Magnesium in PDB 1yst: Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution

The structure of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution, PDB code: 1yst was solved by B.Arnoux, J.F.Gaucher, A.Ducruix, F.Reiss-Husson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	143.700, 139.800, 78.650, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / n/a

The structure of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution (pdb code 1yst). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution, PDB code: 1yst:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg307 b:25.7 occ:1.00 MG M:BCL307 0.0 25.7 1.0 NB M:BCL307 1.9 25.4 1.0 ND M:BCL307 2.1 23.2 1.0 NC M:BCL307 2.1 21.2 1.0 NA M:BCL307 2.1 19.5 1.0 NE2 M:HIS182 2.3 24.4 1.0 C4B M:BCL307 2.9 26.6 1.0 C1B M:BCL307 2.9 22.2 1.0 C4D M:BCL307 2.9 22.9 1.0 C1C M:BCL307 3.0 21.9 1.0 C4C M:BCL307 3.1 19.9 1.0 C4A M:BCL307 3.1 16.5 1.0 C1A M:BCL307 3.1 22.4 1.0 CD2 M:HIS182 3.2 19.6 1.0 C1D M:BCL307 3.2 18.4 1.0 CHC M:BCL307 3.3 23.6 1.0 CE1 M:HIS182 3.3 24.0 1.0 CHB M:BCL307 3.4 14.8 1.0 CHA M:BCL307 3.4 20.9 1.0 CHD M:BCL307 3.5 14.9 1.0 C2B M:BCL307 4.1 23.1 1.0 C3B M:BCL307 4.1 25.5 1.0 C3D M:BCL307 4.2 23.7 1.0 C2D M:BCL307 4.4 18.9 1.0 C2C M:BCL307 4.4 24.1 1.0 C3A M:BCL307 4.4 18.2 1.0 CG M:HIS182 4.4 22.8 1.0 C3C M:BCL307 4.4 22.2 1.0 ND1 M:HIS182 4.4 17.6 1.0 C2A M:BCL307 4.5 23.1 1.0 CE2 L:PHE181 4.5 31.6 1.0 CBD M:BCL307 4.9 23.1 1.0 CBC M:BCL307 5.0 21.0 1.0

Magnesium binding site 2 out of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg274 b:22.9 occ:1.00 MG L:BCL274 0.0 22.9 1.0 NB L:BCL274 1.9 27.2 1.0 ND L:BCL274 2.0 15.3 1.0 NC L:BCL274 2.0 20.5 1.0 NA L:BCL274 2.1 23.0 1.0 NE2 L:HIS173 2.2 22.7 1.0 C4D L:BCL274 2.9 21.4 1.0 C4B L:BCL274 2.9 29.3 1.0 C1B L:BCL274 2.9 28.8 1.0 C4A L:BCL274 3.0 22.9 1.0 CE1 L:HIS173 3.0 29.3 1.0 C1D L:BCL274 3.1 19.0 1.0 C1A L:BCL274 3.1 26.5 1.0 C4C L:BCL274 3.1 19.1 1.0 C1C L:BCL274 3.1 24.5 1.0 CD2 L:HIS173 3.2 24.9 1.0 CHB L:BCL274 3.3 26.2 1.0 CHC L:BCL274 3.4 28.3 1.0 CHA L:BCL274 3.4 27.3 1.0 CHD L:BCL274 3.5 18.6 1.0 OBB M:BCL308 3.7 35.5 1.0 CBB M:BCL308 3.8 30.4 1.0 CAB M:BCL308 3.9 33.5 1.0 C3D L:BCL274 4.1 22.2 1.0 C2B L:BCL274 4.1 29.6 1.0 C3B L:BCL274 4.2 29.9 1.0 ND1 L:HIS173 4.2 21.9 1.0 C2D L:BCL274 4.2 22.3 1.0 CG L:HIS173 4.3 21.4 1.0 C3A L:BCL274 4.4 24.2 1.0 C2C L:BCL274 4.5 21.4 1.0 C2A L:BCL274 4.5 25.2 1.0 C3C L:BCL274 4.6 17.8 1.0 CBD L:BCL274 4.9 24.1 1.0 C3B M:BCL308 4.9 32.4 1.0

Magnesium binding site 3 out of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg308 b:28.8 occ:1.00 MG M:BCL308 0.0 28.8 1.0 NB M:BCL308 1.9 28.2 1.0 NC M:BCL308 2.0 27.9 1.0 ND M:BCL308 2.0 27.0 1.0 NA M:BCL308 2.3 21.1 1.0 NE2 M:HIS202 2.4 28.5 1.0 C4B M:BCL308 2.8 30.5 1.0 C4D M:BCL308 2.9 25.3 1.0 C1C M:BCL308 2.9 30.1 1.0 C1B M:BCL308 3.0 32.5 1.0 C4C M:BCL308 3.0 30.4 1.0 C1D M:BCL308 3.0 29.3 1.0 CD2 M:HIS202 3.2 32.8 1.0 CHC M:BCL308 3.2 34.9 1.0 C4A M:BCL308 3.2 20.0 1.0 C1A M:BCL308 3.2 20.6 1.0 CE1 M:HIS202 3.3 26.3 1.0 CHD M:BCL308 3.4 34.0 1.0 CHA M:BCL308 3.5 24.8 1.0 CHB M:BCL308 3.5 27.0 1.0 OBB L:BCL274 3.6 30.8 1.0 CBB L:BCL274 4.0 29.8 1.0 CAB L:BCL274 4.0 29.5 1.0 C3D M:BCL308 4.1 28.4 1.0 C2D M:BCL308 4.1 27.8 1.0 C3B M:BCL308 4.1 32.4 1.0 C2B M:BCL308 4.2 34.4 1.0 C3C M:BCL308 4.2 28.6 1.0 C2C M:BCL308 4.2 29.0 1.0 CG M:HIS202 4.3 25.8 1.0 ND1 M:HIS202 4.3 21.9 1.0 C3A M:BCL308 4.6 14.8 1.0 C2A M:BCL308 4.6 18.9 1.0 CBD M:BCL308 4.9 30.6 1.0 C3B L:BCL274 4.9 29.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg275 b:18.8 occ:1.00 MG L:BCL275 0.0 18.8 1.0 NC L:BCL275 1.9 21.4 1.0 ND L:BCL275 2.0 20.5 1.0 NB L:BCL275 2.1 21.1 1.0 NA L:BCL275 2.2 21.3 1.0 NE2 L:HIS153 2.3 20.8 1.0 C4C L:BCL275 2.9 25.0 1.0 C4D L:BCL275 2.9 23.3 1.0 C1C L:BCL275 3.0 23.3 1.0 C1D L:BCL275 3.0 20.6 1.0 C4B L:BCL275 3.1 16.9 1.0 C1B L:BCL275 3.1 21.4 1.0 CD2 L:HIS153 3.2 24.9 1.0 C4A L:BCL275 3.2 19.3 1.0 C1A L:BCL275 3.2 22.1 1.0 CE1 L:HIS153 3.3 22.8 1.0 CHD L:BCL275 3.3 25.2 1.0 CHC L:BCL275 3.4 18.0 1.0 CHA L:BCL275 3.5 23.6 1.0 CHB L:BCL275 3.5 22.2 1.0 C3D L:BCL275 4.2 25.5 1.0 C2D L:BCL275 4.2 17.4 1.0 C3C L:BCL275 4.2 22.8 1.0 C3B L:BCL275 4.3 14.2 1.0 C2C L:BCL275 4.3 22.3 1.0 C2B L:BCL275 4.3 17.9 1.0 CG L:HIS153 4.4 25.1 1.0 ND1 L:HIS153 4.4 21.5 1.0 C3A L:BCL275 4.5 20.3 1.0 C2A L:BCL275 4.6 21.4 1.0 CBD L:BCL275 5.0 25.2 1.0

B.Arnoux, J.F.Gaucher, A.Ducruix, F.Reiss-Husson. Structure of the Photochemical Reaction Centre of A Spheroidene-Containing Purple-Bacterium, Rhodobacter Sphaeroides Y, at 3 A Resolution. Acta Crystallogr.,Sect.D V. 51 368 1995.
ISSN: ISSN 0907-4449
PubMed: 15299304
DOI: 10.1107/S0907444994013120