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Magnesium in PDB 2c3u: Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form

Enzymatic activity of Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form

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

Protein crystallography data

The structure of Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form, PDB code: 2c3u 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) 49.48 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.176, 146.810, 212.860, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.8

Other elements in 2c3u:

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

Iron (Fe) 24 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, Oxygen Inhibited Form (pdb code 2c3u). 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, Oxygen Inhibited Form, PDB code: 2c3u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2c3u

Go back to Magnesium Binding Sites List in 2c3u
Magnesium binding site 1 out of 2 in the Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form


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, Oxygen Inhibited Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2238

b:7.4
occ:1.00
O21 A:2TP2236 2.0 12.8 1.0
O A:HOH2271 2.1 17.6 1.0
OD1 A:ASP963 2.1 14.3 1.0
O12 A:2TP2236 2.1 14.9 1.0
O A:VAL993 2.1 18.8 1.0
OG1 A:THR991 2.3 11.3 1.0
CG A:ASP963 3.1 14.3 1.0
P2 A:2TP2236 3.2 17.5 1.0
P1 A:2TP2236 3.2 17.5 1.0
O11 A:2TP2236 3.3 14.8 1.0
C A:VAL993 3.3 20.1 1.0
CB A:THR991 3.5 15.7 1.0
OD2 A:ASP963 3.7 13.6 1.0
O22 A:2TP2236 3.7 18.1 1.0
N A:ASP963 3.8 13.1 1.0
N A:SER995 3.9 13.2 1.0
CG2 A:THR991 3.9 12.9 1.0
N A:THR991 4.0 13.2 1.0
N A:VAL993 4.0 18.5 1.0
OG A:SER995 4.0 16.6 1.0
O5G A:2TP2236 4.0 14.4 1.0
CA A:THR991 4.2 14.9 1.0
N A:TYR994 4.2 20.6 1.0
CA A:TYR994 4.3 17.2 1.0
CA A:VAL993 4.3 18.0 1.0
CB A:ASP963 4.3 11.4 1.0
N A:GLY964 4.3 11.1 1.0
O23 A:2TP2236 4.4 14.4 1.0
CB A:SER995 4.5 14.6 1.0
O13 A:2TP2236 4.5 17.3 1.0
CA A:GLY962 4.5 10.6 1.0
C A:THR991 4.5 17.7 1.0
O A:MET989 4.5 16.8 1.0
CA A:ASP963 4.5 12.8 1.0
C A:GLY962 4.6 13.1 1.0
N A:GLU992 4.6 18.8 1.0
C A:TYR994 4.6 15.6 1.0
CA A:SER995 4.8 14.1 1.0
CG1 A:VAL993 4.8 14.4 1.0
C A:ASP963 5.0 12.0 1.0

Magnesium binding site 2 out of 2 in 2c3u

Go back to Magnesium Binding Sites List in 2c3u
Magnesium binding site 2 out of 2 in the Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form


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, Oxygen Inhibited Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2238

b:1.4
occ:1.00
O22 B:2TP2236 2.1 7.5 1.0
O13 B:2TP2236 2.1 10.6 1.0
OD1 B:ASP963 2.2 10.4 1.0
O B:VAL993 2.2 13.2 1.0
O B:HOH2359 2.2 10.1 1.0
OG1 B:THR991 2.3 7.1 1.0
CG B:ASP963 3.2 9.5 1.0
P2 B:2TP2236 3.2 8.4 1.0
P1 B:2TP2236 3.3 11.4 1.0
O11 B:2TP2236 3.4 9.4 1.0
C B:VAL993 3.4 14.7 1.0
CB B:THR991 3.6 9.5 1.0
OD2 B:ASP963 3.6 6.4 1.0
O21 B:2TP2236 3.8 12.7 1.0
N B:ASP963 3.8 9.4 1.0
N B:SER995 3.9 11.0 1.0
OG B:SER995 3.9 15.5 1.0
N B:THR991 3.9 11.9 1.0
O5G B:2TP2236 4.1 11.4 1.0
CG2 B:THR991 4.1 8.9 1.0
N B:VAL993 4.1 14.0 1.0
CA B:THR991 4.2 11.0 1.0
CA B:TYR994 4.3 14.6 1.0
N B:TYR994 4.3 13.5 1.0
CB B:ASP963 4.4 11.1 1.0
N B:GLY964 4.4 9.1 1.0
O23 B:2TP2236 4.4 9.5 1.0
CA B:VAL993 4.4 13.2 1.0
CB B:SER995 4.5 14.0 1.0
O12 B:2TP2236 4.5 7.0 1.0
O B:MET989 4.5 12.9 1.0
C B:THR991 4.5 12.5 1.0
CA B:GLY962 4.5 4.9 1.0
N B:GLU992 4.5 14.3 1.0
C B:TYR994 4.6 13.2 1.0
CA B:ASP963 4.6 7.3 1.0
C B:GLY962 4.6 8.5 1.0
CG1 B:VAL993 4.8 12.6 1.0
CA B:SER995 4.8 13.1 1.0
OE2 B:GLU817 4.9 13.2 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 22:10:43 2024

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