Calcium in PDB 2c3y: Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus

All present enzymatic activity of Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus:
1.2.7.1;

The structure of Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3y was solved by C.Cavazza, C.Contreras-Martel, L.Pieulle, E.Chabriere, E.C.Hatchikian, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.081, 145.639, 211.619, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.8

The structure of Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Calcium atom in the Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus (pdb code 2c3y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2238 b:39.9 occ:1.00 OD1 A:ASN985 2.8 15.9 1.0 O A:PHE1059 2.8 16.3 1.0 O A:GLY1061 2.8 12.4 1.0 OD2 A:ASP983 2.8 19.6 1.0 O A:ALA1056 3.0 12.9 1.0 OG A:SER1063 3.2 15.8 1.0 O A:GLU1057 3.7 16.9 1.0 CG A:ASN985 3.7 15.0 1.0 O A:VAL984 3.7 14.0 1.0 O A:HOH2755 3.7 17.4 1.0 C A:PHE1059 3.9 16.5 1.0 CB A:SER1063 3.9 14.3 1.0 CG A:ASP983 4.0 18.9 1.0 C A:GLY1061 4.0 14.6 1.0 C A:ALA1056 4.1 14.4 1.0 C A:GLU1057 4.1 16.9 1.0 ND2 A:ASN985 4.1 14.5 1.0 CA A:GLU1057 4.2 16.7 1.0 CB A:PHE1059 4.2 17.0 1.0 C A:VAL984 4.3 13.0 1.0 N A:PHE1059 4.3 16.5 1.0 N A:GLY1061 4.3 17.9 1.0 N A:VAL984 4.4 14.3 1.0 CA A:PHE1059 4.4 16.2 1.0 N A:SER1063 4.4 12.0 1.0 O A:HOH2707 4.5 16.5 1.0 C A:ASP983 4.6 15.2 1.0 N A:GLU1057 4.6 15.4 1.0 CA A:ASP983 4.7 16.2 1.0 C A:PRO1062 4.7 11.2 1.0 OD1 A:ASP983 4.7 18.8 1.0 CD2 A:PHE1059 4.7 17.0 1.0 CA A:SER1063 4.8 12.8 1.0 N A:ASN985 4.8 11.4 1.0 CA A:GLY1061 4.9 15.3 1.0 CB A:ASN985 4.9 12.8 1.0 CA A:PRO1062 4.9 11.6 1.0 CA A:VAL984 4.9 13.5 1.0 N A:PRO1062 4.9 13.5 1.0 CB A:ASP983 4.9 17.6 1.0 CA A:ASN985 5.0 13.9 1.0 CG A:PHE1059 5.0 16.9 1.0 N A:SER1058 5.0 17.7 1.0 N A:PRO1060 5.0 16.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2238 b:38.2 occ:1.00 OD1 B:ASN985 2.7 14.0 1.0 O B:GLY1061 2.8 13.4 1.0 O B:PHE1059 2.8 17.1 1.0 OD2 B:ASP983 2.8 20.6 1.0 O B:ALA1056 3.0 13.5 1.0 OG B:SER1063 3.1 17.6 1.0 O B:VAL984 3.5 15.4 1.0 O B:HOH2925 3.6 19.1 1.0 O B:GLU1057 3.7 13.8 1.0 CG B:ASN985 3.7 12.2 1.0 C B:PHE1059 3.8 15.6 1.0 CB B:SER1063 3.9 11.7 1.0 C B:GLY1061 4.0 14.5 1.0 CG B:ASP983 4.0 19.9 1.0 CB B:PHE1059 4.1 15.1 1.0 C B:ALA1056 4.1 11.0 1.0 C B:VAL984 4.2 14.3 1.0 C B:GLU1057 4.2 13.8 1.0 ND2 B:ASN985 4.2 13.7 1.0 N B:VAL984 4.3 15.6 1.0 N B:SER1063 4.3 12.5 1.0 N B:GLY1061 4.3 18.1 1.0 N B:PHE1059 4.3 13.1 1.0 CA B:PHE1059 4.3 14.3 1.0 CA B:GLU1057 4.4 12.8 1.0 O B:HOH2923 4.4 24.9 1.0 CD2 B:PHE1059 4.5 13.2 1.0 C B:ASP983 4.6 16.2 1.0 CA B:ASP983 4.6 16.4 1.0 C B:PRO1062 4.6 12.4 1.0 N B:GLU1057 4.7 10.9 1.0 CA B:SER1063 4.8 12.8 1.0 OD1 B:ASP983 4.8 21.6 1.0 N B:ASN985 4.8 13.2 1.0 CA B:VAL984 4.8 15.4 1.0 CG B:PHE1059 4.8 12.7 1.0 CA B:PRO1062 4.8 12.8 1.0 CA B:GLY1061 4.8 16.0 1.0 N B:PRO1062 4.9 14.4 1.0 CB B:ASN985 4.9 11.9 1.0 CB B:ASP983 4.9 17.7 1.0 CA B:ASN985 4.9 13.0 1.0 N B:PRO1060 5.0 17.2 1.0

C.Cavazza, C.Contreras-Martel, L.Pieulle, E.Chabriere, E.C.Hatchikian, J.C.Fontecilla-Camps. Flexibility of Thiamine Diphosphate Revealed By Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate. Structure V. 14 217 2006.
ISSN: ISSN 0969-2126
PubMed: 16472741
DOI: 10.1016/J.STR.2005.10.013