Magnesium in PDB 6z1j: Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene, PDB code: 6z1j was solved by A.G.Gabdulkhakov, T.Y.Fufina, L.G.Vasilieva, C.Betzel, G.K.Selikhanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.07 / 2.10
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.890, 99.890, 238.520, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.4

Other elements in 6z1j:

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene (pdb code 6z1j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene, PDB code: 6z1j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6z1j

Go back to Magnesium Binding Sites List in 6z1j
Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:29.6
occ:1.00
 MG L:BCL301 0.0 29.6 1.0
ND L:BCL301 2.0 28.1 1.0
NB L:BCL301 2.1 29.3 1.0
NC L:BCL301 2.1 28.3 1.0
NA L:BCL301 2.2 24.8 1.0
NE2 M:HIS182 2.5 34.1 1.0
C4D L:BCL301 3.0 28.1 1.0
C1B L:BCL301 3.1 26.9 1.0
C4B L:BCL301 3.1 27.0 1.0
C1C L:BCL301 3.1 25.7 1.0
C1D L:BCL301 3.1 28.1 1.0
C4A L:BCL301 3.1 29.5 1.0
C4C L:BCL301 3.2 28.7 1.0
C1A L:BCL301 3.2 27.8 1.0
CD2 M:HIS182 3.3 31.5 1.0
CHC L:BCL301 3.4 28.4 1.0
CHB L:BCL301 3.4 27.6 1.0
CHA L:BCL301 3.5 27.4 1.0
CHD L:BCL301 3.5 27.5 1.0
CE1 M:HIS182 3.6 34.5 1.0
C3D L:BCL301 4.2 28.2 1.0
C2D L:BCL301 4.3 28.5 1.0
C2B L:BCL301 4.3 31.0 1.0
C3B L:BCL301 4.3 32.0 1.0
CBB M:BPH403 4.4 27.3 1.0
C3A L:BCL301 4.4 35.2 1.0
C2C L:BCL301 4.4 24.6 1.0
C3C L:BCL301 4.5 26.5 1.0
C2A L:BCL301 4.5 28.6 1.0
CG M:HIS182 4.5 38.5 1.0
ND1 M:HIS182 4.6 33.0 1.0
CE2 L:PHE181 4.8 24.3 1.0
CBD L:BCL301 4.9 27.7 1.0
CBA L:BCL301 4.9 30.4 1.0

Magnesium binding site 2 out of 4 in 6z1j

Go back to Magnesium Binding Sites List in 6z1j
Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:31.6
occ:1.00
 MG L:BCL302 0.0 31.6 1.0
ND L:BCL302 2.0 27.7 1.0
NB L:BCL302 2.1 26.7 1.0
NC L:BCL302 2.1 26.9 1.0
NA L:BCL302 2.2 26.8 1.0
NE2 L:HIS173 2.5 24.8 1.0
C4D L:BCL302 3.0 30.2 1.0
C1B L:BCL302 3.1 32.7 1.0
C4B L:BCL302 3.1 33.0 1.0
C1C L:BCL302 3.1 29.1 1.0
C4A L:BCL302 3.1 26.3 1.0
C1D L:BCL302 3.2 31.5 1.0
C4C L:BCL302 3.2 29.7 1.0
C1A L:BCL302 3.2 26.4 1.0
CE1 L:HIS173 3.4 29.8 1.0
CHB L:BCL302 3.4 21.9 1.0
CHC L:BCL302 3.4 25.3 1.0
CHA L:BCL302 3.5 30.5 1.0
CD2 L:HIS173 3.5 28.5 1.0
CHD L:BCL302 3.5 26.0 1.0
OBB M:BCL401 3.6 31.7 1.0
CAB M:BCL401 3.6 28.4 1.0
CBB M:BCL401 3.7 26.3 1.0
C3D L:BCL302 4.3 30.0 1.0
C2B L:BCL302 4.3 32.1 1.0
C2D L:BCL302 4.3 31.9 1.0
C3B L:BCL302 4.3 31.3 1.0
C3B M:BCL401 4.4 31.0 1.0
C3A L:BCL302 4.4 26.4 1.0
C2C L:BCL302 4.5 30.1 1.0
C3C L:BCL302 4.5 26.7 1.0
C2A L:BCL302 4.5 27.5 1.0
ND1 L:HIS173 4.5 27.1 1.0
CG L:HIS173 4.6 27.6 1.0
CD2 L:PHE167 4.8 30.5 1.0
CBD L:BCL302 5.0 29.1 1.0

Magnesium binding site 3 out of 4 in 6z1j

Go back to Magnesium Binding Sites List in 6z1j
Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg401

b:27.4
occ:1.00
 MG M:BCL401 0.0 27.4 1.0
ND M:BCL401 2.0 33.5 1.0
NB M:BCL401 2.1 26.0 1.0
NC M:BCL401 2.1 29.6 1.0
NA M:BCL401 2.2 26.8 1.0
NE2 M:HIS202 2.4 22.5 1.0
C4D M:BCL401 3.0 29.7 1.0
C4B M:BCL401 3.1 30.1 1.0
C1C M:BCL401 3.1 29.9 1.0
C1B M:BCL401 3.1 30.8 1.0
C4A M:BCL401 3.1 26.8 1.0
C1D M:BCL401 3.2 32.9 1.0
C4C M:BCL401 3.2 32.3 1.0
C1A M:BCL401 3.2 28.5 1.0
CHC M:BCL401 3.4 28.6 1.0
CHB M:BCL401 3.4 23.9 1.0
CE1 M:HIS202 3.4 23.9 1.0
CD2 M:HIS202 3.4 23.7 1.0
CHA M:BCL401 3.4 27.6 1.0
CHD M:BCL401 3.5 28.6 1.0
CBB L:BCL302 3.6 26.0 1.0
CAB L:BCL302 3.8 30.1 1.0
OBB L:BCL302 3.9 30.1 1.0
C3D M:BCL401 4.2 31.1 1.0
C2D M:BCL401 4.3 31.9 1.0
C2B M:BCL401 4.3 27.1 1.0
C3B M:BCL401 4.4 31.0 1.0
C2C M:BCL401 4.4 27.6 1.0
C3B L:BCL302 4.4 31.3 1.0
C3C M:BCL401 4.5 29.6 1.0
C3A M:BCL401 4.5 28.7 1.0
C2A M:BCL401 4.5 25.1 1.0
ND1 M:HIS202 4.5 26.0 1.0
CG M:HIS202 4.6 30.6 1.0
CBD M:BCL401 4.9 30.5 1.0

Magnesium binding site 4 out of 4 in 6z1j

Go back to Magnesium Binding Sites List in 6z1j
Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Co-Crystallization with Spheroidene within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg402

b:28.5
occ:1.00
 MG M:BCL402 0.0 28.5 1.0
ND M:BCL402 2.0 29.5 1.0
NB M:BCL402 2.1 24.8 1.0
NC M:BCL402 2.1 24.2 1.0
NA M:BCL402 2.2 24.2 1.0
NE2 L:HIS153 2.5 29.7 1.0
C4D M:BCL402 3.0 25.8 1.0
C1B M:BCL402 3.1 22.0 1.0
C4B M:BCL402 3.1 29.0 1.0
C1C M:BCL402 3.1 28.0 1.0
C4A M:BCL402 3.1 25.9 1.0
C1D M:BCL402 3.1 31.2 1.0
C4C M:BCL402 3.1 20.0 1.0
C1A M:BCL402 3.2 25.5 1.0
CD2 L:HIS153 3.3 33.2 1.0
CHB M:BCL402 3.4 23.5 1.0
CHC M:BCL402 3.4 26.2 1.0
CHA M:BCL402 3.4 26.7 1.0
CHD M:BCL402 3.5 22.2 1.0
CE1 L:HIS153 3.6 33.4 1.0
CBB L:BPH303 4.2 24.0 1.0
C3D M:BCL402 4.2 25.9 1.0
C2D M:BCL402 4.3 26.9 1.0
C2B M:BCL402 4.3 24.9 1.0
C3B M:BCL402 4.3 26.6 1.0
C2C M:BCL402 4.4 25.8 1.0
C3A M:BCL402 4.4 25.2 1.0
C3C M:BCL402 4.4 27.1 1.0
C2A M:BCL402 4.5 25.6 1.0
CG L:HIS153 4.5 30.4 1.0
ND1 L:HIS153 4.7 32.5 1.0
CE2 M:TYR210 4.7 23.3 1.0
CD1 L:LEU154 4.7 29.0 1.0
C19 L:BPH303 4.8 25.1 1.0
CBC M:BCL402 4.9 26.4 1.0
CBA M:BCL402 4.9 24.2 1.0
CBD M:BCL402 4.9 27.6 1.0

Reference:

G.Selikhanov, T.Fufina, L.Vasilieva, C.Betzel, A.Gabdulkhakov. Novel Approaches For the Lipid Sponge Phase Crystallization of the Rhodobacter Sphaeroides Photosynthetic Reaction Center. Iucrj V. 7 1084 2020.
ISSN: ESSN 2052-2525
PubMed: 33209319
DOI: 10.1107/S2052252520012142
Page generated: Tue Dec 15 02:52:56 2020

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