Magnesium in PDB 8c88: Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv

Protein crystallography data

The structure of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c88 was solved by A.Gabdulkhakov, G.Selikhanov, T.Fufina, L.Vasilieva, A.Atamas, D.Yukhimchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.42 / 2.75
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.91, 100.91, 237.02, 90, 90, 90
R / Rfree (%) 19.9 / 27.1

Other elements in 8c88:

The structure of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv (pdb code 8c88). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c88:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8c88

Go back to Magnesium Binding Sites List in 8c88
Magnesium binding site 1 out of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg502

b:62.5
occ:1.00
 MG L:BCL502 0.0 62.5 1.0
NE2 L:HIS173 1.9 61.1 1.0
ND L:BCL502 2.0 64.9 1.0
NB L:BCL502 2.1 65.6 1.0
NC L:BCL502 2.2 62.4 1.0
NA L:BCL502 2.2 67.1 1.0
CE1 L:HIS173 2.7 58.0 1.0
C4D L:BCL502 3.0 61.6 1.0
C1B L:BCL502 3.1 58.1 1.0
CD2 L:HIS173 3.1 61.9 1.0
C4B L:BCL502 3.1 61.6 1.0
C4A L:BCL502 3.1 61.8 1.0
C1D L:BCL502 3.2 60.3 1.0
C1C L:BCL502 3.2 65.1 1.0
C4C L:BCL502 3.2 63.2 1.0
C1A L:BCL502 3.2 61.5 1.0
CHB L:BCL502 3.4 58.6 1.0
CHC L:BCL502 3.4 60.7 1.0
CHA L:BCL502 3.5 63.2 1.0
CHD L:BCL502 3.5 64.6 1.0
CBB M:BCL403 3.8 58.0 1.0
ND1 L:HIS173 3.9 56.2 1.0
CAB M:BCL403 3.9 62.6 1.0
OBB M:BCL403 3.9 66.4 1.0
CG L:HIS173 4.1 55.4 1.0
C3D L:BCL502 4.2 64.9 1.0
C2D L:BCL502 4.3 64.6 1.0
C2B L:BCL502 4.3 55.7 1.0
C3A L:BCL502 4.4 53.7 1.0
C3B L:BCL502 4.4 62.0 1.0
C2C L:BCL502 4.5 59.7 1.0
C2A L:BCL502 4.5 55.0 1.0
C3C L:BCL502 4.5 60.8 1.0
CD2 L:PHE167 4.7 62.9 1.0
C3B M:BCL403 4.7 60.1 1.0
CMA L:BCL502 4.8 56.4 1.0
CBD L:BCL502 5.0 64.6 1.0

Magnesium binding site 2 out of 4 in 8c88

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Magnesium binding site 2 out of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg503

b:52.4
occ:1.00
 MG L:BCL503 0.0 52.4 1.0
NE2 L:HIS153 1.9 66.7 1.0
ND L:BCL503 2.0 47.2 1.0
NB L:BCL503 2.1 55.3 1.0
NC L:BCL503 2.1 50.1 1.0
NA L:BCL503 2.2 53.4 1.0
CE1 L:HIS153 2.8 60.2 1.0
C4D L:BCL503 3.0 53.1 1.0
CD2 L:HIS153 3.1 59.0 1.0
C4B L:BCL503 3.1 55.5 1.0
C1C L:BCL503 3.1 52.3 1.0
C1B L:BCL503 3.1 55.8 1.0
C4A L:BCL503 3.2 51.2 1.0
C1D L:BCL503 3.2 52.7 1.0
C4C L:BCL503 3.2 47.9 1.0
C1A L:BCL503 3.2 54.2 1.0
CHC L:BCL503 3.4 55.0 1.0
CHB L:BCL503 3.4 55.8 1.0
CHA L:BCL503 3.5 53.3 1.0
CHD L:BCL503 3.5 51.4 1.0
ND1 L:HIS153 4.0 59.5 1.0
CG L:HIS153 4.1 56.7 1.0
C3D L:BCL503 4.2 53.1 1.0
C2D L:BCL503 4.3 50.1 1.0
C2B L:BCL503 4.4 56.2 1.0
C2C L:BCL503 4.4 52.7 1.0
C3B L:BCL503 4.4 55.8 1.0
CBB L:BPH504 4.4 52.5 1.0
C3A L:BCL503 4.4 51.6 1.0
C19 L:BPH504 4.5 57.3 1.0
C3C L:BCL503 4.5 44.5 1.0
C2A L:BCL503 4.5 56.1 1.0
CMA L:BCL503 4.8 48.5 1.0
CE2 M:TYR210 4.8 54.3 1.0
CMC L:BCL503 4.9 57.9 1.0
CD1 L:LEU154 4.9 57.4 1.0
CBD L:BCL503 4.9 52.7 1.0

Magnesium binding site 3 out of 4 in 8c88

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Magnesium binding site 3 out of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg402

b:58.4
occ:1.00
 MG M:BCL402 0.0 58.4 1.0
NE2 M:HIS182 1.9 68.4 1.0
ND M:BCL402 2.0 58.1 1.0
NB M:BCL402 2.1 59.5 1.0
NC M:BCL402 2.2 59.9 1.0
NA M:BCL402 2.2 59.6 1.0
CE1 M:HIS182 2.9 58.8 1.0
CD2 M:HIS182 2.9 59.9 1.0
C4D M:BCL402 3.0 59.8 1.0
C1B M:BCL402 3.1 59.0 1.0
C4B M:BCL402 3.1 61.0 1.0
C4A M:BCL402 3.2 57.9 1.0
C1C M:BCL402 3.2 63.3 1.0
C1D M:BCL402 3.2 58.9 1.0
C4C M:BCL402 3.2 54.8 1.0
C1A M:BCL402 3.2 60.1 1.0
CHB M:BCL402 3.4 55.7 1.0
CHC M:BCL402 3.4 57.6 1.0
CHD M:BCL402 3.5 54.0 1.0
CHA M:BCL402 3.5 60.7 1.0
ND1 M:HIS182 4.0 54.8 1.0
CG M:HIS182 4.0 60.1 1.0
C3D M:BCL402 4.3 56.5 1.0
C2B M:BCL402 4.3 54.6 1.0
C2D M:BCL402 4.3 58.6 1.0
C3B M:BCL402 4.4 62.4 1.0
C2C M:BCL402 4.4 57.3 1.0
CBB M:BPH404 4.4 58.9 1.0
C3A M:BCL402 4.5 54.9 1.0
C3C M:BCL402 4.5 52.7 1.0
C2A M:BCL402 4.5 55.9 1.0
CBD M:BCL402 5.0 56.6 1.0

Magnesium binding site 4 out of 4 in 8c88

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Magnesium binding site 4 out of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg403

b:58.3
occ:1.00
 MG M:BCL403 0.0 58.3 1.0
NE2 M:HIS202 1.9 57.4 1.0
ND M:BCL403 2.1 55.6 1.0
NB M:BCL403 2.1 59.8 1.0
NC M:BCL403 2.1 62.4 1.0
NA M:BCL403 2.2 57.2 1.0
CE1 M:HIS202 2.8 50.6 1.0
C4D M:BCL403 3.0 51.3 1.0
CD2 M:HIS202 3.0 51.2 1.0
C1B M:BCL403 3.1 62.5 1.0
C4B M:BCL403 3.1 54.0 1.0
C1C M:BCL403 3.1 64.5 1.0
C1D M:BCL403 3.2 62.9 1.0
C4A M:BCL403 3.2 55.2 1.0
C4C M:BCL403 3.2 59.6 1.0
C1A M:BCL403 3.3 58.9 1.0
CHC M:BCL403 3.4 55.5 1.0
CHB M:BCL403 3.4 57.4 1.0
CHA M:BCL403 3.5 52.6 1.0
CHD M:BCL403 3.5 56.0 1.0
CBB L:BCL502 3.8 55.3 1.0
OBB L:BCL502 3.9 67.3 1.0
CAB L:BCL502 3.9 61.7 1.0
ND1 M:HIS202 3.9 44.7 1.0
CG M:HIS202 4.1 47.8 1.0
C3D M:BCL403 4.3 54.8 1.0
C2B M:BCL403 4.3 62.2 1.0
C2D M:BCL403 4.4 57.1 1.0
C3B M:BCL403 4.4 60.1 1.0
C2C M:BCL403 4.4 55.1 1.0
C3C M:BCL403 4.5 56.1 1.0
C3A M:BCL403 4.5 56.5 1.0
C2A M:BCL403 4.6 58.3 1.0
C3B L:BCL502 4.8 62.0 1.0
CMC M:BCL403 4.9 45.7 1.0
CBD M:BCL403 4.9 54.5 1.0

Reference:

G.Selikhanov, A.Atamas, D.Yukhimchuk, T.Fufina, L.Vasilieva, A.Gabdulkhakov. Stabilization of Cereibacter Sphaeroides Photosynthetic Reaction Center By the Introduction of Disulfide Bonds. Membranes (Basel) V. 13 2023.
ISSN: ESSN 2077-0375
PubMed: 36837657
DOI: 10.3390/MEMBRANES13020154
Page generated: Thu Oct 3 20:11:09 2024

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