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Magnesium in PDB 2wjm: Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)

Protein crystallography data

The structure of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose), PDB code: 2wjm was solved by A.B.Woehri, W.Y.Wahlgren, E.Malmerberg, L.C.Johansson, R.Neutze, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 176.78 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.450, 138.498, 177.770, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.1

Other elements in 2wjm:

The structure of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) (pdb code 2wjm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose), PDB code: 2wjm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2wjm

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Magnesium binding site 1 out of 4 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:24.5
occ:1.00
MG L:BCB301 0.0 24.5 1.0
NA L:BCB301 2.0 25.3 1.0
ND L:BCB301 2.0 26.1 1.0
NB L:BCB301 2.0 23.9 1.0
NC L:BCB301 2.1 25.0 1.0
NE2 L:HIS173 2.4 30.6 1.0
C4D L:BCB301 3.0 25.4 1.0
C4A L:BCB301 3.0 24.1 1.0
C1A L:BCB301 3.0 25.2 1.0
C1B L:BCB301 3.0 22.0 1.0
C4B L:BCB301 3.1 24.1 1.0
C1D L:BCB301 3.1 24.9 1.0
C4C L:BCB301 3.1 22.9 1.0
C1C L:BCB301 3.1 22.4 1.0
CD2 L:HIS173 3.3 25.8 1.0
CHB L:BCB301 3.4 22.9 1.0
CHA L:BCB301 3.4 24.1 1.0
CBB M:BCB402 3.4 23.2 1.0
CE1 L:HIS173 3.4 28.0 1.0
CAB M:BCB402 3.5 21.0 1.0
CHC L:BCB301 3.5 23.3 1.0
OBB M:BCB402 3.5 22.9 1.0
CHD L:BCB301 3.6 24.6 1.0
C3B M:BCB402 4.2 20.6 1.0
C3D L:BCB301 4.3 24.0 1.0
C3A L:BCB301 4.3 25.9 1.0
C2D L:BCB301 4.3 24.0 1.0
C2A L:BCB301 4.3 26.2 1.0
C3B L:BCB301 4.4 21.7 1.0
C2B L:BCB301 4.4 23.7 1.0
CD1 L:TRP167 4.4 30.7 1.0
C3C L:BCB301 4.4 23.3 1.0
NE1 L:TRP167 4.4 29.9 1.0
CG L:HIS173 4.5 29.2 1.0
ND1 L:HIS173 4.5 29.0 1.0
C2C L:BCB301 4.5 22.8 1.0
CBD L:BCB301 4.8 24.0 1.0
C2B M:BCB402 4.9 20.7 1.0

Magnesium binding site 2 out of 4 in 2wjm

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Magnesium binding site 2 out of 4 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:25.6
occ:1.00
MG L:BCB302 0.0 25.6 1.0
NA L:BCB302 2.0 25.1 1.0
ND L:BCB302 2.0 23.6 1.0
NB L:BCB302 2.1 24.8 1.0
NC L:BCB302 2.1 25.0 1.0
NE2 L:HIS153 2.4 30.2 1.0
C4D L:BCB302 3.0 24.2 1.0
C1A L:BCB302 3.0 25.3 1.0
C1B L:BCB302 3.0 23.8 1.0
C4A L:BCB302 3.0 25.4 1.0
C4B L:BCB302 3.1 23.0 1.0
C1C L:BCB302 3.1 25.4 1.0
C4C L:BCB302 3.1 26.2 1.0
C1D L:BCB302 3.1 25.8 1.0
CD2 L:HIS153 3.3 27.4 1.0
CE1 L:HIS153 3.4 28.7 1.0
CHA L:BCB302 3.4 23.9 1.0
CHB L:BCB302 3.4 24.4 1.0
CHC L:BCB302 3.5 23.9 1.0
CHD L:BCB302 3.6 24.3 1.0
OBB L:BPB303 4.1 34.0 1.0
C3D L:BCB302 4.3 23.4 1.0
C3B L:BCB302 4.3 24.5 1.0
C2A L:BCB302 4.3 24.4 1.0
C3A L:BCB302 4.4 23.6 1.0
C3C L:BCB302 4.4 25.0 1.0
C2D L:BCB302 4.4 24.6 1.0
C2B L:BCB302 4.4 25.5 1.0
CE2 M:TYR208 4.4 30.2 1.0
ND1 L:HIS153 4.5 27.4 1.0
C2C L:BCB302 4.5 27.4 1.0
CG L:HIS153 4.5 29.0 1.0
C19 L:BPB303 4.7 33.4 1.0
CBA L:BCB302 4.8 24.0 1.0
CBD L:BCB302 4.8 25.6 1.0
CD2 L:LEU154 4.9 31.1 1.0

Magnesium binding site 3 out of 4 in 2wjm

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Magnesium binding site 3 out of 4 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg401

b:23.9
occ:1.00
MG M:BCB401 0.0 23.9 1.0
ND M:BCB401 2.0 22.4 1.0
NA M:BCB401 2.0 22.4 1.0
NB M:BCB401 2.0 23.6 1.0
NC M:BCB401 2.1 23.3 1.0
NE2 M:HIS180 2.4 30.4 1.0
C4D M:BCB401 3.0 21.0 1.0
C1A M:BCB401 3.0 22.1 1.0
C4A M:BCB401 3.0 22.8 1.0
C1B M:BCB401 3.0 21.7 1.0
C4B M:BCB401 3.1 22.9 1.0
C1D M:BCB401 3.1 21.7 1.0
C4C M:BCB401 3.1 22.7 1.0
C1C M:BCB401 3.1 23.9 1.0
CD2 M:HIS180 3.2 29.4 1.0
CHB M:BCB401 3.4 25.0 1.0
CHA M:BCB401 3.4 21.4 1.0
CE1 M:HIS180 3.5 29.7 1.0
CHD M:BCB401 3.5 22.4 1.0
CHC M:BCB401 3.5 22.8 1.0
OBB M:BPB403 4.1 33.0 1.0
C3D M:BCB401 4.3 21.6 1.0
C2D M:BCB401 4.3 21.7 1.0
C2A M:BCB401 4.3 23.3 1.0
C3B M:BCB401 4.3 24.7 1.0
C3A M:BCB401 4.4 22.5 1.0
C3C M:BCB401 4.4 23.5 1.0
C2B M:BCB401 4.4 24.0 1.0
CG M:HIS180 4.4 30.1 1.0
C2C M:BCB401 4.5 24.9 1.0
ND1 M:HIS180 4.5 29.4 1.0
CE2 L:PHE181 4.6 30.9 1.0
CBA M:BCB401 4.7 25.6 1.0
C22 M:NS5405 4.9 38.4 1.0
CBD M:BCB401 4.9 22.9 1.0

Magnesium binding site 4 out of 4 in 2wjm

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Magnesium binding site 4 out of 4 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg402

b:21.5
occ:1.00
MG M:BCB402 0.0 21.5 1.0
NA M:BCB402 2.0 21.3 1.0
NB M:BCB402 2.0 22.5 1.0
ND M:BCB402 2.0 20.5 1.0
NC M:BCB402 2.0 21.3 1.0
NE2 M:HIS200 2.3 31.5 1.0
C4D M:BCB402 3.0 21.6 1.0
C1A M:BCB402 3.0 22.2 1.0
C4A M:BCB402 3.0 21.4 1.0
C1B M:BCB402 3.0 19.7 1.0
C4B M:BCB402 3.0 20.9 1.0
C1C M:BCB402 3.1 20.1 1.0
C4C M:BCB402 3.1 21.6 1.0
C1D M:BCB402 3.1 21.4 1.0
CD2 M:HIS200 3.2 30.4 1.0
CHA M:BCB402 3.3 20.9 1.0
CBB L:BCB301 3.4 20.1 1.0
CE1 M:HIS200 3.4 30.8 1.0
CHB M:BCB402 3.4 21.7 1.0
CHC M:BCB402 3.4 21.3 1.0
CHD M:BCB402 3.6 20.8 1.0
CAB L:BCB301 3.6 23.9 1.0
OBB L:BCB301 3.9 24.1 1.0
C3D M:BCB402 4.3 20.8 1.0
C3B L:BCB301 4.3 21.7 1.0
C3B M:BCB402 4.3 20.6 1.0
C3C M:BCB402 4.3 21.2 1.0
C2A M:BCB402 4.3 23.4 1.0
C3A M:BCB402 4.3 23.3 1.0
C2B M:BCB402 4.4 20.7 1.0
C2D M:BCB402 4.4 20.6 1.0
CG M:HIS200 4.4 31.1 1.0
C2C M:BCB402 4.4 22.6 1.0
ND1 M:HIS200 4.4 30.9 1.0
CD1 M:ILE204 4.7 30.4 1.0
CBD M:BCB402 4.8 22.0 1.0
CMC M:BCB402 5.0 21.9 1.0

Reference:

A.B.Wohri, W.Y.Wahlgren, E.Malmerberg, L.C.Johansson, R.Neutze, G.Katona. Lipidic Sponge Phase Crystal Structure of A Photosynthetic Reaction Center Reveals Lipids on the Protein Surface. Biochemistry V. 48 9831 2009.
ISSN: ISSN 1520-4995
PubMed: 19743880
DOI: 10.1021/BI900545E
Page generated: Wed Aug 14 06:07:49 2024

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