Iron in PDB 7d1u: 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;

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

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 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 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 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 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 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 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

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