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Zinc in PDB 1dv6: Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+, PDB code: 1dv6 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) 27.52 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.517, 141.517, 278.506, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ (pdb code 1dv6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+, PDB code: 1dv6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1dv6

Go back to Zinc Binding Sites List in 1dv6
Zinc 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 ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1010

b:57.0
occ:1.00
O H:HOH1082 2.2 52.8 1.0
ND1 H:HIS126 2.2 56.4 1.0
ND1 H:HIS128 2.2 57.6 1.0
OD2 H:ASP124 2.3 53.8 1.0
CG H:ASP124 2.9 51.3 1.0
OD1 H:ASP124 2.9 51.4 1.0
CG H:HIS128 3.2 56.8 1.0
CG H:HIS126 3.2 56.1 1.0
CE1 H:HIS126 3.2 56.8 1.0
CE1 H:HIS128 3.3 57.5 1.0
CB H:HIS128 3.5 53.8 1.0
CB H:HIS126 3.5 55.7 1.0
CB H:ASP124 4.3 50.4 1.0
CD2 H:HIS128 4.3 57.0 1.0
CD2 H:HIS126 4.4 56.2 1.0
NE2 H:HIS126 4.4 56.8 1.0
NE2 H:HIS128 4.4 58.0 1.0
O L:HOH1016 4.4 44.1 1.0
N H:HIS126 4.5 53.7 1.0
CA H:HIS126 4.6 54.5 1.0
N H:HIS128 4.6 52.1 1.0
CA H:HIS128 4.6 52.3 1.0

Zinc binding site 2 out of 2 in 1dv6

Go back to Zinc Binding Sites List in 1dv6
Zinc 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 ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn2010

b:60.7
occ:1.00
ND1 T:HIS126 2.3 58.7 1.0
OD2 T:ASP124 2.3 55.6 1.0
ND1 T:HIS128 2.3 58.7 1.0
CG T:ASP124 3.0 53.9 1.0
OD1 T:ASP124 3.2 54.5 1.0
CE1 T:HIS126 3.2 59.1 1.0
CG T:HIS128 3.3 57.6 1.0
CE1 T:HIS128 3.3 58.5 1.0
CG T:HIS126 3.4 58.1 1.0
CB T:HIS128 3.6 55.0 1.0
CB T:HIS126 3.7 57.4 1.0
CB T:ASP124 4.4 52.3 1.0
NE2 T:HIS126 4.4 59.2 1.0
CD2 T:HIS126 4.5 58.6 1.0
CD2 T:HIS128 4.5 57.9 1.0
NE2 T:HIS128 4.5 58.6 1.0
N T:HIS126 4.7 55.8 1.0
CA T:HIS128 4.8 53.9 1.0
N T:HIS128 4.8 54.1 1.0
CA T:HIS126 4.8 56.4 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 Sep 25 21:20:29 2020
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