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Iron in PDB 1w5c: Photosystem II From Thermosynechococcus Elongatus

Protein crystallography data

The structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 1w5c was solved by J.Biesiadka, B.Loll, J.Kern, K.-D.Irrgang, A.Zouni, W.Saenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.0 / 3.2
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.517, 224.612, 305.632, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1w5c:

The structure of Photosystem II From Thermosynechococcus Elongatus also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Photosystem II From Thermosynechococcus Elongatus (pdb code 1w5c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Photosystem II From Thermosynechococcus Elongatus, PDB code: 1w5c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1w5c

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Iron binding site 1 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1350

b:45.2
occ:1.00
 NE2 A:HIS215 2.0 45.2 1.0
NE2 A:HIS272 2.1 45.2 1.0
NE2 D:HIS214 2.1 45.2 1.0
NE2 D:HIS268 2.3 45.2 1.0
CE1 A:HIS272 2.7 45.2 1.0
CE1 A:HIS215 2.8 45.2 1.0
CD2 D:HIS214 3.0 45.2 1.0
CD2 A:HIS215 3.1 45.2 1.0
CE1 D:HIS214 3.1 45.2 1.0
CE1 D:HIS268 3.2 45.2 1.0
CD2 A:HIS272 3.3 45.2 1.0
CD2 D:HIS268 3.3 45.2 1.0
ND1 A:HIS272 4.0 45.2 1.0
ND1 A:HIS215 4.0 45.2 1.0
OH D:TYR244 4.0 45.2 1.0
CG A:HIS215 4.2 45.2 1.0
ND1 D:HIS214 4.2 45.2 1.0
CG D:HIS214 4.2 45.2 1.0
CG A:HIS272 4.3 45.2 1.0
ND1 D:HIS268 4.3 45.2 1.0
CG D:HIS268 4.4 45.2 1.0
CG2 D:VAL218 4.8 45.2 1.0
CG2 A:VAL219 4.8 45.2 1.0
OH A:TYR246 4.9 45.2 1.0
CZ D:TYR244 4.9 45.2 1.0

Iron binding site 2 out of 6 in 1w5c

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Iron binding site 2 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1085

b:45.2
occ:1.00
 FE E:HEM1085 0.0 45.2 1.0
NE2 F:HIS24 1.9 45.2 1.0
ND E:HEM1085 2.0 45.2 1.0
NB E:HEM1085 2.0 45.2 1.0
NC E:HEM1085 2.1 45.2 1.0
NA E:HEM1085 2.1 45.2 1.0
NE2 E:HIS23 2.2 45.2 1.0
CD2 E:HIS23 2.6 45.2 1.0
CD2 F:HIS24 2.8 45.2 1.0
CE1 F:HIS24 2.9 45.2 1.0
C4D E:HEM1085 2.9 45.2 1.0
C1D E:HEM1085 3.0 45.2 1.0
C4A E:HEM1085 3.0 45.2 1.0
C4C E:HEM1085 3.0 45.2 1.0
C1B E:HEM1085 3.0 45.2 1.0
C1C E:HEM1085 3.1 45.2 1.0
C4B E:HEM1085 3.1 45.2 1.0
C1A E:HEM1085 3.1 45.2 1.0
CHB E:HEM1085 3.4 45.2 1.0
CHD E:HEM1085 3.4 45.2 1.0
CHA E:HEM1085 3.4 45.2 1.0
CHC E:HEM1085 3.5 45.2 1.0
CE1 E:HIS23 3.5 45.2 1.0
CG E:HIS23 3.9 45.2 1.0
CG F:HIS24 4.0 45.2 1.0
ND1 F:HIS24 4.0 45.2 1.0
C3D E:HEM1085 4.2 45.2 1.0
C2D E:HEM1085 4.2 45.2 1.0
ND1 E:HIS23 4.3 45.2 1.0
C3C E:HEM1085 4.3 45.2 1.0
C2C E:HEM1085 4.3 45.2 1.0
C2B E:HEM1085 4.3 45.2 1.0
C3A E:HEM1085 4.3 45.2 1.0
C3B E:HEM1085 4.3 45.2 1.0
C2A E:HEM1085 4.4 45.2 1.0
NE1 F:TRP20 4.9 45.2 1.0

Iron binding site 3 out of 6 in 1w5c

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Iron binding site 3 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1350

b:45.2
occ:1.00
 NE2 G:HIS215 2.0 45.2 1.0
NE2 J:HIS214 2.1 45.2 1.0
NE2 G:HIS272 2.2 45.2 1.0
NE2 J:HIS268 2.2 45.2 1.0
CE1 G:HIS272 2.8 45.2 1.0
CE1 G:HIS215 2.9 45.2 1.0
CD2 J:HIS214 3.1 45.2 1.0
CE1 J:HIS214 3.1 45.2 1.0
CD2 G:HIS215 3.1 45.2 1.0
CE1 J:HIS268 3.1 45.2 1.0
CD2 J:HIS268 3.2 45.2 1.0
CD2 G:HIS272 3.4 45.2 1.0
OH J:TYR244 4.0 45.2 1.0
ND1 G:HIS272 4.0 45.2 1.0
ND1 G:HIS215 4.0 45.2 1.0
CG G:HIS215 4.2 45.2 1.0
ND1 J:HIS214 4.2 45.2 1.0
CG J:HIS214 4.2 45.2 1.0
ND1 J:HIS268 4.2 45.2 1.0
CG J:HIS268 4.3 45.2 1.0
CG G:HIS272 4.3 45.2 1.0
CG2 G:VAL219 4.7 45.2 1.0
CG2 J:VAL218 4.8 45.2 1.0
OH G:TYR246 4.8 45.2 1.0
CZ J:TYR244 4.9 45.2 1.0

Iron binding site 4 out of 6 in 1w5c

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Iron binding site 4 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe1046

b:45.2
occ:1.00
 FE L:HEM1046 0.0 45.2 1.0
NE2 L:HIS24 1.8 45.2 1.0
ND L:HEM1046 2.0 45.2 1.0
NB L:HEM1046 2.0 45.2 1.0
NC L:HEM1046 2.1 45.2 1.0
NA L:HEM1046 2.1 45.2 1.0
NE2 K:HIS23 2.3 45.2 1.0
CD2 L:HIS24 2.7 45.2 1.0
CD2 K:HIS23 2.7 45.2 1.0
CE1 L:HIS24 2.9 45.2 1.0
C4D L:HEM1046 3.0 45.2 1.0
C4A L:HEM1046 3.0 45.2 1.0
C1B L:HEM1046 3.0 45.2 1.0
C1D L:HEM1046 3.1 45.2 1.0
C1C L:HEM1046 3.1 45.2 1.0
C4B L:HEM1046 3.1 45.2 1.0
C4C L:HEM1046 3.1 45.2 1.0
C1A L:HEM1046 3.1 45.2 1.0
CHB L:HEM1046 3.3 45.2 1.0
CHD L:HEM1046 3.4 45.2 1.0
CHC L:HEM1046 3.4 45.2 1.0
CHA L:HEM1046 3.5 45.2 1.0
CE1 K:HIS23 3.6 45.2 1.0
CG L:HIS24 3.9 45.2 1.0
ND1 L:HIS24 3.9 45.2 1.0
CG K:HIS23 4.0 45.2 1.0
C3D L:HEM1046 4.2 45.2 1.0
C2D L:HEM1046 4.3 45.2 1.0
C2B L:HEM1046 4.3 45.2 1.0
C3B L:HEM1046 4.3 45.2 1.0
C3A L:HEM1046 4.3 45.2 1.0
C2C L:HEM1046 4.3 45.2 1.0
C3C L:HEM1046 4.3 45.2 1.0
ND1 K:HIS23 4.4 45.2 1.0
C2A L:HEM1046 4.4 45.2 1.0
NE1 L:TRP20 4.8 45.2 1.0

Iron binding site 5 out of 6 in 1w5c

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Iron binding site 5 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Fe1138

b:45.2
occ:1.00
 FE T:HEC1138 0.0 45.2 1.0
NA T:HEC1138 2.0 45.2 1.0
NE2 T:HIS92 2.0 45.2 1.0
NB T:HEC1138 2.0 45.2 1.0
ND T:HEC1138 2.0 45.2 1.0
NC T:HEC1138 2.1 45.2 1.0
NE2 T:HIS41 2.1 45.2 1.0
CE1 T:HIS92 2.9 45.2 1.0
CD2 T:HIS92 3.0 45.2 1.0
C4A T:HEC1138 3.0 45.2 1.0
C4D T:HEC1138 3.0 45.2 1.0
C1B T:HEC1138 3.0 45.2 1.0
CE1 T:HIS41 3.1 45.2 1.0
C1D T:HEC1138 3.1 45.2 1.0
C4B T:HEC1138 3.1 45.2 1.0
C1C T:HEC1138 3.1 45.2 1.0
C4C T:HEC1138 3.1 45.2 1.0
CD2 T:HIS41 3.1 45.2 1.0
C1A T:HEC1138 3.1 45.2 1.0
CHB T:HEC1138 3.4 45.2 1.0
CHD T:HEC1138 3.4 45.2 1.0
CHC T:HEC1138 3.4 45.2 1.0
CHA T:HEC1138 3.5 45.2 1.0
ND1 T:HIS92 3.9 45.2 1.0
CG T:HIS92 4.0 45.2 1.0
ND1 T:HIS41 4.2 45.2 1.0
CG T:HIS41 4.2 45.2 1.0
C3A T:HEC1138 4.2 45.2 1.0
C2D T:HEC1138 4.3 45.2 1.0
C3D T:HEC1138 4.3 45.2 1.0
C2A T:HEC1138 4.3 45.2 1.0
C2B T:HEC1138 4.3 45.2 1.0
C3B T:HEC1138 4.3 45.2 1.0
C2C T:HEC1138 4.3 45.2 1.0
C3C T:HEC1138 4.4 45.2 1.0
CE1 T:TYR75 4.8 45.2 1.0

Iron binding site 6 out of 6 in 1w5c

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Iron binding site 6 out of 6 in the Photosystem II From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe1138

b:45.2
occ:1.00
 FE V:HEC1138 0.0 45.2 1.0
ND V:HEC1138 2.0 45.2 1.0
NA V:HEC1138 2.0 45.2 1.0
NE2 V:HIS92 2.0 45.2 1.0
NB V:HEC1138 2.1 45.2 1.0
NC V:HEC1138 2.1 45.2 1.0
NE2 V:HIS41 2.1 45.2 1.0
CE1 V:HIS92 2.9 45.2 1.0
CD2 V:HIS92 3.0 45.2 1.0
C4D V:HEC1138 3.0 45.2 1.0
C4A V:HEC1138 3.0 45.2 1.0
CE1 V:HIS41 3.0 45.2 1.0
C1D V:HEC1138 3.0 45.2 1.0
C1B V:HEC1138 3.1 45.2 1.0
C1A V:HEC1138 3.1 45.2 1.0
C4C V:HEC1138 3.1 45.2 1.0
C1C V:HEC1138 3.1 45.2 1.0
CD2 V:HIS41 3.1 45.2 1.0
C4B V:HEC1138 3.1 45.2 1.0
CHB V:HEC1138 3.4 45.2 1.0
CHD V:HEC1138 3.4 45.2 1.0
CHC V:HEC1138 3.5 45.2 1.0
CHA V:HEC1138 3.5 45.2 1.0
ND1 V:HIS92 4.0 45.2 1.0
CG V:HIS92 4.0 45.2 1.0
ND1 V:HIS41 4.2 45.2 1.0
C3A V:HEC1138 4.2 45.2 1.0
C2D V:HEC1138 4.2 45.2 1.0
CG V:HIS41 4.2 45.2 1.0
C3D V:HEC1138 4.3 45.2 1.0
C2A V:HEC1138 4.3 45.2 1.0
C2B V:HEC1138 4.3 45.2 1.0
C3B V:HEC1138 4.3 45.2 1.0
C2C V:HEC1138 4.4 45.2 1.0
C3C V:HEC1138 4.4 45.2 1.0
CE1 V:TYR75 4.8 45.2 1.0

Reference:

J.Biesiadka, B.Loll, J.Kern, K.-D.Irrgang, A.Zouni. Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster Phys.Chem.Chem.Phys. V. 6 4733 2004.
ISSN: ISSN 1463-9076
Page generated: Sun Dec 13 14:34:56 2020

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