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Magnesium 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:

Iron (Fe) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1eys

Go back to Magnesium Binding Sites List in 1eys
Magnesium binding site 1 out of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
L:Mg602

b:18.9
occ:1.00
MG L:BCL602 0.0 18.9 1.0
NB L:BCL602 2.0 15.6 1.0
ND L:BCL602 2.0 18.9 1.0
NC L:BCL602 2.1 12.8 1.0
NA L:BCL602 2.2 12.6 1.0
NE2 L:HIS181 2.8 19.7 1.0
C4D L:BCL602 2.9 19.7 1.0
C1B L:BCL602 3.0 21.1 1.0
C1D L:BCL602 3.0 17.4 1.0
C4B L:BCL602 3.1 15.6 1.0
C1C L:BCL602 3.1 15.6 1.0
C4A L:BCL602 3.1 15.6 1.0
C4C L:BCL602 3.1 18.5 1.0
C1A L:BCL602 3.2 15.1 1.0
CBB M:BCL603 3.4 12.0 1.0
OBB M:BCL603 3.4 19.2 1.0
CAB M:BCL603 3.4 23.0 1.0
CHD L:BCL602 3.4 19.7 1.0
CHC L:BCL602 3.4 16.9 1.0
CHB L:BCL602 3.4 16.9 1.0
CHA L:BCL602 3.4 14.4 1.0
CE1 L:HIS181 3.7 20.0 1.0
CD2 L:HIS181 3.8 15.2 1.0
C3D L:BCL602 4.2 20.2 1.0
C3B M:BCL603 4.2 18.8 1.0
C2D L:BCL602 4.2 17.3 1.0
C2B L:BCL602 4.3 15.0 1.0
C3B L:BCL602 4.3 19.4 1.0
C3C L:BCL602 4.3 17.1 1.0
C2C L:BCL602 4.4 17.3 1.0
C3A L:BCL602 4.4 18.9 1.0
C2A L:BCL602 4.4 17.6 1.0
ND1 L:HIS181 4.8 18.6 1.0
C4B M:BCL603 4.9 17.6 1.0
CBD L:BCL602 4.9 17.6 1.0
CG L:HIS181 4.9 18.8 1.0
CHC M:BCL603 5.0 21.3 1.0
CG1 L:VAL165 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in 1eys

Go back to Magnesium Binding Sites List in 1eys
Magnesium binding site 2 out of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
L:Mg604

b:26.2
occ:1.00
MG L:BCL604 0.0 26.2 1.0
ND L:BCL604 2.0 24.5 1.0
NB L:BCL604 2.0 23.9 1.0
NC L:BCL604 2.1 24.3 1.0
NA L:BCL604 2.1 22.7 1.0
NE2 L:HIS161 2.8 17.4 1.0
C4D L:BCL604 3.0 22.7 1.0
C1D L:BCL604 3.0 20.2 1.0
C1B L:BCL604 3.1 26.0 1.0
C4B L:BCL604 3.1 22.3 1.0
C1C L:BCL604 3.1 23.6 1.0
C4A L:BCL604 3.1 23.6 1.0
C4C L:BCL604 3.1 22.6 1.0
C1A L:BCL604 3.2 20.5 1.0
CHD L:BCL604 3.4 22.1 1.0
CHC L:BCL604 3.4 21.0 1.0
CHB L:BCL604 3.4 23.6 1.0
CHA L:BCL604 3.5 20.1 1.0
CE1 L:HIS161 3.7 12.3 1.0
CD2 L:HIS161 3.8 17.9 1.0
CBB L:BPH606 3.8 16.1 1.0
C3D L:BCL604 4.2 19.1 1.0
C2D L:BCL604 4.2 19.0 1.0
C3B L:BCL604 4.3 19.4 1.0
C2B L:BCL604 4.3 27.1 1.0
C3C L:BCL604 4.3 23.8 1.0
C2C L:BCL604 4.3 20.5 1.0
C2A L:BCL604 4.4 15.7 1.0
C3A L:BCL604 4.4 19.7 1.0
CE2 M:TYR209 4.5 17.4 1.0
CBA L:BCL604 4.6 17.2 1.0
ND1 L:HIS161 4.8 16.9 1.0
CG L:HIS161 4.9 14.8 1.0
CBD L:BCL604 5.0 19.2 1.0
C20 L:BPH606 5.0 15.6 1.0

Magnesium binding site 3 out of 4 in 1eys

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Magnesium binding site 3 out of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
M:Mg601

b:26.6
occ:1.00
MG M:BCL601 0.0 26.6 1.0
ND M:BCL601 2.0 21.7 1.0
NB M:BCL601 2.0 23.3 1.0
NC M:BCL601 2.1 16.2 1.0
NA M:BCL601 2.1 21.2 1.0
NE2 M:HIS181 2.8 24.7 1.0
C4D M:BCL601 3.0 23.8 1.0
C1D M:BCL601 3.0 22.0 1.0
C1C M:BCL601 3.1 19.1 1.0
C4B M:BCL601 3.1 22.5 1.0
C1B M:BCL601 3.1 23.6 1.0
C4C M:BCL601 3.1 18.8 1.0
C4A M:BCL601 3.1 24.5 1.0
C1A M:BCL601 3.2 27.0 1.0
CHD M:BCL601 3.4 19.6 1.0
CHC M:BCL601 3.4 20.7 1.0
CHB M:BCL601 3.4 20.6 1.0
CHA M:BCL601 3.5 22.4 1.0
CD2 M:HIS181 3.5 24.0 1.0
CE1 M:HIS181 3.8 24.3 1.0
CBB M:BPH605 3.9 26.9 1.0
C3D M:BCL601 4.2 20.3 1.0
C2D M:BCL601 4.2 19.8 1.0
C3C M:BCL601 4.3 18.3 1.0
C3B M:BCL601 4.3 23.4 1.0
C2B M:BCL601 4.3 20.9 1.0
C2C M:BCL601 4.3 21.0 1.0
C3A M:BCL601 4.4 30.2 1.0
C2A M:BCL601 4.4 33.2 1.0
CE2 L:PHE189 4.5 27.8 1.0
CG M:HIS181 4.8 23.8 1.0
ND1 M:HIS181 4.9 24.5 1.0
CBD M:BCL601 5.0 20.2 1.0
CAA M:BCL601 5.0 30.3 1.0

Magnesium binding site 4 out of 4 in 1eys

Go back to Magnesium Binding Sites List in 1eys
Magnesium binding site 4 out of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
M:Mg603

b:24.2
occ:1.00
MG M:BCL603 0.0 24.2 1.0
ND M:BCL603 2.0 22.8 1.0
NB M:BCL603 2.0 18.6 1.0
NC M:BCL603 2.1 22.0 1.0
NA M:BCL603 2.2 19.4 1.0
NE2 M:HIS201 2.7 15.4 1.0
C4D M:BCL603 3.0 24.1 1.0
C1D M:BCL603 3.0 20.9 1.0
CBB L:BCL602 3.0 16.3 1.0
C1C M:BCL603 3.1 21.2 1.0
C4B M:BCL603 3.1 17.6 1.0
C1B M:BCL603 3.1 16.6 1.0
C4C M:BCL603 3.1 16.0 1.0
C4A M:BCL603 3.1 17.7 1.0
C1A M:BCL603 3.2 22.0 1.0
CHD M:BCL603 3.4 19.5 1.0
CAB L:BCL602 3.4 20.6 1.0
CHC M:BCL603 3.4 21.3 1.0
CHA M:BCL603 3.5 25.4 1.0
CHB M:BCL603 3.5 17.1 1.0
CE1 M:HIS201 3.6 11.1 1.0
OBB L:BCL602 3.7 27.2 1.0
CD2 M:HIS201 3.8 7.0 1.0
C3D M:BCL603 4.2 23.2 1.0
C3B L:BCL602 4.2 19.4 1.0
C2D M:BCL603 4.2 24.7 1.0
C2B M:BCL603 4.3 17.9 1.0
C3B M:BCL603 4.3 18.8 1.0
C2C M:BCL603 4.3 23.6 1.0
C3C M:BCL603 4.3 17.6 1.0
C3A M:BCL603 4.4 17.8 1.0
C2A M:BCL603 4.5 14.9 1.0
ND1 M:HIS201 4.8 11.4 1.0
CG M:HIS201 4.9 14.5 1.0
C4B L:BCL602 4.9 15.6 1.0
C2B L:BCL602 4.9 15.0 1.0
CBD M:BCL603 4.9 23.6 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: Tue Aug 13 03:04:35 2024

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