Zinc in PDB 1cpr: St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus

The structure of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus, PDB code: 1cpr was solved by T.H.Tahirov, S.Misaki, T.E.Meyer, M.A.Cusanovich, N.Yasuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.680, 46.850, 40.750, 90.00, 110.94, 90.00
R / Rfree (%)	18.4 / n/a

The structure of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus (pdb code 1cpr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus, PDB code: 1cpr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn130 b:16.1 occ:1.00 OE1 A:GLU34 2.0 8.7 1.0 OD1 A:ASP32 2.1 11.4 1.0 CG A:ASP32 2.9 14.2 1.0 OD2 A:ASP32 3.0 12.5 1.0 ZN A:ZN131 3.2 23.0 0.3 CD A:GLU34 3.2 12.6 1.0 CG A:GLU34 3.8 12.5 1.0 CB A:GLU34 3.9 10.4 1.0 O A:HOH137 4.0 5.6 1.0 OE2 A:GLU34 4.2 16.4 1.0 N A:GLU34 4.3 9.6 1.0 CB A:ASP32 4.4 13.0 1.0 CA A:GLU34 4.7 12.3 1.0 N A:ALA33 4.8 10.5 1.0 CA A:ASP32 5.0 13.2 1.0

Zinc binding site 2 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn131 b:23.0 occ:0.35 O A:HOH137 2.9 5.6 1.0 ZN A:ZN130 3.2 16.1 1.0 OE1 A:GLU34 3.7 8.7 1.0 CD A:GLU34 4.5 12.6 1.0 OD1 A:ASP32 4.7 11.4 1.0 OE2 A:GLU34 4.8 16.4 1.0

Zinc binding site 3 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn132 b:13.5 occ:0.70 ND1 A:HIS122 2.1 7.5 1.0 O A:HOH148 2.4 15.0 1.0 CE1 A:HIS122 3.1 9.4 1.0 CG A:HIS122 3.1 6.3 1.0 CB A:HIS122 3.5 9.0 1.0 NE2 A:HIS122 4.2 8.5 1.0 CD2 A:HIS122 4.3 6.6 1.0 NH1 A:ARG126 4.3 20.2 1.0 O A:CYS118 4.5 8.8 1.0 CA A:LYS119 4.6 11.5 1.0 C A:CYS118 4.7 9.9 1.0 N A:LYS119 4.8 8.8 1.0

Zinc binding site 4 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn133 b:28.2 occ:0.45 OE2 A:GLU11 2.1 29.5 1.0 O2A A:HEM136 2.1 32.6 1.0 O1A A:HEM136 2.4 31.0 1.0 CGA A:HEM136 2.6 25.6 1.0 CD A:GLU11 3.2 27.6 1.0 CG A:GLU11 3.6 23.8 1.0 CE A:LYS15 4.1 35.8 1.0 CBA A:HEM136 4.1 22.5 1.0 O A:HOH179 4.1 42.0 1.0 OE1 A:GLU11 4.3 30.9 1.0 NZ A:LYS15 4.7 41.9 1.0 CB A:GLU11 4.7 12.1 1.0 CAA A:HEM136 4.8 13.7 1.0

Zinc binding site 5 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn134 b:27.8 occ:0.31 ND1 A:HIS89 2.1 28.0 1.0 CG A:HIS89 3.0 24.6 1.0 O A:HOH182 3.1 36.1 1.0 CB A:HIS89 3.2 19.0 1.0 CE1 A:HIS89 3.2 27.8 1.0 O A:LEU47 3.8 22.1 1.0 O A:HOH141 4.0 32.5 1.0 CA A:HIS89 4.1 16.7 1.0 CB A:LEU47 4.2 16.9 1.0 CD2 A:HIS89 4.2 27.6 1.0 NE2 A:HIS89 4.3 29.9 1.0 O A:HIS89 4.5 16.9 1.0 C A:HIS89 4.6 15.8 1.0 C A:LEU47 4.7 22.2 1.0 CD1 A:LEU47 4.7 17.1 1.0 CG A:LEU47 5.0 15.9 1.0

Zinc binding site 6 out of 6 in the St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of St. Louis Cytochrome C' From the Purple Phototropic Bacterium, Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn135 b:28.1 occ:0.25 NE2 A:HIS89 2.1 29.9 1.0 O A:HOH183 2.5 31.3 1.0 O A:HOH172 2.6 41.3 1.0 CE1 A:HIS89 3.0 27.8 1.0 CD2 A:HIS89 3.2 27.6 1.0 OH A:TYR13 3.2 12.6 1.0 O A:THR49 3.6 25.7 1.0 CG1 A:VAL51 3.9 30.0 1.0 CG2 A:VAL51 4.0 31.4 1.0 ND1 A:HIS89 4.2 28.0 1.0 CZ A:TYR13 4.3 10.6 1.0 CG A:HIS89 4.3 24.6 1.0 CE A:MET88 4.4 13.1 1.0 CB A:VAL51 4.6 30.3 1.0 N A:VAL51 4.7 27.1 1.0 O A:LEU47 4.8 22.1 1.0 C A:THR49 4.8 28.7 1.0 O A:GLY85 5.0 16.5 1.0 CE1 A:TYR13 5.0 10.2 1.0

T.H.Tahirov, S.Misaki, T.E.Meyer, M.A.Cusanovich, Y.Higuchi, N.Yasuoka. Structure of Cytochrome C' From Rhodobacter Capsulatus Strain St Louis: An Unusual Molecular Association Induced By Bridging Zn Ions. Acta Crystallogr.,Sect.D V. 53 658 1997.
ISSN: ISSN 0907-4449
PubMed: 15299853
DOI: 10.1107/S0907444997005805