Cadmium in PDB 1ds8: Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+, PDB code: 1ds8 was solved by H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	139.590, 139.590, 272.860, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 25.6

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+ also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Cadmium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+ (pdb code 1ds8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+, PDB code: 1ds8:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd1010 b:42.0 occ:1.00 ND1 H:HIS126 2.3 43.0 1.0 ND1 H:HIS128 2.3 43.9 1.0 OD2 H:ASP124 2.3 41.7 1.0 O H:HOH1043 2.5 43.1 1.0 O H:HOH1048 2.7 50.5 1.0 O H:HOH1086 2.7 45.2 1.0 CG H:ASP124 3.2 40.4 1.0 CG H:HIS126 3.3 42.9 1.0 CE1 H:HIS128 3.3 44.0 1.0 CE1 H:HIS126 3.3 43.0 1.0 CG H:HIS128 3.3 43.4 1.0 OD1 H:ASP124 3.5 39.7 1.0 CB H:HIS126 3.5 42.6 1.0 CB H:HIS128 3.6 42.3 1.0 CD2 H:HIS126 4.4 42.8 1.0 NE2 H:HIS128 4.4 44.4 1.0 CD2 H:HIS128 4.4 43.7 1.0 NE2 H:HIS126 4.4 43.5 1.0 CB H:ASP124 4.5 40.7 1.0 N H:HIS126 4.7 41.8 1.0 CA H:HIS126 4.7 42.4 1.0 O L:HOH1078 4.8 45.3 1.0 CA H:HIS128 4.8 41.5 1.0 N H:HIS128 4.9 41.6 1.0

Cadmium binding site 2 out of 2 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor CD2+ within 5.0Å range: probe atom residue distance (Å) B Occ T:Cd2010 b:53.7 occ:1.00 ND1 T:HIS128 2.3 48.3 1.0 OD2 T:ASP124 2.3 46.4 1.0 ND1 T:HIS126 2.3 48.3 1.0 O T:HOH2027 2.5 67.4 1.0 O T:HOH2066 2.8 64.2 1.0 O T:HOH2095 3.0 65.1 1.0 CE1 T:HIS128 3.3 48.3 1.0 CG T:ASP124 3.3 44.1 1.0 CG T:HIS128 3.3 47.0 1.0 CE1 T:HIS126 3.3 48.4 1.0 CG T:HIS126 3.3 47.1 1.0 OD1 T:ASP124 3.6 44.7 1.0 CB T:HIS128 3.6 44.7 1.0 CB T:HIS126 3.6 45.2 1.0 O R:HOH2041 4.4 58.5 1.0 NE2 T:HIS128 4.4 47.5 1.0 CD2 T:HIS128 4.4 46.6 1.0 NE2 T:HIS126 4.5 47.5 1.0 CD2 T:HIS126 4.5 46.9 1.0 CB T:ASP124 4.5 42.9 1.0 CA T:HIS126 4.8 44.0 1.0 N T:HIS126 4.8 43.5 1.0 CA T:HIS128 4.9 43.2 1.0 N T:HIS128 4.9 43.2 1.0 O T:HOH2053 5.0 64.6 1.0

H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher. Determination of the Binding Sites of the Proton Transfer Inhibitors CD2+ and ZN2+ in Bacterial Reaction Centers. Proc.Natl.Acad.Sci.Usa V. 97 1542 2000.
ISSN: ISSN 0027-8424
PubMed: 10677497
DOI: 10.1073/PNAS.97.4.1542