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Iron in PDB 1eys: Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum

Protein crystallography data

The structure of Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys was solved by T.Nogi, I.Fathir, M.Kobayashi, T.Nozawa, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.299, 196.596, 84.163, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 28.7

Other elements in 1eys:

The structure of Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum (pdb code 1eys). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1eys

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Iron binding site 1 out of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe609

b:31.2
occ:1.00
FE C:HEM609 0.0 31.2 1.0
NC C:HEM609 1.9 28.5 1.0
NB C:HEM609 2.0 28.3 1.0
ND C:HEM609 2.0 26.2 1.0
SD C:MET72 2.1 33.9 1.0
NA C:HEM609 2.2 31.6 1.0
NE2 C:HIS89 2.4 31.0 1.0
C4C C:HEM609 2.9 27.9 1.0
C1D C:HEM609 2.9 27.2 1.0
C1C C:HEM609 3.0 25.6 1.0
C4B C:HEM609 3.0 25.1 1.0
C1B C:HEM609 3.1 33.3 1.0
C4D C:HEM609 3.1 29.7 1.0
C1A C:HEM609 3.2 36.1 1.0
C4A C:HEM609 3.2 33.6 1.0
CHD C:HEM609 3.2 26.7 1.0
CHC C:HEM609 3.3 24.7 1.0
CE C:MET72 3.3 23.6 1.0
CE1 C:HIS89 3.4 30.1 1.0
CD2 C:HIS89 3.4 31.1 1.0
CHA C:HEM609 3.5 34.0 1.0
CHB C:HEM609 3.5 34.0 1.0
CG C:MET72 3.6 26.3 1.0
C3C C:HEM609 4.1 27.0 1.0
C2C C:HEM609 4.1 25.8 1.0
C2D C:HEM609 4.2 25.5 1.0
C3B C:HEM609 4.2 28.6 1.0
C2B C:HEM609 4.3 30.6 1.0
C3D C:HEM609 4.3 23.5 1.0
CB C:MET72 4.3 29.0 1.0
C2A C:HEM609 4.4 32.9 1.0
C3A C:HEM609 4.4 32.2 1.0
ND1 C:HIS89 4.5 29.5 1.0
CG C:HIS89 4.6 29.7 1.0

Iron binding site 2 out of 5 in 1eys

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Iron binding site 2 out of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe610

b:25.8
occ:1.00
FE C:HEM610 0.0 25.8 1.0
SD C:MET108 1.9 31.2 1.0
NA C:HEM610 2.0 27.9 1.0
ND C:HEM610 2.0 22.7 1.0
NB C:HEM610 2.0 20.0 1.0
NC C:HEM610 2.1 24.9 1.0
NE2 C:HIS134 2.5 23.3 1.0
C1A C:HEM610 2.9 23.5 1.0
C4D C:HEM610 2.9 24.6 1.0
C4A C:HEM610 3.0 22.2 1.0
C1B C:HEM610 3.0 26.8 1.0
C1D C:HEM610 3.1 25.8 1.0
C4C C:HEM610 3.1 23.3 1.0
C4B C:HEM610 3.2 27.7 1.0
CE1 C:HIS134 3.2 28.2 1.0
CG C:MET108 3.2 30.1 1.0
CHA C:HEM610 3.2 25.9 1.0
C1C C:HEM610 3.2 21.0 1.0
CE C:MET108 3.3 24.9 1.0
CHB C:HEM610 3.3 25.1 1.0
CHD C:HEM610 3.5 25.6 1.0
CD2 C:HIS134 3.6 24.0 1.0
CHC C:HEM610 3.6 25.4 1.0
CB C:MET108 4.0 30.3 1.0
C2A C:HEM610 4.1 22.8 1.0
C3A C:HEM610 4.2 24.8 1.0
C3D C:HEM610 4.2 27.5 1.0
C2D C:HEM610 4.2 25.3 1.0
C2B C:HEM610 4.3 26.6 1.0
C3B C:HEM610 4.3 23.4 1.0
C3C C:HEM610 4.4 22.0 1.0
ND1 C:HIS134 4.4 28.0 1.0
C2C C:HEM610 4.4 22.9 1.0
CG C:HIS134 4.6 27.9 1.0

Iron binding site 3 out of 5 in 1eys

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Iron binding site 3 out of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe611

b:22.5
occ:1.00
FE C:HEM611 0.0 22.5 1.0
ND C:HEM611 2.0 19.7 1.0
NC C:HEM611 2.0 18.7 1.0
NA C:HEM611 2.0 12.0 1.0
NB C:HEM611 2.0 19.4 1.0
SD C:MET214 2.1 25.8 1.0
NE2 C:HIS229 2.4 24.8 1.0
C4D C:HEM611 3.0 15.0 1.0
C1D C:HEM611 3.0 17.7 1.0
C4C C:HEM611 3.0 22.2 1.0
C1B C:HEM611 3.0 16.4 1.0
C1A C:HEM611 3.0 20.0 1.0
C1C C:HEM611 3.1 17.5 1.0
C4B C:HEM611 3.1 15.9 1.0
CE C:MET214 3.1 28.3 1.0
C4A C:HEM611 3.1 16.5 1.0
CG C:MET214 3.1 16.0 1.0
CD2 C:HIS229 3.4 28.5 1.0
CHD C:HEM611 3.4 20.1 1.0
CHA C:HEM611 3.4 18.8 1.0
CE1 C:HIS229 3.4 28.5 1.0
CHB C:HEM611 3.4 17.1 1.0
CHC C:HEM611 3.4 18.3 1.0
CB C:MET214 3.9 18.7 1.0
C2D C:HEM611 4.2 17.1 1.0
C3D C:HEM611 4.2 19.7 1.0
C2B C:HEM611 4.2 18.4 1.0
C3C C:HEM611 4.2 18.7 1.0
C3B C:HEM611 4.3 20.4 1.0
C2C C:HEM611 4.3 18.0 1.0
C2A C:HEM611 4.3 20.0 1.0
C3A C:HEM611 4.3 16.6 1.0
ND1 C:HIS229 4.5 26.6 1.0
CG C:HIS229 4.5 25.5 1.0
CA C:MET214 4.9 17.3 1.0

Iron binding site 4 out of 5 in 1eys

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Iron binding site 4 out of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe612

b:21.1
occ:1.00
FE C:HEM612 0.0 21.1 1.0
NE2 C:HIS289 1.9 23.4 1.0
ND C:HEM612 2.0 24.8 1.0
NA C:HEM612 2.0 28.8 1.0
NB C:HEM612 2.0 21.8 1.0
NC C:HEM612 2.0 27.4 1.0
NE2 C:HIS122 2.4 26.3 1.0
CE1 C:HIS289 2.7 24.2 1.0
C1B C:HEM612 3.0 25.4 1.0
C4D C:HEM612 3.0 25.8 1.0
C4A C:HEM612 3.0 25.7 1.0
C1A C:HEM612 3.0 28.4 1.0
C1D C:HEM612 3.0 26.9 1.0
C4C C:HEM612 3.1 25.4 1.0
CD2 C:HIS289 3.1 28.5 1.0
C4B C:HEM612 3.1 24.5 1.0
C1C C:HEM612 3.1 24.9 1.0
CE1 C:HIS122 3.2 25.0 1.0
CHB C:HEM612 3.4 26.2 1.0
CHA C:HEM612 3.4 25.4 1.0
CHD C:HEM612 3.4 26.6 1.0
CHC C:HEM612 3.4 27.1 1.0
CD2 C:HIS122 3.5 26.8 1.0
ND1 C:HIS289 3.9 27.1 1.0
CG C:HIS289 4.1 26.5 1.0
C2B C:HEM612 4.2 24.1 1.0
C3D C:HEM612 4.2 24.2 1.0
C2D C:HEM612 4.2 23.6 1.0
C2A C:HEM612 4.3 29.3 1.0
C3A C:HEM612 4.3 27.9 1.0
C3B C:HEM612 4.3 24.2 1.0
C3C C:HEM612 4.3 27.1 1.0
C2C C:HEM612 4.3 23.2 1.0
ND1 C:HIS122 4.4 24.4 1.0
CG C:HIS122 4.6 24.1 1.0
CB C:ALA250 4.9 28.2 1.0
CD C:PRO295 4.9 32.8 1.0

Iron binding site 5 out of 5 in 1eys

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Iron binding site 5 out of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe607

b:35.7
occ:1.00
NE2 M:HIS218 1.8 26.4 1.0
NE2 L:HIS198 1.9 33.2 1.0
NE2 M:HIS265 1.9 29.1 1.0
NE2 L:HIS238 2.0 25.3 1.0
OE2 M:GLU233 2.3 32.6 1.0
OE1 M:GLU233 2.4 38.2 1.0
CE1 M:HIS218 2.6 28.6 1.0
CD M:GLU233 2.6 34.9 1.0
CE1 M:HIS265 2.7 30.7 1.0
CE1 L:HIS238 2.8 25.7 1.0
CE1 L:HIS198 2.9 35.7 1.0
CD2 L:HIS198 2.9 30.4 1.0
CD2 M:HIS218 3.0 26.2 1.0
CD2 M:HIS265 3.2 33.1 1.0
CD2 L:HIS238 3.2 23.9 1.0
ND1 M:HIS218 3.8 28.6 1.0
ND1 M:HIS265 3.9 26.7 1.0
ND1 L:HIS238 4.0 22.1 1.0
CG M:HIS218 4.0 22.0 1.0
ND1 L:HIS198 4.0 32.1 1.0
CG L:HIS198 4.0 31.5 1.0
CG M:GLU233 4.1 34.0 1.0
CG M:HIS265 4.1 28.7 1.0
CG L:HIS238 4.2 23.7 1.0
CG1 M:ILE222 4.6 21.9 1.0
CG1 L:ILE202 4.7 33.9 1.0
O M:HOH916 4.9 35.3 1.0
CB M:GLU233 5.0 33.6 1.0

Reference:

T.Nogi, I.Fathir, M.Kobayashi, T.Nozawa, K.Miki. Crystal Structures of Photosynthetic Reaction Center and High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum: Thermostability and Electron Transfer. Proc.Natl.Acad.Sci.Usa V. 97 13561 2000.
ISSN: ISSN 0027-8424
PubMed: 11095707
DOI: 10.1073/PNAS.240224997
Page generated: Sat Aug 3 04:38:57 2024

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