Magnesium in PDB 3prc: Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)

The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted), PDB code: 3prc was solved by C.R.D.Lancaster, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	223.500, 223.500, 113.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) (pdb code 3prc). 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 Rhodopseudomonas Viridis (Qb- Depleted), PDB code: 3prc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


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 Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg302 b:12.0 occ:1.00 MG L:BCB302 0.0 12.0 1.0 ND L:BCB302 2.0 10.0 1.0 NB L:BCB302 2.0 8.4 1.0 NC L:BCB302 2.1 8.1 1.0 NE2 L:HIS173 2.1 10.7 1.0 NA L:BCB302 2.2 12.3 1.0 C4D L:BCB302 2.9 11.4 1.0 CE1 L:HIS173 3.0 10.2 1.0 C1D L:BCB302 3.0 11.1 1.0 C4B L:BCB302 3.1 8.8 1.0 C1C L:BCB302 3.1 9.8 1.0 C1B L:BCB302 3.1 11.2 1.0 C4C L:BCB302 3.1 10.3 1.0 CD2 L:HIS173 3.1 8.7 1.0 C4A L:BCB302 3.2 12.6 1.0 C1A L:BCB302 3.2 12.4 1.0 CHC L:BCB302 3.4 10.1 1.0 CHD L:BCB302 3.4 10.2 1.0 CHA L:BCB302 3.5 13.6 1.0 CHB L:BCB302 3.5 10.7 1.0 CBB M:BCB806 3.5 13.0 1.0 CAB M:BCB806 3.7 10.6 1.0 OBB M:BCB806 3.8 11.1 1.0 ND1 L:HIS173 4.2 8.1 1.0 C3D L:BCB302 4.2 13.0 1.0 CG L:HIS173 4.2 9.7 1.0 C2D L:BCB302 4.3 11.0 1.0 C3B L:BCB302 4.3 11.1 1.0 C2B L:BCB302 4.3 11.5 1.0 CD1 L:TRP167 4.3 7.5 1.0 NE1 L:TRP167 4.3 9.5 1.0 C3C L:BCB302 4.3 9.1 1.0 C2C L:BCB302 4.3 8.7 1.0 C3B M:BCB806 4.4 7.8 1.0 C3A L:BCB302 4.5 14.2 1.0 C2A L:BCB302 4.5 12.8 1.0 CBD L:BCB302 4.9 14.7 1.0

Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


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 Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg304 b:13.4 occ:1.00 MG L:BCB304 0.0 13.4 1.0 ND L:BCB304 2.0 10.5 1.0 NB L:BCB304 2.0 13.4 1.0 NC L:BCB304 2.1 11.2 1.0 NE2 L:HIS153 2.1 11.6 1.0 NA L:BCB304 2.2 10.4 1.0 C4D L:BCB304 3.0 11.0 1.0 C4B L:BCB304 3.0 14.1 1.0 C1B L:BCB304 3.1 13.1 1.0 C1C L:BCB304 3.1 12.4 1.0 C1D L:BCB304 3.1 11.9 1.0 CE1 L:HIS153 3.1 10.4 1.0 C4C L:BCB304 3.1 11.0 1.0 CD2 L:HIS153 3.2 9.1 1.0 C4A L:BCB304 3.2 9.8 1.0 C1A L:BCB304 3.2 10.7 1.0 CHC L:BCB304 3.4 13.2 1.0 CHD L:BCB304 3.5 11.5 1.0 CHB L:BCB304 3.5 11.3 1.0 CHA L:BCB304 3.5 12.3 1.0 C3D L:BCB304 4.2 11.3 1.0 ND1 L:HIS153 4.2 10.6 1.0 C2D L:BCB304 4.3 10.4 1.0 C3B L:BCB304 4.3 14.0 1.0 C2B L:BCB304 4.3 13.2 1.0 CG L:HIS153 4.3 10.2 1.0 C2C L:BCB304 4.3 12.6 1.0 C3C L:BCB304 4.4 11.5 1.0 OBB L:BPB402 4.4 18.0 1.0 C3A L:BCB304 4.5 8.1 1.0 C2A L:BCB304 4.5 10.3 1.0 CE2 M:TYR208 4.6 11.2 1.0 CD2 L:LEU154 4.8 14.3 1.0 C20 L:BPB402 4.9 7.3 1.0 CBA L:BCB304 4.9 11.2 1.0 CBD L:BCB304 5.0 12.5 1.0

Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


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 Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg805 b:17.1 occ:1.00 MG M:BCB805 0.0 17.1 1.0 NB M:BCB805 2.0 17.2 1.0 ND M:BCB805 2.0 16.3 1.0 NE2 M:HIS180 2.1 16.2 1.0 NC M:BCB805 2.1 13.0 1.0 NA M:BCB805 2.2 16.9 1.0 CD2 M:HIS180 3.0 15.0 1.0 C4D M:BCB805 3.0 17.9 1.0 C4B M:BCB805 3.0 17.2 1.0 C1B M:BCB805 3.1 18.7 1.0 C1C M:BCB805 3.1 13.7 1.0 C1D M:BCB805 3.1 13.6 1.0 C4A M:BCB805 3.2 19.2 1.0 C4C M:BCB805 3.2 11.6 1.0 CE1 M:HIS180 3.2 14.9 1.0 C1A M:BCB805 3.2 17.3 1.0 CHC M:BCB805 3.4 14.8 1.0 CHB M:BCB805 3.5 17.9 1.0 CHA M:BCB805 3.5 18.1 1.0 CHD M:BCB805 3.5 13.4 1.0 CG M:HIS180 4.2 14.1 1.0 C3D M:BCB805 4.2 16.9 1.0 ND1 M:HIS180 4.3 14.8 1.0 C2B M:BCB805 4.3 19.4 1.0 C3B M:BCB805 4.3 18.7 1.0 C2D M:BCB805 4.3 14.6 1.0 C2C M:BCB805 4.4 12.0 1.0 C3C M:BCB805 4.4 11.7 1.0 OBB M:BPB401 4.5 26.5 1.0 C3A M:BCB805 4.5 17.6 1.0 C2A M:BCB805 4.5 17.7 1.0 CBA M:BCB805 4.9 27.7 1.0 CBD M:BCB805 5.0 15.9 1.0

Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


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 Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg806 b:12.8 occ:1.00 MG M:BCB806 0.0 12.8 1.0 ND M:BCB806 2.0 12.9 1.0 NB M:BCB806 2.1 10.2 1.0 NC M:BCB806 2.1 12.0 1.0 NE2 M:HIS200 2.1 11.8 1.0 NA M:BCB806 2.2 12.4 1.0 C4D M:BCB806 3.0 14.6 1.0 C1C M:BCB806 3.0 10.9 1.0 C4B M:BCB806 3.1 9.5 1.0 CD2 M:HIS200 3.1 9.3 1.0 C1B M:BCB806 3.1 9.0 1.0 C1D M:BCB806 3.1 12.1 1.0 CE1 M:HIS200 3.1 9.6 1.0 C4C M:BCB806 3.1 11.7 1.0 C1A M:BCB806 3.2 14.1 1.0 C4A M:BCB806 3.2 10.1 1.0 CHC M:BCB806 3.4 8.8 1.0 CHA M:BCB806 3.4 13.5 1.0 CHD M:BCB806 3.5 11.9 1.0 CHB M:BCB806 3.5 9.3 1.0 CBB L:BCB302 3.8 9.3 1.0 CAB L:BCB302 3.9 11.6 1.0 OBB L:BCB302 4.0 10.1 1.0 C3D M:BCB806 4.2 12.6 1.0 ND1 M:HIS200 4.2 10.8 1.0 CG M:HIS200 4.3 11.7 1.0 C3B M:BCB806 4.3 7.8 1.0 C2B M:BCB806 4.3 8.0 1.0 C2C M:BCB806 4.3 7.8 1.0 C2D M:BCB806 4.3 12.3 1.0 C3C M:BCB806 4.3 9.4 1.0 C2A M:BCB806 4.5 12.2 1.0 C3A M:BCB806 4.5 10.1 1.0 C3B L:BCB302 4.5 11.1 1.0 CMC M:BCB806 4.9 4.8 1.0 CD1 M:ILE204 4.9 10.8 1.0 CBD M:BCB806 4.9 13.4 1.0

C.R.Lancaster, H.Michel. The Coupling of Light-Induced Electron Transfer and Proton Uptake As Derived From Crystal Structures of Reaction Centres From Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb. Structure V. 5 1339 1997.
ISSN: ISSN 0969-2126
PubMed: 9351808
DOI: 10.1016/S0969-2126(97)00285-2