Iron in PDB 7d1u: Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution:
1.10.3.9;

Other elements in 7d1u:

The structure of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution (pdb code 7d1u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution, PDB code: 7d1u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7d1u

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Iron binding site 1 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:8.0
occ:1.00
NE2 A:HIS215 2.0 10.3 1.0
NE2 D:HIS214 2.2 8.3 1.0
NE2 D:HIS268 2.2 9.1 1.0
NE2 A:HIS272 2.2 11.9 1.0
O3 A:BCT414 2.3 12.4 1.0
O2 A:BCT414 2.3 12.5 1.0
C A:BCT414 2.8 12.5 1.0
CE1 A:HIS215 2.9 10.3 1.0
CE1 D:HIS268 3.1 9.1 1.0
CE1 A:HIS272 3.1 11.9 1.0
CD2 A:HIS215 3.1 10.3 1.0
CD2 D:HIS214 3.1 8.3 1.0
CE1 D:HIS214 3.2 8.3 1.0
CD2 D:HIS268 3.2 9.1 1.0
CD2 A:HIS272 3.3 11.9 1.0
O1 A:BCT414 3.9 12.5 1.0
ND1 A:HIS215 4.1 10.4 1.0
CG A:HIS215 4.2 10.3 1.0
ND1 D:HIS268 4.2 9.1 1.0
ND1 A:HIS272 4.3 11.9 1.0
ND1 D:HIS214 4.3 8.3 1.0
CG D:HIS214 4.3 8.3 1.0
CG D:HIS268 4.3 9.1 1.0
CG A:HIS272 4.4 11.9 1.0
CG2 A:VAL219 4.6 12.1 1.0
OH A:TYR246 4.8 20.3 1.0
OH D:TYR244 4.8 14.5 1.0
CG2 D:VAL218 4.8 9.8 1.0

Iron binding site 2 out of 6 in 7d1u

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Iron binding site 2 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:21.6
occ:1.00
FE E:HEM103 0.0 21.6 1.0
NC E:HEM103 2.0 21.6 1.0
ND E:HEM103 2.0 21.6 1.0
NE2 F:HIS24 2.0 20.0 1.0
NA E:HEM103 2.1 21.6 1.0
NB E:HEM103 2.1 21.6 1.0
NE2 E:HIS23 2.1 26.8 1.0
CE1 E:HIS23 3.0 26.7 1.0
C1A E:HEM103 3.0 21.7 1.0
C4D E:HEM103 3.0 21.7 1.0
C1C E:HEM103 3.0 21.6 1.0
CD2 F:HIS24 3.0 19.9 1.0
CE1 F:HIS24 3.0 20.0 1.0
C1D E:HEM103 3.0 21.6 1.0
C4A E:HEM103 3.0 21.7 1.0
C4B E:HEM103 3.1 21.6 1.0
C4C E:HEM103 3.1 21.6 1.0
C1B E:HEM103 3.1 21.6 1.0
CD2 E:HIS23 3.2 26.8 1.0
CHA E:HEM103 3.4 21.7 1.0
CHC E:HEM103 3.4 21.6 1.0
CHD E:HEM103 3.4 21.6 1.0
CHB E:HEM103 3.4 21.7 1.0
ND1 E:HIS23 4.1 26.8 1.0
ND1 F:HIS24 4.1 19.9 1.0
CG F:HIS24 4.2 19.9 1.0
C2A E:HEM103 4.2 21.8 1.0
C3D E:HEM103 4.2 21.7 1.0
C3A E:HEM103 4.2 21.7 1.0
C2D E:HEM103 4.2 21.7 1.0
C2C E:HEM103 4.2 21.5 1.0
CG E:HIS23 4.2 26.9 1.0
C3C E:HEM103 4.3 21.6 1.0
C3B E:HEM103 4.3 21.7 1.0
C2B E:HEM103 4.3 21.7 1.0
CE1 E:TYR19 4.8 27.4 1.0
NE1 F:TRP20 4.9 22.7 1.0

Iron binding site 3 out of 6 in 7d1u

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Iron binding site 3 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:22.1
occ:1.00
FE V:HEC201 0.0 22.1 1.0
NE2 V:HIS41 1.9 19.9 1.0
ND V:HEC201 2.0 22.2 1.0
NB V:HEC201 2.0 22.2 1.0
NC V:HEC201 2.0 22.2 1.0
NA V:HEC201 2.1 22.1 1.0
NE2 V:HIS92 2.2 24.9 1.0
CE1 V:HIS41 2.9 19.9 1.0
CD2 V:HIS41 2.9 20.0 1.0
C1D V:HEC201 3.0 22.2 1.0
C1B V:HEC201 3.0 22.2 1.0
C4C V:HEC201 3.0 22.2 1.0
C4D V:HEC201 3.0 22.2 1.0
C4A V:HEC201 3.1 22.1 1.0
C4B V:HEC201 3.1 22.2 1.0
C1C V:HEC201 3.1 22.2 1.0
C1A V:HEC201 3.1 22.1 1.0
CE1 V:HIS92 3.1 25.0 1.0
CD2 V:HIS92 3.1 25.0 1.0
CHD V:HEC201 3.3 22.2 1.0
CHB V:HEC201 3.4 22.1 1.0
CHC V:HEC201 3.4 22.2 1.0
CHA V:HEC201 3.4 22.2 1.0
ND1 V:HIS41 4.0 19.9 1.0
CG V:HIS41 4.1 20.0 1.0
C2D V:HEC201 4.2 22.2 1.0
C2B V:HEC201 4.2 22.3 1.0
C3D V:HEC201 4.2 22.3 1.0
ND1 V:HIS92 4.2 25.1 1.0
C3C V:HEC201 4.2 22.3 1.0
C3B V:HEC201 4.3 22.3 1.0
CG V:HIS92 4.3 25.1 1.0
C3A V:HEC201 4.3 22.1 1.0
C2C V:HEC201 4.3 22.3 1.0
C2A V:HEC201 4.3 22.2 1.0
CE2 V:TYR75 4.9 26.2 1.0

Iron binding site 4 out of 6 in 7d1u

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Iron binding site 4 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe402

b:8.0
occ:1.00
NE2 a:HIS215 2.0 10.3 1.0
NE2 d:HIS214 2.2 8.3 1.0
NE2 d:HIS268 2.2 9.2 1.0
NE2 a:HIS272 2.2 11.8 1.0
O3 a:BCT414 2.3 12.4 1.0
O2 a:BCT414 2.3 12.4 1.0
C a:BCT414 2.8 12.4 1.0
CE1 a:HIS215 2.9 10.3 1.0
CE1 d:HIS268 3.1 9.2 1.0
CE1 a:HIS272 3.1 11.9 1.0
CD2 a:HIS215 3.1 10.3 1.0
CD2 d:HIS214 3.1 8.3 1.0
CE1 d:HIS214 3.2 8.3 1.0
CD2 d:HIS268 3.2 9.2 1.0
CD2 a:HIS272 3.3 11.9 1.0
O1 a:BCT414 3.9 12.5 1.0
ND1 a:HIS215 4.1 10.4 1.0
CG a:HIS215 4.2 10.3 1.0
ND1 d:HIS268 4.2 9.2 1.0
ND1 a:HIS272 4.3 11.9 1.0
ND1 d:HIS214 4.3 8.3 1.0
CG d:HIS214 4.3 8.3 1.0
CG d:HIS268 4.3 9.2 1.0
CG a:HIS272 4.4 11.9 1.0
CG2 a:VAL219 4.6 12.1 1.0
OH a:TYR246 4.8 20.4 1.0
OH d:TYR244 4.8 14.6 1.0
CG2 d:VAL218 4.8 9.8 1.0

Iron binding site 5 out of 6 in 7d1u

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Iron binding site 5 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe103

b:21.8
occ:1.00
FE e:HEM103 0.0 21.8 1.0
NC e:HEM103 2.0 21.7 1.0
ND e:HEM103 2.0 21.8 1.0
NE2 f:HIS24 2.0 20.1 1.0
NA e:HEM103 2.1 21.8 1.0
NB e:HEM103 2.1 21.8 1.0
NE2 e:HIS23 2.1 27.0 1.0
CE1 e:HIS23 3.0 26.9 1.0
C1A e:HEM103 3.0 21.8 1.0
C4D e:HEM103 3.0 21.8 1.0
C1C e:HEM103 3.0 21.7 1.0
CD2 f:HIS24 3.0 20.1 1.0
CE1 f:HIS24 3.0 20.2 1.0
C1D e:HEM103 3.0 21.8 1.0
C4A e:HEM103 3.0 21.8 1.0
C4B e:HEM103 3.1 21.8 1.0
C4C e:HEM103 3.1 21.7 1.0
C1B e:HEM103 3.1 21.8 1.0
CD2 e:HIS23 3.2 27.0 1.0
CHA e:HEM103 3.4 21.8 1.0
CHC e:HEM103 3.4 21.7 1.0
CHD e:HEM103 3.4 21.8 1.0
CHB e:HEM103 3.4 21.8 1.0
ND1 e:HIS23 4.1 27.0 1.0
ND1 f:HIS24 4.1 20.1 1.0
CG f:HIS24 4.2 20.1 1.0
C2A e:HEM103 4.2 21.9 1.0
C3D e:HEM103 4.2 21.8 1.0
C3A e:HEM103 4.2 21.9 1.0
C2D e:HEM103 4.2 21.8 1.0
C2C e:HEM103 4.2 21.7 1.0
CG e:HIS23 4.2 27.1 1.0
C3C e:HEM103 4.3 21.7 1.0
C3B e:HEM103 4.3 21.8 1.0
C2B e:HEM103 4.3 21.8 1.0
CE1 e:TYR19 4.8 27.6 1.0
NE1 f:TRP20 4.9 22.9 1.0

Iron binding site 6 out of 6 in 7d1u

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Iron binding site 6 out of 6 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:22.5
occ:1.00
FE v:HEC201 0.0 22.5 1.0
NE2 v:HIS41 1.9 20.0 1.0
ND v:HEC201 2.0 22.5 1.0
NB v:HEC201 2.0 22.5 1.0
NC v:HEC201 2.0 22.5 1.0
NA v:HEC201 2.1 22.5 1.0
NE2 v:HIS92 2.2 25.0 1.0
CE1 v:HIS41 2.9 20.0 1.0
CD2 v:HIS41 2.9 20.0 1.0
C1D v:HEC201 3.0 22.5 1.0
C1B v:HEC201 3.0 22.6 1.0
C4C v:HEC201 3.0 22.6 1.0
C4D v:HEC201 3.0 22.5 1.0
C4A v:HEC201 3.1 22.5 1.0
C4B v:HEC201 3.1 22.6 1.0
C1C v:HEC201 3.1 22.5 1.0
C1A v:HEC201 3.1 22.5 1.0
CE1 v:HIS92 3.1 25.0 1.0
CD2 v:HIS92 3.1 25.0 1.0
CHD v:HEC201 3.3 22.6 1.0
CHB v:HEC201 3.4 22.5 1.0
CHC v:HEC201 3.4 22.6 1.0
CHA v:HEC201 3.4 22.5 1.0
ND1 v:HIS41 4.0 20.0 1.0
CG v:HIS41 4.1 20.0 1.0
C2D v:HEC201 4.2 22.6 1.0
C2B v:HEC201 4.2 22.6 1.0
C3D v:HEC201 4.2 22.6 1.0
ND1 v:HIS92 4.2 25.1 1.0
C3C v:HEC201 4.2 22.6 1.0
C3B v:HEC201 4.3 22.7 1.0
CG v:HIS92 4.3 25.2 1.0
C3A v:HEC201 4.3 22.5 1.0
C2C v:HEC201 4.3 22.6 1.0
C2A v:HEC201 4.3 22.5 1.0
CE2 v:TYR75 4.9 26.2 1.0

Reference:

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3
Page generated: Sat Apr 3 15:54:23 2021

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