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Cadmium in PDB 1dv3: Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+, PDB code: 1dv3 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) 27.80 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.250, 141.250, 275.330, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 25.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ (pdb code 1dv3). 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-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+, PDB code: 1dv3:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1dv3

Go back to Cadmium Binding Sites List in 1dv3
Cadmium binding site 1 out of 2 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-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-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd1010

b:43.9
occ:1.00
ND1 H:HIS128 2.3 41.8 1.0
ND1 H:HIS126 2.3 41.2 1.0
O H:HOH1030 2.3 39.4 1.0
OD2 H:ASP124 2.3 40.4 1.0
O H:HOH1094 2.7 46.2 1.0
O H:HOH1029 2.9 47.6 1.0
CG H:ASP124 3.2 37.9 1.0
CG H:HIS128 3.2 42.1 1.0
CE1 H:HIS128 3.3 42.6 1.0
CG H:HIS126 3.3 41.2 1.0
CE1 H:HIS126 3.3 41.2 1.0
OD1 H:ASP124 3.5 36.4 1.0
CB H:HIS128 3.5 38.9 1.0
CB H:HIS126 3.6 40.4 1.0
CD2 H:HIS128 4.4 41.5 1.0
NE2 H:HIS128 4.4 42.1 1.0
CD2 H:HIS126 4.4 40.2 1.0
NE2 H:HIS126 4.4 40.6 1.0
CB H:ASP124 4.5 37.1 1.0
O L:HOH1020 4.6 40.8 1.0
N H:HIS126 4.7 39.9 1.0
CA H:HIS126 4.7 40.4 1.0
CA H:HIS128 4.8 37.6 1.0
N H:HIS128 4.8 37.9 1.0

Cadmium binding site 2 out of 2 in 1dv3

Go back to Cadmium Binding Sites List in 1dv3
Cadmium binding site 2 out of 2 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-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-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd2010

b:56.9
occ:1.00
OD2 T:ASP124 2.3 46.6 1.0
ND1 T:HIS128 2.3 48.1 1.0
ND1 T:HIS126 2.3 47.4 1.0
O T:HOH2023 2.6 56.2 1.0
O T:HOH2024 2.9 44.3 1.0
CG T:ASP124 3.2 43.3 1.0
CE1 T:HIS126 3.3 46.9 1.0
CG T:HIS128 3.3 46.4 1.0
CE1 T:HIS128 3.3 47.8 1.0
CG T:HIS126 3.3 46.0 1.0
OD1 T:ASP124 3.5 44.9 1.0
CB T:HIS128 3.6 42.5 1.0
CB T:HIS126 3.7 44.4 1.0
CD2 T:HIS128 4.5 45.8 1.0
NE2 T:HIS126 4.5 45.2 1.0
NE2 T:HIS128 4.5 46.8 1.0
CD2 T:HIS126 4.5 44.7 1.0
CB T:ASP124 4.5 40.6 1.0
N T:HIS126 4.8 42.5 1.0
CA T:HIS126 4.8 43.6 1.0
CA T:HIS128 4.8 41.2 1.0
N T:HIS128 4.9 41.4 1.0

Reference:

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
Page generated: Fri Aug 28 11:45:16 2020
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