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Iron in PDB 4il6: Structure of Sr-Substituted Photosystem II

Enzymatic activity of Structure of Sr-Substituted Photosystem II

All present enzymatic activity of Structure of Sr-Substituted Photosystem II:
1.10.3.9;

Protein crystallography data

The structure of Structure of Sr-Substituted Photosystem II, PDB code: 4il6 was solved by F.H.M.Koua, Y.Umena, K.Kawakami, N.Kamiya, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.860, 228.790, 285.760, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.5

Other elements in 4il6:

The structure of Structure of Sr-Substituted Photosystem II also contains other interesting chemical elements:

Strontium (Sr) 2 atoms
Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Sr-Substituted Photosystem II (pdb code 4il6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Sr-Substituted Photosystem II, PDB code: 4il6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4il6

Go back to Iron Binding Sites List in 4il6
Iron binding site 1 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:29.3
occ:1.00
 NE2 A:HIS215 2.1 28.4 1.0
NE2 D:HIS214 2.1 25.9 1.0
NE2 D:HIS268 2.2 25.8 1.0
NE2 A:HIS272 2.3 27.5 1.0
O1 D:BCT401 2.3 38.2 1.0
O2 D:BCT401 2.4 38.8 1.0
C D:BCT401 2.7 37.9 1.0
CE1 A:HIS215 3.0 27.7 1.0
CD2 D:HIS214 3.1 25.6 1.0
CE1 D:HIS214 3.1 25.2 1.0
CE1 D:HIS268 3.1 25.9 1.0
CD2 A:HIS215 3.1 28.0 1.0
CE1 A:HIS272 3.2 27.3 1.0
CD2 D:HIS268 3.3 26.0 1.0
CD2 A:HIS272 3.3 27.7 1.0
O3 D:BCT401 4.0 41.4 1.0
ND1 A:HIS215 4.1 28.2 1.0
ND1 D:HIS214 4.2 26.1 1.0
CG D:HIS214 4.2 25.9 1.0
CG A:HIS215 4.3 27.6 1.0
ND1 D:HIS268 4.3 26.4 1.0
CG D:HIS268 4.4 26.1 1.0
ND1 A:HIS272 4.4 27.0 1.0
CG A:HIS272 4.5 28.3 1.0
CG2 A:VAL219 4.6 27.9 1.0
CG2 D:VAL218 4.8 24.9 1.0
OH D:TYR244 4.8 31.5 1.0

Iron binding site 2 out of 6 in 4il6

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Iron binding site 2 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:39.7
occ:1.00
 FE F:HEM101 0.0 39.7 1.0
NE2 F:HIS24 2.1 37.5 1.0
NB F:HEM101 2.1 40.8 1.0
NA F:HEM101 2.1 41.7 1.0
ND F:HEM101 2.1 40.5 1.0
NC F:HEM101 2.1 41.1 1.0
NE2 E:HIS23 2.1 42.2 1.0
CE1 F:HIS24 3.0 36.6 1.0
C4D F:HEM101 3.0 41.6 1.0
C1A F:HEM101 3.1 41.2 1.0
CD2 F:HIS24 3.1 36.4 1.0
C4B F:HEM101 3.1 41.7 1.0
C1D F:HEM101 3.1 41.1 1.0
C4A F:HEM101 3.1 41.4 1.0
CE1 E:HIS23 3.1 41.0 1.0
C1B F:HEM101 3.1 41.2 1.0
C1C F:HEM101 3.1 39.6 1.0
CD2 E:HIS23 3.1 41.2 1.0
C4C F:HEM101 3.1 40.2 1.0
CHA F:HEM101 3.4 40.7 1.0
CHC F:HEM101 3.4 39.6 1.0
CHD F:HEM101 3.5 40.5 1.0
CHB F:HEM101 3.5 41.0 1.0
ND1 F:HIS24 4.2 36.1 1.0
CG F:HIS24 4.2 36.5 1.0
ND1 E:HIS23 4.2 40.7 1.0
C3D F:HEM101 4.3 41.0 1.0
C2A F:HEM101 4.3 42.0 1.0
C2D F:HEM101 4.3 40.4 1.0
CG E:HIS23 4.3 41.3 1.0
C3A F:HEM101 4.3 42.0 1.0
C3B F:HEM101 4.3 41.4 1.0
C2B F:HEM101 4.3 41.5 1.0
C2C F:HEM101 4.3 40.1 1.0
C3C F:HEM101 4.3 40.0 1.0
NE1 F:TRP20 4.8 35.9 1.0
CE2 E:TYR19 4.9 44.8 1.0

Iron binding site 3 out of 6 in 4il6

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Iron binding site 3 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:26.6
occ:1.00
 FE V:HEM201 0.0 26.6 1.0
NE2 V:HIS41 2.0 24.5 1.0
NC V:HEM201 2.0 26.6 1.0
NA V:HEM201 2.0 26.9 1.0
ND V:HEM201 2.1 26.6 1.0
NB V:HEM201 2.1 27.5 1.0
NE2 V:HIS92 2.1 28.9 1.0
CD2 V:HIS41 3.0 24.3 1.0
C4C V:HEM201 3.0 27.0 1.0
C4A V:HEM201 3.1 26.8 1.0
CE1 V:HIS41 3.1 24.0 1.0
C1C V:HEM201 3.1 26.6 1.0
C4D V:HEM201 3.1 26.7 1.0
C1D V:HEM201 3.1 26.8 1.0
C1A V:HEM201 3.1 26.9 1.0
C1B V:HEM201 3.1 27.1 1.0
CD2 V:HIS92 3.1 28.4 1.0
CE1 V:HIS92 3.1 29.0 1.0
C4B V:HEM201 3.1 26.8 1.0
CHD V:HEM201 3.4 26.3 1.0
CHB V:HEM201 3.4 26.5 1.0
CHA V:HEM201 3.4 27.0 1.0
CHC V:HEM201 3.5 26.7 1.0
CG V:HIS41 4.2 24.3 1.0
ND1 V:HIS41 4.2 24.9 1.0
ND1 V:HIS92 4.2 28.2 1.0
CG V:HIS92 4.2 28.6 1.0
C3C V:HEM201 4.3 26.3 1.0
C2C V:HEM201 4.3 26.2 1.0
C3A V:HEM201 4.3 26.6 1.0
C2A V:HEM201 4.3 27.0 1.0
C3D V:HEM201 4.3 26.7 1.0
C2D V:HEM201 4.3 26.7 1.0
C2B V:HEM201 4.3 27.1 1.0
C3B V:HEM201 4.3 27.8 1.0
CE1 V:TYR75 4.7 28.8 1.0

Iron binding site 4 out of 6 in 4il6

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Iron binding site 4 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe404

b:29.9
occ:1.00
 NE2 a:HIS215 2.0 31.3 1.0
NE2 d:HIS214 2.1 28.6 1.0
O2 d:BCT401 2.2 40.6 1.0
NE2 d:HIS268 2.2 28.6 1.0
NE2 a:HIS272 2.3 31.8 1.0
O1 d:BCT401 2.4 40.6 1.0
C d:BCT401 2.6 41.3 1.0
CE1 a:HIS215 2.9 31.4 1.0
CD2 d:HIS214 3.1 27.4 1.0
CE1 d:HIS214 3.1 27.6 1.0
CD2 a:HIS215 3.1 30.8 1.0
CD2 d:HIS268 3.2 28.7 1.0
CE1 a:HIS272 3.2 31.6 1.0
CE1 d:HIS268 3.2 27.5 1.0
CD2 a:HIS272 3.3 31.6 1.0
O3 d:BCT401 3.9 42.9 1.0
ND1 a:HIS215 4.1 32.1 1.0
CG a:HIS215 4.2 30.7 1.0
ND1 d:HIS214 4.2 28.5 1.0
CG d:HIS214 4.3 27.8 1.0
ND1 d:HIS268 4.3 28.2 1.0
CG d:HIS268 4.4 28.2 1.0
ND1 a:HIS272 4.4 32.0 1.0
CG a:HIS272 4.5 32.2 1.0
CG2 a:VAL219 4.6 29.5 1.0
CG2 d:VAL218 4.8 28.9 1.0

Iron binding site 5 out of 6 in 4il6

Go back to Iron Binding Sites List in 4il6
Iron binding site 5 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:44.0
occ:1.00
 FE f:HEM101 0.0 44.0 1.0
NC f:HEM101 2.1 43.6 1.0
NA f:HEM101 2.1 46.6 1.0
NB f:HEM101 2.1 44.5 1.0
NE2 f:HIS24 2.1 44.8 1.0
ND f:HEM101 2.1 43.7 1.0
NE2 e:HIS23 2.1 48.2 1.0
CD2 f:HIS24 3.0 43.0 1.0
CD2 e:HIS23 3.0 46.5 1.0
C4D f:HEM101 3.1 45.0 1.0
C1C f:HEM101 3.1 43.1 1.0
C1A f:HEM101 3.1 47.3 1.0
C4C f:HEM101 3.1 42.6 1.0
C1D f:HEM101 3.1 43.8 1.0
C4B f:HEM101 3.1 44.4 1.0
C4A f:HEM101 3.1 46.5 1.0
C1B f:HEM101 3.1 45.1 1.0
CE1 f:HIS24 3.1 43.9 1.0
CE1 e:HIS23 3.1 46.5 1.0
CHA f:HEM101 3.4 45.5 1.0
CHC f:HEM101 3.4 43.3 1.0
CHD f:HEM101 3.4 42.6 1.0
CHB f:HEM101 3.5 45.5 1.0
CG f:HIS24 4.2 42.4 1.0
ND1 f:HIS24 4.2 42.7 1.0
CG e:HIS23 4.2 46.4 1.0
ND1 e:HIS23 4.2 46.5 1.0
C2C f:HEM101 4.3 43.0 1.0
C3D f:HEM101 4.3 43.8 1.0
C2A f:HEM101 4.3 49.1 1.0
C3C f:HEM101 4.3 42.2 1.0
C2D f:HEM101 4.3 43.8 1.0
C3A f:HEM101 4.3 48.0 1.0
C3B f:HEM101 4.3 44.5 1.0
C2B f:HEM101 4.3 45.1 1.0
CE2 e:TYR19 4.8 48.9 1.0

Iron binding site 6 out of 6 in 4il6

Go back to Iron Binding Sites List in 4il6
Iron binding site 6 out of 6 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Sr-Substituted Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:32.6
occ:1.00
 FE v:HEM201 0.0 32.6 1.0
NB v:HEM201 2.0 33.7 1.0
NC v:HEM201 2.1 32.5 1.0
NA v:HEM201 2.1 32.9 1.0
NE2 v:HIS41 2.1 31.6 1.0
NE2 v:HIS92 2.1 33.6 1.0
ND v:HEM201 2.1 32.6 1.0
CE1 v:HIS92 3.0 32.6 1.0
CD2 v:HIS41 3.0 31.3 1.0
C1B v:HEM201 3.0 33.7 1.0
C4B v:HEM201 3.0 33.8 1.0
C4A v:HEM201 3.1 33.6 1.0
CD2 v:HIS92 3.1 33.5 1.0
C4C v:HEM201 3.1 32.2 1.0
C1C v:HEM201 3.1 32.6 1.0
CE1 v:HIS41 3.1 31.0 1.0
C4D v:HEM201 3.1 32.9 1.0
C1A v:HEM201 3.1 33.3 1.0
C1D v:HEM201 3.1 32.0 1.0
CHB v:HEM201 3.4 33.9 1.0
CHC v:HEM201 3.4 33.1 1.0
CHD v:HEM201 3.4 31.9 1.0
CHA v:HEM201 3.4 32.4 1.0
ND1 v:HIS92 4.1 33.3 1.0
CG v:HIS41 4.2 32.0 1.0
ND1 v:HIS41 4.2 31.5 1.0
CG v:HIS92 4.2 34.2 1.0
C3B v:HEM201 4.2 34.1 1.0
C2B v:HEM201 4.2 34.5 1.0
C3A v:HEM201 4.3 34.2 1.0
C3C v:HEM201 4.3 32.1 1.0
C2C v:HEM201 4.3 32.2 1.0
C3D v:HEM201 4.3 31.8 1.0
C2A v:HEM201 4.3 34.0 1.0
C2D v:HEM201 4.3 31.7 1.0
CE1 v:TYR75 4.8 34.9 1.0

Reference:

F.H.Koua, Y.Umena, K.Kawakami, J.R.Shen. Structure of Sr-Substituted Photosystem II at 2.1 A Resolution and Its Implications in the Mechanism of Water Oxidation Proc.Natl.Acad.Sci.Usa V. 110 3889 2013.
ISSN: ISSN 0027-8424
PubMed: 23426624
DOI: 10.1073/PNAS.1219922110
Page generated: Mon Aug 5 04:11:19 2024

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