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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:

Calcium (Ca) 7 atoms
Chlorine (Cl) 12 atoms
Manganese (Mn) 8 atoms
Magnesium (Mg) 74 atoms

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

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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

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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

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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

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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

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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

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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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