Iron in PDB 3a0b: Crystal Structure of Br-Substituted Photosystem II Complex

The structure of Crystal Structure of Br-Substituted Photosystem II Complex, PDB code: 3a0b was solved by K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.70 / 3.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.589, 226.394, 307.514, 90.00, 90.00, 90.00
R / Rfree (%)	30.2 / 35.8

The structure of Crystal Structure of Br-Substituted Photosystem II Complex also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Magnesium	(Mg)	70 atoms
Manganese	(Mn)	8 atoms
Calcium	(Ca)	2 atoms

The binding sites of Iron atom in the Crystal Structure of Br-Substituted Photosystem II Complex (pdb code 3a0b). 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 Br-Substituted Photosystem II Complex, PDB code: 3a0b:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:0.7 occ:1.00 NE2 A:HIS272 2.1 0.7 1.0 NE2 A:HIS215 2.3 0.1 1.0 NE2 D:HIS268 2.3 0.1 1.0 CE1 A:HIS215 2.7 0.6 1.0 NE2 D:HIS214 2.7 0.8 1.0 CE1 D:HIS268 2.9 0.0 1.0 OH D:TYR244 3.1 0.1 1.0 CD2 A:HIS272 3.1 0.9 1.0 CE1 A:HIS272 3.1 1.0 1.0 CE1 D:HIS214 3.4 0.7 1.0 CD2 A:HIS215 3.5 0.2 1.0 CD2 D:HIS268 3.6 1.0 1.0 OH A:TYR246 3.8 0.9 1.0 CD2 D:HIS214 3.9 0.0 1.0 ND1 A:HIS215 4.0 0.5 1.0 CZ D:TYR244 4.0 0.6 1.0 ND1 A:HIS272 4.2 0.2 1.0 ND1 D:HIS268 4.2 0.6 1.0 CE1 D:TYR244 4.2 0.3 1.0 CG A:HIS272 4.2 0.6 1.0 CZ A:TYR246 4.4 0.7 1.0 CG A:HIS215 4.4 0.0 1.0 CG D:HIS268 4.5 0.8 1.0 CG1 A:VAL219 4.6 0.1 1.0 CE1 A:TYR246 4.6 0.6 1.0 ND1 D:HIS214 4.7 0.7 1.0 CD2 D:LEU267 4.8 0.7 1.0 CG D:HIS214 4.9 0.1 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe1040 b:0.0 occ:1.00 FE E:HEM1040 0.0 0.0 1.0 NC E:HEM1040 2.1 0.5 1.0 NA E:HEM1040 2.1 0.2 1.0 NB E:HEM1040 2.1 0.9 1.0 ND E:HEM1040 2.1 0.1 1.0 NE2 F:HIS24 2.3 0.8 1.0 NE2 E:HIS23 2.9 0.7 1.0 CE1 F:HIS24 3.0 0.0 1.0 C4C E:HEM1040 3.1 0.6 1.0 C1A E:HEM1040 3.1 0.4 1.0 C1C E:HEM1040 3.1 0.3 1.0 C4A E:HEM1040 3.1 0.2 1.0 C1D E:HEM1040 3.1 0.7 1.0 C4D E:HEM1040 3.1 0.9 1.0 C4B E:HEM1040 3.1 0.6 1.0 C1B E:HEM1040 3.1 0.4 1.0 CHD E:HEM1040 3.4 0.2 1.0 CHA E:HEM1040 3.4 0.0 1.0 CHC E:HEM1040 3.5 0.2 1.0 CHB E:HEM1040 3.5 0.6 1.0 CD2 F:HIS24 3.5 0.9 1.0 CD2 E:HIS23 3.7 0.1 1.0 CE1 E:HIS23 3.9 0.1 1.0 ND1 F:HIS24 4.2 0.2 1.0 C3C E:HEM1040 4.3 0.6 1.0 C2A E:HEM1040 4.3 0.8 1.0 C2C E:HEM1040 4.3 0.8 1.0 C3A E:HEM1040 4.3 0.1 1.0 C3B E:HEM1040 4.3 0.4 1.0 C2B E:HEM1040 4.3 0.4 1.0 C3D E:HEM1040 4.3 0.1 1.0 C2D E:HEM1040 4.3 0.3 1.0 CG F:HIS24 4.5 0.3 1.0 NE1 F:TRP20 4.7 0.1 1.0 CG E:HIS23 4.8 0.6 1.0 ND1 E:HIS23 4.9 0.8 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ V:Fe1041 b:81.4 occ:1.00 FE V:HEM1041 0.0 81.4 1.0 NA V:HEM1041 2.1 0.2 1.0 NC V:HEM1041 2.1 0.3 1.0 NB V:HEM1041 2.1 1.0 1.0 ND V:HEM1041 2.1 0.5 1.0 NE2 V:HIS118 2.3 0.3 1.0 NE2 V:HIS67 2.4 0.4 1.0 CE1 V:HIS67 2.9 0.6 1.0 C1A V:HEM1041 3.1 0.4 1.0 C4C V:HEM1041 3.1 0.2 1.0 C4A V:HEM1041 3.1 0.4 1.0 C1C V:HEM1041 3.1 0.2 1.0 C4D V:HEM1041 3.1 0.3 1.0 C1D V:HEM1041 3.1 0.1 1.0 C1B V:HEM1041 3.1 0.6 1.0 C4B V:HEM1041 3.1 0.8 1.0 CE1 V:HIS118 3.1 0.8 1.0 CD2 V:HIS118 3.3 0.1 1.0 CD2 V:HIS67 3.3 0.2 1.0 CHA V:HEM1041 3.4 0.0 1.0 CHD V:HEM1041 3.4 0.4 1.0 CHC V:HEM1041 3.5 0.1 1.0 CHB V:HEM1041 3.5 0.1 1.0 ND1 V:HIS67 3.9 0.4 1.0 CG V:HIS67 4.1 0.3 1.0 ND1 V:HIS118 4.2 0.4 1.0 C2A V:HEM1041 4.3 1.0 1.0 C3C V:HEM1041 4.3 0.8 1.0 C3A V:HEM1041 4.3 0.9 1.0 C2C V:HEM1041 4.3 0.5 1.0 C3B V:HEM1041 4.3 0.8 1.0 C2B V:HEM1041 4.3 0.9 1.0 C2D V:HEM1041 4.3 0.1 1.0 C3D V:HEM1041 4.3 0.9 1.0 CG V:HIS118 4.3 0.8 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe6002 b:0.4 occ:1.00 NE2 a:HIS5272 2.0 0.7 1.0 NE2 a:HIS5215 2.1 0.6 1.0 CE1 a:HIS5272 2.5 0.1 1.0 CE1 a:HIS5215 2.6 0.0 1.0 NE2 d:HIS5214 2.7 0.6 1.0 NE2 d:HIS5268 2.7 0.8 1.0 OH d:TYR5244 3.1 1.0 1.0 CD2 a:HIS5272 3.3 0.1 1.0 CD2 a:HIS5215 3.4 0.9 1.0 CE1 d:HIS5214 3.4 0.9 1.0 CD2 d:HIS5268 3.5 0.7 1.0 OH a:TYR5246 3.7 0.1 1.0 ND1 a:HIS5272 3.7 0.5 1.0 CE1 d:HIS5268 3.8 0.4 1.0 CD2 d:HIS5214 3.9 0.1 1.0 ND1 a:HIS5215 3.9 0.0 1.0 CZ d:TYR5244 4.1 0.5 1.0 CG a:HIS5272 4.1 0.6 1.0 CG a:HIS5215 4.3 0.7 1.0 CZ a:TYR5246 4.3 1.0 1.0 CE1 d:TYR5244 4.4 0.8 1.0 CE1 a:TYR5246 4.5 0.5 1.0 ND1 d:HIS5214 4.7 0.6 1.0 CG d:HIS5268 4.7 0.8 1.0 ND1 d:HIS5268 4.8 1.0 1.0 NZ d:LYS5264 4.9 0.2 1.0 CG d:HIS5214 4.9 0.8 1.0 CG2 d:VAL5218 5.0 0.3 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ e:Fe6040 b:1.0 occ:1.00 FE e:HEM6040 0.0 1.0 1.0 NC e:HEM6040 2.1 0.2 1.0 NA e:HEM6040 2.1 0.1 1.0 NB e:HEM6040 2.1 0.1 1.0 ND e:HEM6040 2.1 0.9 1.0 NE2 f:HIS5024 2.5 0.5 1.0 NE2 e:HIS5023 2.8 0.3 1.0 C4C e:HEM6040 3.1 0.2 1.0 C1A e:HEM6040 3.1 0.5 1.0 C4A e:HEM6040 3.1 0.8 1.0 C1C e:HEM6040 3.1 0.1 1.0 C1D e:HEM6040 3.1 0.6 1.0 C4D e:HEM6040 3.1 0.7 1.0 C1B e:HEM6040 3.1 0.6 1.0 C4B e:HEM6040 3.1 0.8 1.0 CHD e:HEM6040 3.4 1.0 1.0 CHA e:HEM6040 3.4 1.0 1.0 CE1 f:HIS5024 3.4 0.8 1.0 CHB e:HEM6040 3.5 0.8 1.0 CHC e:HEM6040 3.5 0.2 1.0 CE1 e:HIS5023 3.5 0.6 1.0 CD2 f:HIS5024 3.5 0.5 1.0 CD2 e:HIS5023 3.8 0.4 1.0 C2A e:HEM6040 4.3 1.0 1.0 C3C e:HEM6040 4.3 0.3 1.0 C3A e:HEM6040 4.3 0.2 1.0 C2C e:HEM6040 4.3 0.7 1.0 C3B e:HEM6040 4.3 0.1 1.0 C2B e:HEM6040 4.3 0.5 1.0 C3D e:HEM6040 4.3 0.7 1.0 C2D e:HEM6040 4.3 0.6 1.0 ND1 f:HIS5024 4.6 0.4 1.0 ND1 e:HIS5023 4.6 1.0 1.0 CG f:HIS5024 4.7 0.4 1.0 CG e:HIS5023 4.8 0.5 1.0 NE1 f:TRP5020 4.8 0.8 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Br-Substituted 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 Br-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ v:Fe6041 b:99.8 occ:1.00 FE v:HEM6041 0.0 99.8 1.0 NA v:HEM6041 2.1 0.3 1.0 NC v:HEM6041 2.1 0.9 1.0 NB v:HEM6041 2.1 0.9 1.0 ND v:HEM6041 2.1 0.3 1.0 NE2 v:HIS5118 2.8 0.8 1.0 NE2 v:HIS5067 2.9 0.0 1.0 CD2 v:HIS5067 3.0 0.9 1.0 C1A v:HEM6041 3.1 0.5 1.0 C4C v:HEM6041 3.1 0.5 1.0 C4A v:HEM6041 3.1 0.1 1.0 C1C v:HEM6041 3.1 0.3 1.0 C4D v:HEM6041 3.1 0.9 1.0 C1D v:HEM6041 3.1 0.7 1.0 C4B v:HEM6041 3.1 0.6 1.0 C1B v:HEM6041 3.1 0.5 1.0 CE1 v:HIS5118 3.3 0.7 1.0 CHA v:HEM6041 3.4 0.6 1.0 CHD v:HEM6041 3.4 0.2 1.0 CHC v:HEM6041 3.5 0.3 1.0 CHB v:HEM6041 3.5 0.7 1.0 CD2 v:HIS5118 3.8 0.3 1.0 CE1 v:HIS5067 4.1 1.0 1.0 C2A v:HEM6041 4.3 0.9 1.0 C3C v:HEM6041 4.3 0.3 1.0 C2C v:HEM6041 4.3 0.2 1.0 C3A v:HEM6041 4.3 0.2 1.0 ND1 v:HIS5118 4.3 0.9 1.0 C3B v:HEM6041 4.3 0.2 1.0 C2B v:HEM6041 4.3 0.5 1.0 C2D v:HEM6041 4.3 1.0 1.0 C3D v:HEM6041 4.3 0.0 1.0 CG v:HIS5067 4.4 0.6 1.0 CG v:HIS5118 4.6 0.5 1.0 OG1 v:THR5072 4.7 0.8 1.0 ND1 v:HIS5067 4.9 0.1 1.0

K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen. Location of Chloride and Its Possible Functions in Oxygen-Evolving Photosystem II Revealed By X-Ray Crystallography Proc.Natl.Acad.Sci.Usa V. 106 8567 2009.
ISSN: ISSN 0027-8424
PubMed: 19433803
DOI: 10.1073/PNAS.0812797106