Magnesium in PDB 7od5: F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization

The structure of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization, PDB code: 7od5 was solved by A.G.Gabdulkhakov, G.K.Selikhanov, T.Y.Fufina, L.G.Vasilieva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 2.10
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.984, 99.984, 238.124, 90, 90, 90
R / Rfree (%)	17.9 / 22.1

The structure of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization (pdb code 7od5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization, PDB code: 7od5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg504 b:32.1 occ:1.00 MG L:BCL504 0.0 32.1 1.0 ND L:BCL504 2.0 31.1 1.0 NB L:BCL504 2.1 32.3 1.0 NC L:BCL504 2.1 30.8 1.0 NA L:BCL504 2.2 35.0 1.0 NE2 M:HIS182 2.5 31.9 1.0 C4D L:BCL504 3.0 30.6 1.0 C1B L:BCL504 3.1 31.2 1.0 C4B L:BCL504 3.1 30.4 1.0 C1C L:BCL504 3.1 34.6 1.0 C1D L:BCL504 3.1 29.5 1.0 C4A L:BCL504 3.1 35.1 1.0 C4C L:BCL504 3.2 32.6 1.0 C1A L:BCL504 3.2 31.3 1.0 CD2 M:HIS182 3.3 35.9 1.0 CHC L:BCL504 3.4 29.6 1.0 CHB L:BCL504 3.4 29.6 1.0 CHA L:BCL504 3.5 32.8 1.0 CHD L:BCL504 3.5 28.9 1.0 CE1 M:HIS182 3.6 36.9 1.0 C3D L:BCL504 4.2 31.1 1.0 C2D L:BCL504 4.3 29.6 1.0 C2B L:BCL504 4.3 31.9 1.0 C3B L:BCL504 4.3 38.5 1.0 C3A L:BCL504 4.4 36.7 1.0 CBB M:BPH406 4.4 31.1 1.0 C2C L:BCL504 4.4 31.5 1.0 C2A L:BCL504 4.5 32.4 1.0 C3C L:BCL504 4.5 29.6 1.0 CG M:HIS182 4.5 41.1 1.0 ND1 M:HIS182 4.6 37.5 1.0 CE2 L:PHE181 4.8 26.2 1.0 CBA L:BCL504 4.9 38.1 1.0 CBD L:BCL504 4.9 33.2 1.0 CMA L:BCL504 5.0 37.9 1.0

Magnesium binding site 2 out of 4 in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg505 b:32.0 occ:1.00 MG L:BCL505 0.0 32.0 1.0 ND L:BCL505 2.0 34.0 1.0 NB L:BCL505 2.1 30.7 1.0 NC L:BCL505 2.1 31.6 1.0 NA L:BCL505 2.2 30.9 1.0 NE2 L:HIS173 2.4 30.9 1.0 C4D L:BCL505 3.0 31.6 1.0 C1B L:BCL505 3.1 33.2 1.0 C4B L:BCL505 3.1 33.8 1.0 C1C L:BCL505 3.1 38.3 1.0 C4A L:BCL505 3.1 29.8 1.0 C1D L:BCL505 3.2 35.3 1.0 C4C L:BCL505 3.2 34.1 1.0 C1A L:BCL505 3.2 31.5 1.0 CE1 L:HIS173 3.4 33.9 1.0 CHB L:BCL505 3.4 25.3 1.0 CHC L:BCL505 3.4 30.8 1.0 CD2 L:HIS173 3.4 28.4 1.0 CHA L:BCL505 3.5 34.3 1.0 CHD L:BCL505 3.5 32.0 1.0 CBB M:BCL404 3.5 29.2 1.0 CAB M:BCL404 4.0 27.4 1.0 C3D L:BCL505 4.3 33.5 1.0 C2B L:BCL505 4.3 34.9 1.0 C2D L:BCL505 4.4 37.8 1.0 C3B L:BCL505 4.4 33.8 1.0 C3A L:BCL505 4.4 30.1 1.0 C2C L:BCL505 4.5 32.1 1.0 C3C L:BCL505 4.5 32.9 1.0 OBB M:BCL404 4.5 31.1 1.0 C2A L:BCL505 4.5 32.6 1.0 ND1 L:HIS173 4.5 31.4 1.0 C3B M:BCL404 4.6 35.0 1.0 CG L:HIS173 4.6 32.3 1.0 CD1 L:PHE167 4.7 35.6 1.0 CMA L:BCL505 5.0 29.9 1.0 CBD L:BCL505 5.0 32.0 1.0

Magnesium binding site 3 out of 4 in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg404 b:31.2 occ:1.00 MG M:BCL404 0.0 31.2 1.0 ND M:BCL404 2.0 29.6 1.0 NB M:BCL404 2.1 30.5 1.0 NC M:BCL404 2.1 37.2 1.0 NA M:BCL404 2.2 29.6 1.0 NE2 M:HIS202 2.4 25.8 1.0 C4D M:BCL404 3.0 29.7 1.0 C4B M:BCL404 3.1 32.7 1.0 C1C M:BCL404 3.1 34.7 1.0 C1B M:BCL404 3.1 33.4 1.0 C4A M:BCL404 3.1 32.1 1.0 C1D M:BCL404 3.1 35.6 1.0 C4C M:BCL404 3.2 34.3 1.0 C1A M:BCL404 3.2 33.7 1.0 CHC M:BCL404 3.4 30.3 1.0 CD2 M:HIS202 3.4 32.4 1.0 CE1 M:HIS202 3.4 29.4 1.0 CHB M:BCL404 3.4 25.9 1.0 CHA M:BCL404 3.4 30.0 1.0 CHD M:BCL404 3.5 32.7 1.0 CBB L:BCL505 3.7 30.0 1.0 CAB L:BCL505 3.8 34.8 1.0 OBB L:BCL505 3.9 31.1 1.0 C3D M:BCL404 4.2 34.5 1.0 C2B M:BCL404 4.3 31.7 1.0 C2D M:BCL404 4.3 38.3 1.0 C3B M:BCL404 4.4 35.0 1.0 C2C M:BCL404 4.4 28.3 1.0 C3B L:BCL505 4.4 33.8 1.0 C3C M:BCL404 4.4 34.3 1.0 C3A M:BCL404 4.5 36.0 1.0 C2A M:BCL404 4.5 31.3 1.0 ND1 M:HIS202 4.5 34.2 1.0 CG M:HIS202 4.5 35.5 1.0 CBD M:BCL404 4.9 30.9 1.0

Magnesium binding site 4 out of 4 in the F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of F(M197)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv Lsp Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg405 b:33.1 occ:1.00 MG M:BCL405 0.0 33.1 1.0 ND M:BCL405 2.0 30.3 1.0 NB M:BCL405 2.1 31.1 1.0 NC M:BCL405 2.1 29.8 1.0 NA M:BCL405 2.2 28.1 1.0 NE2 L:HIS153 2.6 35.3 1.0 C4D M:BCL405 3.0 28.6 1.0 C4B M:BCL405 3.1 29.3 1.0 C1B M:BCL405 3.1 27.2 1.0 C1C M:BCL405 3.1 32.4 1.0 C4A M:BCL405 3.1 27.9 1.0 C1D M:BCL405 3.2 32.8 1.0 C4C M:BCL405 3.2 25.6 1.0 C1A M:BCL405 3.2 31.6 1.0 CD2 L:HIS153 3.2 33.5 1.0 CHC M:BCL405 3.4 27.2 1.0 CHB M:BCL405 3.4 26.4 1.0 CHA M:BCL405 3.5 30.8 1.0 CHD M:BCL405 3.5 27.6 1.0 CE1 L:HIS153 3.7 36.4 1.0 C3D M:BCL405 4.2 31.3 1.0 CBB L:BPH506 4.2 29.6 1.0 C2D M:BCL405 4.3 28.8 1.0 C2B M:BCL405 4.3 25.4 1.0 C3B M:BCL405 4.3 30.7 1.0 C2C M:BCL405 4.4 32.9 1.0 C3A M:BCL405 4.4 34.3 1.0 C3C M:BCL405 4.4 34.3 1.0 CG L:HIS153 4.5 35.2 1.0 C2A M:BCL405 4.5 33.6 1.0 CE2 M:TYR210 4.6 26.3 1.0 ND1 L:HIS153 4.7 33.8 1.0 CD1 L:LEU154 4.7 31.6 1.0 CBC M:BCL405 4.9 29.9 1.0 C19 L:BPH506 4.9 31.0 1.0 CBD M:BCL405 4.9 29.9 1.0 CBA M:BCL405 4.9 29.7 1.0

G.Selikhanov, T.Fufina, S.Guenther, A.Meents, A.Gabdulkhakov, L.Vasilieva. X-Ray Structure of the Rhodobacter Sphaeroides Reaction Center with An M197 Phe→His Substitution Clarifies the Properties of the Mutant Complex. Iucrj V. 9 261 2022.
ISSN: ESSN 2052-2525
PubMed: 35371503
DOI: 10.1107/S2052252521013178