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

Protein crystallography data

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

Other elements in 3a0b:

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

Iron Binding Sites:

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 3a0b

Go back to Iron Binding Sites List in 3a0b
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 3a0b

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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 3a0b

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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 3a0b

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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 3a0b

Go back to Iron Binding Sites List in 3a0b
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 3a0b

Go back to Iron Binding Sites List in 3a0b
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

Reference:

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
Page generated: Sun Dec 13 14:59:40 2020

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