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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2c3m:

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

Magnesium Binding Sites:

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 2c3m

Go back to Magnesium Binding Sites List in 2c3m
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 2c3m

Go back to Magnesium Binding Sites List in 2c3m
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

Reference:

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
Page generated: Tue Aug 13 22:09:48 2024

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