Magnesium in PDB 6z02: Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization, PDB code: 6z02 was solved by A.G.Gabdulkhakov, G.K.Selikhanov, T.Y.Fufina, L.G.Vasilieva, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.20 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.850, 139.850, 185.370, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 22.6

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization also contains other interesting chemical elements:

Potassium	(K)	1 atom
Iron	(Fe)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization (pdb code 6z02). 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 in Surfo Crystallization, PDB code: 6z02:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization


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 in Surfo Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg301 b:32.7 occ:1.00 MG L:BCL301 0.0 32.7 1.0 ND L:BCL301 2.0 29.1 1.0 NB L:BCL301 2.1 28.9 1.0 NC L:BCL301 2.1 33.3 1.0 NA L:BCL301 2.2 28.3 1.0 NE2 L:HIS173 2.4 25.7 1.0 C4D L:BCL301 3.0 31.3 1.0 C1B L:BCL301 3.1 27.4 1.0 C4B L:BCL301 3.1 30.6 1.0 C1C L:BCL301 3.1 29.4 1.0 C4A L:BCL301 3.1 26.8 1.0 C1D L:BCL301 3.1 32.2 1.0 C4C L:BCL301 3.2 28.7 1.0 C1A L:BCL301 3.2 31.7 1.0 CD2 L:HIS173 3.3 19.7 1.0 CHB L:BCL301 3.4 25.9 1.0 CHC L:BCL301 3.4 28.6 1.0 CE1 L:HIS173 3.4 26.0 1.0 CHA L:BCL301 3.5 34.4 1.0 CHD L:BCL301 3.5 23.5 1.0 CBB M:BCL402 3.6 25.1 1.0 CAB M:BCL402 3.7 33.1 1.0 OBB M:BCL402 3.8 31.5 1.0 C3D L:BCL301 4.2 28.9 1.0 C2D L:BCL301 4.3 34.5 1.0 C2B L:BCL301 4.3 29.3 1.0 C3B L:BCL301 4.4 23.0 1.0 C3A L:BCL301 4.4 28.1 1.0 C2C L:BCL301 4.4 28.8 1.0 C3C L:BCL301 4.5 29.1 1.0 CG L:HIS173 4.5 25.2 1.0 C3B M:BCL402 4.5 26.8 1.0 ND1 L:HIS173 4.5 23.4 1.0 C2A L:BCL301 4.5 26.8 1.0 CD2 L:PHE167 4.6 29.2 1.0 CMA L:BCL301 5.0 29.4 1.0 CBD L:BCL301 5.0 30.0 1.0

Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization


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 in Surfo Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg401 b:29.9 occ:1.00 MG M:BCL401 0.0 29.9 1.0 ND M:BCL401 2.0 29.7 1.0 NB M:BCL401 2.1 31.7 1.0 NC M:BCL401 2.1 26.7 1.0 NA M:BCL401 2.2 27.8 1.0 NE2 M:HIS182 2.3 27.3 1.0 C4D M:BCL401 3.0 27.6 1.0 C4B M:BCL401 3.1 27.8 1.0 C1B M:BCL401 3.1 29.3 1.0 C1C M:BCL401 3.1 28.5 1.0 C1D M:BCL401 3.1 26.2 1.0 CD2 M:HIS182 3.1 31.5 1.0 C4C M:BCL401 3.1 29.2 1.0 C4A M:BCL401 3.1 28.8 1.0 C1A M:BCL401 3.2 29.5 1.0 CE1 M:HIS182 3.3 27.9 1.0 CHC M:BCL401 3.4 26.5 1.0 CHB M:BCL401 3.4 26.4 1.0 CHA M:BCL401 3.5 31.2 1.0 CHD M:BCL401 3.5 28.5 1.0 C3D M:BCL401 4.2 22.9 1.0 C2D M:BCL401 4.3 29.9 1.0 C2B M:BCL401 4.3 31.6 1.0 C3B M:BCL401 4.3 31.8 1.0 CG M:HIS182 4.3 31.3 1.0 C2C M:BCL401 4.4 31.6 1.0 ND1 M:HIS182 4.4 31.5 1.0 C3C M:BCL401 4.4 26.9 1.0 C3A M:BCL401 4.4 29.5 1.0 C2A M:BCL401 4.5 31.4 1.0 CBB M:BPH404 4.7 28.8 1.0 CBD M:BCL401 4.9 28.4 1.0 CM5 M:SPN407 5.0 33.6 1.0 CE2 L:PHE181 5.0 30.5 1.0

Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization


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 in Surfo Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg402 b:25.9 occ:1.00 MG M:BCL402 0.0 25.9 1.0 ND M:BCL402 2.0 22.3 1.0 NB M:BCL402 2.1 25.2 1.0 NC M:BCL402 2.2 25.1 1.0 NA M:BCL402 2.2 22.1 1.0 NE2 M:HIS202 2.3 24.3 1.0 C4D M:BCL402 3.0 28.9 1.0 C4B M:BCL402 3.1 28.6 1.0 C1B M:BCL402 3.1 29.9 1.0 C1C M:BCL402 3.1 28.2 1.0 C4A M:BCL402 3.2 25.4 1.0 C1D M:BCL402 3.2 28.6 1.0 C4C M:BCL402 3.2 28.9 1.0 C1A M:BCL402 3.2 25.1 1.0 CD2 M:HIS202 3.3 25.0 1.0 CE1 M:HIS202 3.3 24.4 1.0 CHC M:BCL402 3.4 24.6 1.0 CHB M:BCL402 3.4 25.9 1.0 CHA M:BCL402 3.4 22.0 1.0 CHD M:BCL402 3.5 25.6 1.0 CBB L:BCL301 3.7 27.2 1.0 CAB L:BCL301 3.8 27.9 1.0 OBB L:BCL301 4.0 29.1 1.0 C3D M:BCL402 4.2 28.3 1.0 C2B M:BCL402 4.3 27.1 1.0 C2D M:BCL402 4.3 26.5 1.0 C3B M:BCL402 4.4 26.8 1.0 C2C M:BCL402 4.4 35.6 1.0 ND1 M:HIS202 4.4 24.0 1.0 CG M:HIS202 4.4 26.0 1.0 C3A M:BCL402 4.5 28.1 1.0 C3C M:BCL402 4.5 30.7 1.0 C2A M:BCL402 4.5 27.7 1.0 C3B L:BCL301 4.5 23.0 1.0 CBD M:BCL402 4.9 28.0 1.0

Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv in Surfo Crystallization


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 in Surfo Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg403 b:30.7 occ:1.00 MG M:BCL403 0.0 30.7 1.0 ND M:BCL403 2.0 21.2 1.0 NB M:BCL403 2.1 26.7 1.0 NC M:BCL403 2.1 22.5 1.0 NA M:BCL403 2.1 24.2 1.0 NE2 L:HIS153 2.4 31.0 1.0 C4D M:BCL403 3.0 20.9 1.0 C1C M:BCL403 3.1 27.1 1.0 C4B M:BCL403 3.1 27.2 1.0 C1B M:BCL403 3.1 26.0 1.0 C4A M:BCL403 3.1 23.6 1.0 C4C M:BCL403 3.1 23.7 1.0 C1D M:BCL403 3.1 20.6 1.0 C1A M:BCL403 3.2 24.1 1.0 CD2 L:HIS153 3.2 32.8 1.0 CHC M:BCL403 3.4 30.4 1.0 CHB M:BCL403 3.4 26.8 1.0 CHA M:BCL403 3.4 23.4 1.0 CHD M:BCL403 3.5 24.8 1.0 CE1 L:HIS153 3.5 38.4 1.0 C3D M:BCL403 4.2 20.3 1.0 CBB L:BPH302 4.3 30.0 1.0 C2D M:BCL403 4.3 27.1 1.0 C2B M:BCL403 4.3 29.7 1.0 C3B M:BCL403 4.4 25.3 1.0 C3A M:BCL403 4.4 26.0 1.0 C2C M:BCL403 4.4 29.8 1.0 C3C M:BCL403 4.4 24.6 1.0 C2A M:BCL403 4.4 25.5 1.0 CG L:HIS153 4.5 34.4 1.0 ND1 L:HIS153 4.6 33.1 1.0 CE2 M:TYR210 4.6 31.2 1.0 CD1 L:LEU154 4.8 28.5 1.0 CBC M:BCL403 4.8 26.3 1.0 CBA M:BCL403 4.9 28.0 1.0 C19 L:BPH302 4.9 36.1 1.0 CBD M:BCL403 4.9 26.6 1.0

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