Iron in PDB 7cji: Photosystem II Structure in the S1 State

Enzymatic activity of Photosystem II Structure in the S1 State

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

Protein crystallography data

The structure of Photosystem II Structure in the S1 State, PDB code: 7cji 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) 39.93 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.02, 231.7, 288.32, 90, 90, 90
R / Rfree (%) 16 / 20.8

Other elements in 7cji:

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

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

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 1 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

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

b:61.2
occ:1.00
NE2 A:HIS215 2.1 56.8 1.0
O2 D:BCT401 2.1 59.3 1.0
NE2 D:HIS214 2.1 55.3 1.0
O1 D:BCT401 2.2 64.6 1.0
NE2 A:HIS272 2.3 55.7 1.0
NE2 D:HIS268 2.3 51.5 1.0
C D:BCT401 2.4 65.4 1.0
CE1 A:HIS215 2.8 47.0 1.0
CE1 D:HIS214 3.0 46.2 1.0
CD2 D:HIS214 3.1 47.3 1.0
CE1 A:HIS272 3.2 53.9 1.0
CD2 A:HIS215 3.2 45.9 1.0
CE1 D:HIS268 3.3 47.9 1.0
CD2 D:HIS268 3.3 45.9 1.0
CD2 A:HIS272 3.3 52.5 1.0
O3 D:BCT401 3.7 66.2 1.0
ND1 A:HIS215 4.0 49.9 1.0
ND1 D:HIS214 4.1 45.7 1.0
CG D:HIS214 4.2 45.4 1.0
CG A:HIS215 4.2 48.3 1.0
ND1 A:HIS272 4.4 56.7 1.0
ND1 D:HIS268 4.4 48.9 1.0
CG A:HIS272 4.4 56.6 1.0
CG D:HIS268 4.4 49.8 1.0
CG2 A:VAL219 4.6 55.2 1.0
CG2 D:VAL218 4.8 47.7 1.0

Iron binding site 2 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 2 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

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

b:75.7
occ:1.00
FE E:HEM103 0.0 75.7 1.0
ND E:HEM103 2.0 71.1 1.0
NA E:HEM103 2.0 73.6 1.0
NC E:HEM103 2.1 70.2 1.0
NE2 F:HIS24 2.1 79.5 1.0
NB E:HEM103 2.1 71.3 1.0
NE2 E:HIS23 2.1 79.1 1.0
C4D E:HEM103 2.9 70.4 1.0
C1A E:HEM103 3.0 76.0 1.0
C1D E:HEM103 3.0 67.8 1.0
CD2 E:HIS23 3.0 79.2 1.0
CE1 F:HIS24 3.0 80.5 1.0
C4C E:HEM103 3.0 66.4 1.0
C4A E:HEM103 3.1 72.6 1.0
CD2 F:HIS24 3.1 80.4 1.0
C4B E:HEM103 3.1 67.4 1.0
C1B E:HEM103 3.1 69.8 1.0
C1C E:HEM103 3.1 69.5 1.0
CE1 E:HIS23 3.2 78.7 1.0
CHA E:HEM103 3.3 74.5 1.0
CHD E:HEM103 3.4 63.0 1.0
CHB E:HEM103 3.5 71.2 1.0
CHC E:HEM103 3.5 67.1 1.0
ND1 F:HIS24 4.1 80.5 1.0
C3D E:HEM103 4.2 71.1 1.0
C2A E:HEM103 4.2 84.5 1.0
C2D E:HEM103 4.2 69.5 1.0
CG F:HIS24 4.2 79.2 1.0
CG E:HIS23 4.2 75.2 1.0
C3A E:HEM103 4.2 84.9 1.0
ND1 E:HIS23 4.2 76.2 1.0
C3C E:HEM103 4.3 66.5 1.0
C2C E:HEM103 4.3 68.8 1.0
C2B E:HEM103 4.3 68.5 1.0
C3B E:HEM103 4.3 71.4 1.0
CE2 E:TYR19 4.9 72.0 1.0

Iron binding site 3 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 3 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

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

b:57.5
occ:1.00
FE V:HEC201 0.0 57.5 1.0
NA V:HEC201 2.0 55.6 1.0
ND V:HEC201 2.1 51.4 1.0
NC V:HEC201 2.1 53.7 1.0
NB V:HEC201 2.1 55.1 1.0
NE2 V:HIS41 2.1 51.0 1.0
NE2 V:HIS92 2.1 52.9 1.0
CD2 V:HIS92 3.0 55.5 1.0
C4A V:HEC201 3.0 56.6 1.0
CD2 V:HIS41 3.0 50.9 1.0
C1D V:HEC201 3.0 51.0 1.0
C1B V:HEC201 3.1 52.8 1.0
C4C V:HEC201 3.1 55.8 1.0
C4D V:HEC201 3.1 51.5 1.0
C1A V:HEC201 3.1 54.4 1.0
CE1 V:HIS41 3.1 56.3 1.0
C1C V:HEC201 3.1 58.4 1.0
C4B V:HEC201 3.1 52.5 1.0
CE1 V:HIS92 3.1 53.5 1.0
CHD V:HEC201 3.4 50.8 1.0
CHB V:HEC201 3.4 52.9 1.0
CHA V:HEC201 3.5 51.9 1.0
CHC V:HEC201 3.5 55.6 1.0
CG V:HIS92 4.2 67.7 1.0
ND1 V:HIS41 4.2 50.0 1.0
CG V:HIS41 4.2 50.3 1.0
ND1 V:HIS92 4.2 54.0 1.0
C3A V:HEC201 4.3 58.8 1.0
C3D V:HEC201 4.3 51.2 1.0
C2A V:HEC201 4.3 53.3 1.0
C2D V:HEC201 4.3 50.9 1.0
C2B V:HEC201 4.3 53.2 1.0
C2C V:HEC201 4.3 62.8 1.0
C3B V:HEC201 4.3 53.0 1.0
C3C V:HEC201 4.3 58.8 1.0
CE1 V:TYR75 4.8 54.2 1.0
OH V:TYR75 4.9 61.0 1.0

Iron binding site 4 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 4 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

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

b:61.0
occ:1.00
O2 d:BCT401 2.1 58.0 1.0
NE2 d:HIS214 2.1 54.4 1.0
NE2 a:HIS215 2.2 54.8 1.0
NE2 a:HIS272 2.3 51.9 1.0
O1 d:BCT401 2.3 57.5 1.0
NE2 d:HIS268 2.4 52.3 1.0
C d:BCT401 2.5 64.5 1.0
CE1 a:HIS215 3.0 55.4 1.0
CE1 d:HIS214 3.1 48.9 1.0
CD2 d:HIS214 3.2 48.1 1.0
CE1 a:HIS272 3.2 51.7 1.0
CD2 a:HIS272 3.3 49.9 1.0
CE1 d:HIS268 3.3 50.4 1.0
CD2 a:HIS215 3.3 50.4 1.0
CD2 d:HIS268 3.4 50.4 1.0
O3 d:BCT401 3.8 67.8 1.0
ND1 a:HIS215 4.2 50.9 1.0
ND1 d:HIS214 4.2 48.0 1.0
CG d:HIS214 4.3 53.6 1.0
ND1 a:HIS272 4.4 54.5 1.0
CG a:HIS215 4.4 53.1 1.0
CG a:HIS272 4.4 52.2 1.0
ND1 d:HIS268 4.5 50.0 1.0
CG d:HIS268 4.6 51.4 1.0
CG2 a:VAL219 4.7 50.4 1.0
CG2 d:VAL218 4.7 49.8 1.0
OH d:TYR244 4.9 58.7 1.0

Iron binding site 5 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 5 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:87.0
occ:1.00
FE f:HEM101 0.0 87.0 1.0
ND f:HEM101 2.0 76.8 1.0
NA f:HEM101 2.0 88.5 1.0
NC f:HEM101 2.1 82.7 1.0
NE2 e:HIS23 2.1 85.6 1.0
NE2 f:HIS24 2.1 80.3 1.0
NB f:HEM101 2.1 77.0 1.0
CD2 f:HIS24 2.9 82.6 1.0
C4D f:HEM101 2.9 80.5 1.0
C1D f:HEM101 3.0 73.2 1.0
C1A f:HEM101 3.0 82.4 1.0
CE1 e:HIS23 3.0 81.9 1.0
C4C f:HEM101 3.0 74.0 1.0
C4A f:HEM101 3.1 90.5 1.0
C4B f:HEM101 3.1 80.0 1.0
C1B f:HEM101 3.1 83.4 1.0
C1C f:HEM101 3.1 78.7 1.0
CD2 e:HIS23 3.1 82.7 1.0
CE1 f:HIS24 3.2 82.9 1.0
CHA f:HEM101 3.3 80.5 1.0
CHD f:HEM101 3.4 70.5 1.0
CHB f:HEM101 3.5 86.8 1.0
CHC f:HEM101 3.5 76.2 1.0
CG f:HIS24 4.1 81.7 1.0
ND1 e:HIS23 4.2 86.7 1.0
C3D f:HEM101 4.2 84.0 1.0
ND1 f:HIS24 4.2 87.1 1.0
C2A f:HEM101 4.2 94.6 1.0
C2D f:HEM101 4.2 81.0 1.0
C3A f:HEM101 4.2 95.8 1.0
CG e:HIS23 4.2 87.5 1.0
C3C f:HEM101 4.2 76.0 1.0
C2C f:HEM101 4.3 82.1 1.0
C2B f:HEM101 4.3 84.4 1.0
C3B f:HEM101 4.3 84.8 1.0
CE2 e:TYR19 4.8 79.2 1.0
NE1 f:TRP20 4.9 85.3 1.0

Iron binding site 6 out of 6 in 7cji

Go back to Iron Binding Sites List in 7cji
Iron binding site 6 out of 6 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe203

b:65.9
occ:1.00
FE v:HEC203 0.0 65.9 1.0
NA v:HEC203 2.0 61.9 1.0
ND v:HEC203 2.0 67.0 1.0
NE2 v:HIS41 2.1 60.1 1.0
NB v:HEC203 2.1 68.9 1.0
NE2 v:HIS92 2.1 62.5 1.0
NC v:HEC203 2.1 66.3 1.0
C1A v:HEC203 3.0 61.8 1.0
C4D v:HEC203 3.0 65.5 1.0
CE1 v:HIS41 3.0 62.3 1.0
C4A v:HEC203 3.0 66.9 1.0
CD2 v:HIS92 3.0 62.4 1.0
C1D v:HEC203 3.1 63.7 1.0
C1B v:HEC203 3.1 64.0 1.0
CE1 v:HIS92 3.1 63.3 1.0
C4B v:HEC203 3.1 67.7 1.0
CD2 v:HIS41 3.1 60.0 1.0
C1C v:HEC203 3.1 66.4 1.0
C4C v:HEC203 3.1 69.5 1.0
CHA v:HEC203 3.3 61.4 1.0
CHB v:HEC203 3.4 68.5 1.0
CHD v:HEC203 3.5 63.6 1.0
CHC v:HEC203 3.5 69.6 1.0
ND1 v:HIS41 4.1 64.8 1.0
CG v:HIS92 4.2 64.2 1.0
ND1 v:HIS92 4.2 63.8 1.0
C2A v:HEC203 4.2 63.1 1.0
C3A v:HEC203 4.2 65.2 1.0
CG v:HIS41 4.2 67.6 1.0
C3D v:HEC203 4.2 65.3 1.0
C2D v:HEC203 4.3 71.9 1.0
C2B v:HEC203 4.3 63.1 1.0
C3B v:HEC203 4.3 64.2 1.0
C2C v:HEC203 4.4 69.1 1.0
C3C v:HEC203 4.4 70.8 1.0
CE1 v:TYR75 4.8 64.4 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 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521002177
Page generated: Sat Jul 10 15:14:51 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy