Magnesium in PDB 2c3m: Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus

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

The structure of Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3m 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)	51.12 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.021, 146.158, 211.737, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.2

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

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

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus (pdb code 2c3m). 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 Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure 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 Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2238 b:9.3 occ:1.00 OD1 A:ASP963 2.0 12.4 1.0 O1B A:TPP2236 2.1 12.8 1.0 O2A A:TPP2236 2.1 11.9 1.0 O A:VAL993 2.1 10.0 1.0 O A:HOH2487 2.2 13.7 1.0 OG1 A:THR991 2.3 11.9 1.0 CG A:ASP963 3.0 12.7 1.0 PA A:TPP2236 3.3 12.6 1.0 PB A:TPP2236 3.3 12.1 1.0 C A:VAL993 3.4 14.5 1.0 O3A A:TPP2236 3.4 13.0 1.0 OD2 A:ASP963 3.5 16.9 1.0 CB A:THR991 3.6 13.8 1.0 N A:ASP963 3.7 13.3 1.0 O2B A:TPP2236 3.8 13.2 1.0 N A:THR991 3.9 12.8 1.0 N A:SER995 3.9 12.9 1.0 CG2 A:THR991 4.0 11.4 1.0 N A:VAL993 4.0 16.1 1.0 O7 A:TPP2236 4.1 10.8 1.0 OG A:SER995 4.1 12.9 1.0 CA A:THR991 4.2 13.2 1.0 CA A:TYR994 4.2 11.7 1.0 N A:TYR994 4.2 12.9 1.0 CB A:ASP963 4.2 14.2 1.0 N A:GLY964 4.3 11.8 1.0 CA A:VAL993 4.4 14.9 1.0 O A:MET989 4.4 15.8 1.0 O1A A:TPP2236 4.4 13.5 1.0 C A:THR991 4.5 12.9 1.0 N A:GLU992 4.5 14.2 1.0 CA A:GLY962 4.5 12.8 1.0 CA A:ASP963 4.5 12.0 1.0 O3B A:TPP2236 4.5 14.7 1.0 C A:GLY962 4.5 13.0 1.0 C A:TYR994 4.6 13.7 1.0 CB A:SER995 4.6 14.5 1.0 CG2 A:VAL993 4.9 15.9 1.0 C A:ASP963 4.9 11.8 1.0 CA A:SER995 4.9 14.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure 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 Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2238 b:5.8 occ:1.00 O1B B:TPP2236 2.1 9.0 1.0 OD1 B:ASP963 2.1 10.7 1.0 O2A B:TPP2236 2.2 11.0 1.0 O B:VAL993 2.2 10.8 1.0 O B:HOH2575 2.2 12.0 1.0 OG1 B:THR991 2.3 7.4 1.0 CG B:ASP963 3.1 10.0 1.0 PB B:TPP2236 3.2 11.8 1.0 PA B:TPP2236 3.3 9.9 1.0 O3A B:TPP2236 3.4 9.2 1.0 C B:VAL993 3.4 11.6 1.0 CB B:THR991 3.6 7.9 1.0 OD2 B:ASP963 3.6 12.1 1.0 O2B B:TPP2236 3.7 10.9 1.0 N B:ASP963 3.8 9.6 1.0 N B:THR991 3.8 10.9 1.0 N B:SER995 3.9 11.9 1.0 OG B:SER995 3.9 12.9 1.0 O7 B:TPP2236 4.1 12.0 1.0 N B:VAL993 4.1 11.1 1.0 CG2 B:THR991 4.1 7.8 1.0 CA B:THR991 4.1 7.4 1.0 CA B:TYR994 4.2 8.9 1.0 N B:TYR994 4.2 11.2 1.0 CB B:ASP963 4.3 10.4 1.0 N B:GLY964 4.4 12.1 1.0 CA B:VAL993 4.4 9.9 1.0 O3B B:TPP2236 4.4 10.6 1.0 C B:THR991 4.4 9.9 1.0 CB B:SER995 4.5 11.6 1.0 O1A B:TPP2236 4.5 7.6 1.0 O B:MET989 4.5 14.3 1.0 N B:GLU992 4.5 10.5 1.0 C B:TYR994 4.5 11.9 1.0 CA B:GLY962 4.5 9.1 1.0 CA B:ASP963 4.5 10.1 1.0 C B:GLY962 4.6 9.0 1.0 CA B:SER995 4.8 10.1 1.0 CG2 B:VAL993 4.8 13.7 1.0 OE2 B:GLU817 5.0 10.3 1.0 C B:ASP963 5.0 11.6 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