:BCT401 3.7 64.9 1.0
ND1 a:HIS215 4.2 44.4 1.0
ND1 d:HIS214 4.2 45.6 1.0
CG d:HIS214 4.3 46.7 1.0
CG a:HIS215 4.4 45.8 1.0
ND1 a:HIS272 4.4 52.0 1.0
ND1 d:HIS268 4.4 47.5 1.0
CG a:HIS272 4.5 48.1 1.0
CG d:HIS268 4.5 47.8 1.0
CG2 a:VAL219 4.7 43.5 1.0
CG2 d:VAL218 4.8 43.6 1.0
OH d:TYR244 5.0 55.0 1.0

Iron binding site 5 out of 6 in 7cou

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Iron binding site 5 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:81.4
occ:1.00
FE e:HEC102 0.0 81.4 1.0
ND e:HEC102 2.0 70.4 1.0
NA e:HEC102 2.0 83.8 1.0
NC e:HEC102 2.1 78.1 1.0
NE2 e:HIS23 2.1 84.6 1.0
NE2 f:HIS24 2.1 76.1 1.0
NB e:HEC102 2.1 71.4 1.0
CD2 f:HIS24 2.9 75.8 1.0
C4D e:HEC102 2.9 74.5 1.0
C1D e:HEC102 3.0 67.9 1.0
C1A e:HEC102 3.0 78.8 1.0
C4C e:HEC102 3.0 70.1 1.0
C4A e:HEC102 3.1 90.5 1.0
CE1 e:HIS23 3.1 81.5 1.0
C4B e:HEC102 3.1 73.1 1.0
C1B e:HEC102 3.1 78.3 1.0
CD2 e:HIS23 3.1 79.8 1.0
C1C e:HEC102 3.1 72.8 1.0
CE1 f:HIS24 3.2 76.8 1.0
CHA e:HEC102 3.3 75.0 1.0
CHD e:HEC102 3.4 64.7 1.0
CHB e:HEC102 3.5 87.2 1.0
CHC e:HEC102 3.5 68.6 1.0
CG f:HIS24 4.1 74.9 1.0
C3D e:HEC102 4.2 75.0 1.0
ND1 e:HIS23 4.2 84.4 1.0
C2A e:HEC102 4.2 95.2 1.0
C2D e:HEC102 4.2 75.5 1.0
ND1 f:HIS24 4.2 78.6 1.0
CG e:HIS23 4.2 84.7 1.0
C3A e:HEC102 4.2 98.2 1.0
C3C e:HEC102 4.2 71.9 1.0
C2C e:HEC102 4.3 75.2 1.0
C2B e:HEC102 4.3 78.0 1.0
C3B e:HEC102 4.3 78.0 1.0
NE1 f:TRP20 4.9 85.4 1.0
CE2 e:TYR19 4.9 81.6 1.0

Iron binding site 6 out of 6 in 7cou

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Iron binding site 6 out of 6 in the Structure of Cyanobacterial Photosystem II in the Dark S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Cyanobacterial Photosystem II in the Dark S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe202

b:61.4
occ:1.00
FE v:HEC202 0.0 61.4 1.0
NA v:HEC202 2.0 56.9 1.0
ND v:HEC202 2.0 61.1 1.0
NC v:HEC202 2.1 56.4 1.0
NE2 v:HIS41 2.1 53.8 1.0
NB v:HEC202 2.1 63.1 1.0
NE2 v:HIS92 2.1 56.2 1.0
CE1 v:HIS41 3.0 54.0 1.0
CD2 v:HIS92 3.0 56.0 1.0
C1A v:HEC202 3.0 57.5 1.0
C4D v:HEC202 3.0 61.9 1.0
C4A v:HEC202 3.0 59.2 1.0
C1D v:HEC202 3.1 59.7 1.0
C1C v:HEC202 3.1 57.6 1.0
C4B v:HEC202 3.1 63.8 1.0
C4C v:HEC202 3.1 61.4 1.0
C1B v:HEC202 3.1 58.1 1.0
CD2 v:HIS41 3.1 53.7 1.0
CE1 v:HIS92 3.1 60.2 1.0
CHA v:HEC202 3.4 55.0 1.0
CHC v:HEC202 3.4 60.4 1.0
CHD v:HEC202 3.4 53.4 1.0
CHB v:HEC202 3.5 62.3 1.0
ND1 v:HIS41 4.1 58.2 1.0
CG v:HIS92 4.2 57.7 1.0
ND1 v:HIS92 4.2 61.4 1.0
C2A v:HEC202 4.2 57.3 1.0
CG v:HIS41 4.2 59.5 1.0
C3A v:HEC202 4.2 59.5 1.0
C3D v:HEC202 4.2 60.8 1.0
C2D v:HEC202 4.3 64.0 1.0
C2C v:HEC202 4.3 63.0 1.0
C3B v:HEC202 4.3 56.3 1.0
C2B v:HEC202 4.3 56.7 1.0
C3C v:HEC202 4.3 59.7 1.0
CE1 v:TYR75 4.9 58.1 1.0

Reference:

H.Li, , Y.Nakajima, T.Nomura, M.Sugahara, S.Yonekura, S.K.Chan, T.Nakane, T.Yamane, Y.Umena, M.Suzuki, T.Masuda, T.Motomura, H.Naitow, Y.Matsuura, T.Kimura, K.Tono, S.Owada, Y.Joti, R.Tanaka, E.Nango, F.Akita, M.Kubo, S.Iwata, J.R.Shen, M.Suga. Capturing Structural Changes of the S1 to S2 Transition of Photosystem II Using Time-Resolved Serial Femtosecond Crystallography Iucrj V. 81 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521002177
Page generated: Sat Jul 10 15:19:30 2021

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