Magnesium 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:

Iron	(Fe)	24 atoms
Calcium	(Ca)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Radical Form of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3y:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2237 b:15.5 occ:1.00 OD1 A:ASP963 2.1 10.8 1.0 O12 A:HTL2236 2.1 12.0 1.0 O23 A:HTL2236 2.1 11.4 1.0 O A:VAL993 2.2 13.5 1.0 O A:HOH2710 2.2 10.3 1.0 OG1 A:THR991 2.2 13.8 1.0 CG A:ASP963 3.1 9.1 1.0 P1 A:HTL2236 3.2 13.2 1.0 P2 A:HTL2236 3.2 12.0 1.0 O11 A:HTL2236 3.4 11.2 1.0 C A:VAL993 3.4 15.2 1.0 CB A:THR991 3.5 14.7 1.0 OD2 A:ASP963 3.6 10.9 1.0 O21 A:HTL2236 3.7 11.2 1.0 N A:ASP963 3.8 10.1 1.0 N A:SER995 3.8 11.6 1.0 N A:THR991 3.9 13.4 1.0 OG A:SER995 3.9 11.2 1.0 CG2 A:THR991 4.0 12.2 1.0 N A:VAL993 4.1 13.5 1.0 O5G A:HTL2236 4.1 15.2 1.0 CA A:TYR994 4.1 12.3 1.0 CA A:THR991 4.2 12.0 1.0 N A:TYR994 4.2 13.9 1.0 N A:GLY964 4.2 10.9 1.0 CB A:ASP963 4.3 9.3 1.0 CA A:VAL993 4.4 14.3 1.0 C A:THR991 4.4 11.3 1.0 O13 A:HTL2236 4.5 10.7 1.0 CB A:SER995 4.5 11.0 1.0 O22 A:HTL2236 4.5 12.0 1.0 O A:MET989 4.5 14.9 1.0 C A:TYR994 4.5 12.3 1.0 N A:GLU992 4.5 10.6 1.0 CA A:ASP963 4.5 11.7 1.0 CA A:GLY962 4.6 11.2 1.0 C A:GLY962 4.6 11.3 1.0 CG1 A:VAL993 4.8 14.8 1.0 CA A:SER995 4.8 10.7 1.0 C A:ASP963 4.9 11.8 1.0 OE2 A:GLU817 5.0 13.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2237 b:10.3 occ:1.00 O23 B:HTL2236 2.0 10.4 1.0 O12 B:HTL2236 2.0 14.4 1.0 O B:VAL993 2.2 11.3 1.0 O B:HOH2927 2.2 11.3 1.0 OD1 B:ASP963 2.2 7.5 1.0 OG1 B:THR991 2.3 9.9 1.0 P1 B:HTL2236 3.1 14.4 1.0 P2 B:HTL2236 3.2 13.1 1.0 CG B:ASP963 3.2 9.5 1.0 O11 B:HTL2236 3.3 12.1 1.0 C B:VAL993 3.4 13.2 1.0 CB B:THR991 3.6 11.3 1.0 OD2 B:ASP963 3.6 7.8 1.0 N B:SER995 3.7 9.3 1.0 O21 B:HTL2236 3.8 11.3 1.0 N B:ASP963 3.9 8.7 1.0 N B:THR991 4.0 9.9 1.0 OG B:SER995 4.0 10.3 1.0 CA B:TYR994 4.1 11.6 1.0 O5G B:HTL2236 4.1 13.1 1.0 CG2 B:THR991 4.1 8.6 1.0 N B:VAL993 4.1 10.9 1.0 N B:TYR994 4.2 12.8 1.0 CA B:THR991 4.2 9.8 1.0 N B:GLY964 4.3 10.3 1.0 O22 B:HTL2236 4.3 14.0 1.0 O13 B:HTL2236 4.3 12.5 1.0 CB B:SER995 4.4 9.2 1.0 CA B:VAL993 4.4 12.5 1.0 C B:TYR994 4.4 11.2 1.0 CB B:ASP963 4.4 7.5 1.0 C B:THR991 4.5 8.9 1.0 O B:MET989 4.5 9.1 1.0 CA B:GLY962 4.6 10.1 1.0 N B:GLU992 4.6 9.1 1.0 CA B:ASP963 4.6 9.8 1.0 C B:GLY962 4.7 10.3 1.0 CA B:SER995 4.7 9.6 1.0 CG1 B:VAL993 4.9 12.7 1.0 C B:ASP963 5.0 9.6 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