Iron in PDB 3a0h: Crystal Structure of I-Substituted Photosystem II Complex

The structure of Crystal Structure of I-Substituted Photosystem II Complex, PDB code: 3a0h 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)	20.00 / 4.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.499, 224.702, 304.919, 90.00, 90.00, 90.00
R / Rfree (%)	29 / 32.6

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

Magnesium	(Mg)	70 atoms
Manganese	(Mn)	8 atoms
Iodine	(I)	10 atoms
Calcium	(Ca)	2 atoms

The binding sites of Iron atom in the Crystal Structure of I-Substituted Photosystem II Complex (pdb code 3a0h). 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 I-Substituted Photosystem II Complex, PDB code: 3a0h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1002 b:0.9 occ:1.00 NE2 D:HIS268 2.3 0.3 1.0 NE2 A:HIS215 2.3 0.6 1.0 NE2 A:HIS272 2.5 0.9 1.0 CD2 D:HIS268 2.5 0.2 1.0 NE2 D:HIS214 2.6 0.8 1.0 CE1 A:HIS272 2.7 0.5 1.0 CE1 A:HIS215 2.9 0.2 1.0 CD2 A:HIS215 3.1 0.9 1.0 CE1 D:HIS268 3.1 0.1 1.0 CE1 D:HIS214 3.3 0.8 1.0 CG D:HIS268 3.4 0.6 1.0 ND1 D:HIS268 3.7 0.7 1.0 CD2 A:HIS272 3.7 0.5 1.0 ND1 A:HIS215 3.7 0.4 1.0 OH A:TYR246 3.8 0.9 1.0 CG2 A:VAL219 3.8 0.1 1.0 CD2 D:HIS214 3.8 0.6 1.0 ND1 A:HIS272 3.8 0.5 1.0 CG A:HIS215 3.9 0.8 1.0 OH D:TYR244 4.1 0.1 1.0 CZ A:TYR246 4.3 0.3 1.0 CG A:HIS272 4.4 0.5 1.0 CB D:HIS268 4.5 0.5 1.0 CE2 A:TYR246 4.5 0.1 1.0 ND1 D:HIS214 4.5 0.8 1.0 CG D:HIS214 4.8 0.1 1.0

Iron binding site 2 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe1040 b:0.7 occ:1.00 FE F:HEM1040 0.0 0.7 1.0 NA F:HEM1040 2.1 1.0 1.0 NC F:HEM1040 2.1 0.3 1.0 NB F:HEM1040 2.1 0.6 1.0 ND F:HEM1040 2.1 0.4 1.0 NE2 E:HIS23 2.6 0.8 1.0 CE1 F:HIS24 2.7 0.6 1.0 NE2 F:HIS24 2.7 0.9 1.0 C4C F:HEM1040 3.1 0.1 1.0 C1A F:HEM1040 3.1 0.8 1.0 C1C F:HEM1040 3.1 0.9 1.0 C4A F:HEM1040 3.1 0.1 1.0 C1D F:HEM1040 3.1 0.1 1.0 C4D F:HEM1040 3.1 0.4 1.0 C4B F:HEM1040 3.1 0.4 1.0 C1B F:HEM1040 3.1 0.3 1.0 CD2 E:HIS23 3.4 0.7 1.0 CHA F:HEM1040 3.4 0.6 1.0 CHD F:HEM1040 3.4 0.5 1.0 CHC F:HEM1040 3.5 0.6 1.0 CHB F:HEM1040 3.5 0.4 1.0 CE1 E:HIS23 3.6 0.6 1.0 ND1 F:HIS24 3.9 0.3 1.0 CD2 F:HIS24 4.0 0.3 1.0 C3C F:HEM1040 4.3 0.2 1.0 C2A F:HEM1040 4.3 0.1 1.0 C2C F:HEM1040 4.3 0.4 1.0 C3A F:HEM1040 4.3 0.1 1.0 C3B F:HEM1040 4.3 0.9 1.0 C2B F:HEM1040 4.3 0.6 1.0 C2D F:HEM1040 4.3 0.4 1.0 C3D F:HEM1040 4.3 0.4 1.0 NE1 F:TRP20 4.5 0.2 1.0 CG E:HIS23 4.6 0.0 1.0 CG F:HIS24 4.6 0.9 1.0 ND1 E:HIS23 4.7 0.7 1.0

Iron binding site 3 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ V:Fe1041 b:0.5 occ:1.00 FE V:HEM1041 0.0 0.5 1.0 NA V:HEM1041 2.1 1.0 1.0 NC V:HEM1041 2.1 0.1 1.0 NB V:HEM1041 2.1 0.6 1.0 ND V:HEM1041 2.1 0.7 1.0 NE2 V:HIS118 2.5 0.2 1.0 NE2 V:HIS67 3.0 0.4 1.0 C1A V:HEM1041 3.1 0.3 1.0 C4C V:HEM1041 3.1 0.1 1.0 C4A V:HEM1041 3.1 0.1 1.0 C1C V:HEM1041 3.1 0.2 1.0 C4D V:HEM1041 3.1 0.8 1.0 C1D V:HEM1041 3.1 0.9 1.0 CE1 V:HIS118 3.1 0.7 1.0 C4B V:HEM1041 3.1 0.7 1.0 C1B V:HEM1041 3.1 0.1 1.0 CD2 V:HIS118 3.3 0.6 1.0 CD2 V:HIS67 3.3 0.6 1.0 CHA V:HEM1041 3.4 0.8 1.0 CHD V:HEM1041 3.4 0.9 1.0 CHB V:HEM1041 3.5 0.7 1.0 CHC V:HEM1041 3.5 0.6 1.0 ND1 V:HIS118 4.0 0.8 1.0 CG V:HIS118 4.1 0.8 1.0 CE1 V:HIS67 4.2 0.9 1.0 C3C V:HEM1041 4.3 0.4 1.0 C2A V:HEM1041 4.3 0.4 1.0 C3A V:HEM1041 4.3 0.8 1.0 C2C V:HEM1041 4.3 0.8 1.0 C3B V:HEM1041 4.3 0.6 1.0 C2B V:HEM1041 4.3 0.2 1.0 C3D V:HEM1041 4.3 0.5 1.0 C2D V:HEM1041 4.3 0.4 1.0 CG V:HIS67 4.6 0.8 1.0

Iron binding site 4 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe6002 b:0.9 occ:1.00 NE2 a:HIS5272 2.2 0.9 1.0 NE2 d:HIS5214 2.4 0.8 1.0 NE2 a:HIS5215 2.4 0.6 1.0 NE2 d:HIS5268 2.4 0.3 1.0 CD2 d:HIS5268 2.6 0.2 1.0 CD2 a:HIS5272 2.8 0.5 1.0 CD2 a:HIS5215 3.1 0.9 1.0 CE1 a:HIS5215 3.2 0.2 1.0 CE1 d:HIS5214 3.2 0.8 1.0 CD2 d:HIS5214 3.3 0.6 1.0 CE1 a:HIS5272 3.4 0.5 1.0 CE1 d:HIS5268 3.7 0.1 1.0 CG d:HIS5268 3.9 0.6 1.0 OH a:TYR5246 4.0 0.9 1.0 CG a:HIS5215 4.0 0.8 1.0 ND1 a:HIS5215 4.0 0.4 1.0 OH d:TYR5244 4.1 0.1 1.0 CG a:HIS5272 4.1 0.5 1.0 ND1 d:HIS5214 4.3 0.8 1.0 ND1 a:HIS5272 4.3 0.5 1.0 CG2 a:VAL5219 4.3 0.1 1.0 CG d:HIS5214 4.4 0.1 1.0 ND1 d:HIS5268 4.4 0.7 1.0 CZ a:TYR5246 4.7 0.3 1.0 CZ d:TYR5244 4.8 0.1 1.0 CE1 d:TYR5244 4.9 0.9 1.0

Iron binding site 5 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ f:Fe6040 b:0.7 occ:1.00 FE f:HEM6040 0.0 0.7 1.0 NA f:HEM6040 2.1 1.0 1.0 NC f:HEM6040 2.1 0.3 1.0 NB f:HEM6040 2.1 0.6 1.0 ND f:HEM6040 2.1 0.4 1.0 NE2 e:HIS5023 2.6 0.8 1.0 CE1 f:HIS5024 2.7 0.6 1.0 NE2 f:HIS5024 2.7 0.9 1.0 C4C f:HEM6040 3.1 0.1 1.0 C1A f:HEM6040 3.1 0.8 1.0 C1C f:HEM6040 3.1 0.9 1.0 C4A f:HEM6040 3.1 0.1 1.0 C4D f:HEM6040 3.1 0.4 1.0 C1D f:HEM6040 3.1 0.1 1.0 C4B f:HEM6040 3.1 0.4 1.0 C1B f:HEM6040 3.1 0.3 1.0 CD2 e:HIS5023 3.4 0.7 1.0 CHD f:HEM6040 3.4 0.5 1.0 CHA f:HEM6040 3.4 0.6 1.0 CHB f:HEM6040 3.5 0.4 1.0 CHC f:HEM6040 3.5 0.6 1.0 CE1 e:HIS5023 3.6 0.6 1.0 ND1 f:HIS5024 3.9 0.3 1.0 CD2 f:HIS5024 4.0 0.3 1.0 C3C f:HEM6040 4.3 0.2 1.0 C2A f:HEM6040 4.3 0.1 1.0 C3A f:HEM6040 4.3 0.1 1.0 C2C f:HEM6040 4.3 0.4 1.0 C3B f:HEM6040 4.3 0.9 1.0 C2B f:HEM6040 4.3 0.6 1.0 C2D f:HEM6040 4.3 0.4 1.0 C3D f:HEM6040 4.3 0.4 1.0 NE1 f:TRP5020 4.5 0.2 1.0 CG e:HIS5023 4.6 0.0 1.0 CG f:HIS5024 4.6 0.9 1.0 ND1 e:HIS5023 4.7 0.7 1.0

Iron binding site 6 out of 6 in the Crystal Structure of I-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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ v:Fe6041 b:0.5 occ:1.00 FE v:HEM6041 0.0 0.5 1.0 NC v:HEM6041 2.1 0.1 1.0 NA v:HEM6041 2.1 1.0 1.0 NB v:HEM6041 2.1 0.6 1.0 ND v:HEM6041 2.1 0.7 1.0 NE2 v:HIS5118 2.5 0.2 1.0 NE2 v:HIS5067 3.0 0.4 1.0 C1A v:HEM6041 3.1 0.3 1.0 C4C v:HEM6041 3.1 0.1 1.0 C4A v:HEM6041 3.1 0.1 1.0 C1C v:HEM6041 3.1 0.2 1.0 C4D v:HEM6041 3.1 0.8 1.0 C1D v:HEM6041 3.1 0.9 1.0 CE1 v:HIS5118 3.1 0.7 1.0 C4B v:HEM6041 3.1 0.7 1.0 C1B v:HEM6041 3.1 0.1 1.0 CD2 v:HIS5118 3.3 0.6 1.0 CD2 v:HIS5067 3.3 0.6 1.0 CHA v:HEM6041 3.4 0.8 1.0 CHD v:HEM6041 3.4 0.9 1.0 CHC v:HEM6041 3.5 0.6 1.0 CHB v:HEM6041 3.5 0.7 1.0 ND1 v:HIS5118 4.0 0.8 1.0 CG v:HIS5118 4.1 0.8 1.0 CE1 v:HIS5067 4.2 0.9 1.0 C3C v:HEM6041 4.3 0.4 1.0 C2A v:HEM6041 4.3 0.4 1.0 C2C v:HEM6041 4.3 0.8 1.0 C3A v:HEM6041 4.3 0.8 1.0 C3B v:HEM6041 4.3 0.6 1.0 C2B v:HEM6041 4.3 0.2 1.0 C2D v:HEM6041 4.3 0.4 1.0 C3D v:HEM6041 4.3 0.5 1.0 CG v:HIS5067 4.6 0.8 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