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Calcium in PDB 2c3p: Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus

Enzymatic activity of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus

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

Protein crystallography data

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3p 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) 47.37 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.966, 145.840, 210.822, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.3

Other elements in 2c3p:

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

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus (pdb code 2c3p). 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 Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2c3p

Go back to Calcium Binding Sites List in 2c3p
Calcium binding site 1 out of 2 in the Crystal Structure of the Free Radical Intermediate 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 Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2238

b:57.1
occ:1.00
 OD1 A:ASN985 2.8 11.4 1.0
O A:PHE1059 2.8 14.7 1.0
OD2 A:ASP983 2.8 24.4 1.0
O A:ALA1056 2.9 20.2 1.0
O A:GLY1061 3.0 16.1 1.0
OG A:SER1063 3.1 25.7 1.0
O A:VAL984 3.5 15.6 1.0
O A:GLU1057 3.7 17.7 1.0
CG A:ASN985 3.7 18.6 1.0
O A:HOH2307 3.8 20.1 1.0
CB A:SER1063 3.9 18.2 1.0
C A:PHE1059 3.9 18.8 1.0
CG A:ASP983 4.0 25.6 1.0
C A:ALA1056 4.0 19.3 1.0
C A:GLU1057 4.1 19.8 1.0
C A:VAL984 4.1 19.1 1.0
C A:GLY1061 4.2 19.5 1.0
ND2 A:ASN985 4.2 17.1 1.0
CB A:PHE1059 4.2 13.2 1.0
CA A:GLU1057 4.2 20.0 1.0
N A:SER1063 4.3 12.3 1.0
N A:PHE1059 4.3 13.9 1.0
N A:VAL984 4.4 19.3 1.0
CA A:PHE1059 4.4 15.4 1.0
N A:GLY1061 4.4 22.9 1.0
C A:ASP983 4.5 19.8 1.0
O A:HOH2305 4.6 14.9 1.0
N A:GLU1057 4.6 18.4 1.0
C A:PRO1062 4.7 15.9 1.0
CD2 A:PHE1059 4.7 15.2 1.0
CA A:ASP983 4.7 20.8 1.0
CA A:SER1063 4.8 16.4 1.0
OD1 A:ASP983 4.8 27.7 1.0
N A:ASN985 4.8 14.2 1.0
CA A:VAL984 4.8 18.0 1.0
CB A:ASN985 4.8 14.4 1.0
CA A:ASN985 4.9 13.3 1.0
CA A:PRO1062 4.9 13.0 1.0
CG A:PHE1059 4.9 17.3 1.0
CB A:ASP983 5.0 24.4 1.0
N A:PRO1062 5.0 16.1 1.0
N A:PRO1060 5.0 18.2 1.0

Calcium binding site 2 out of 2 in 2c3p

Go back to Calcium Binding Sites List in 2c3p
Calcium binding site 2 out of 2 in the Crystal Structure of the Free Radical Intermediate 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 Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2238

b:47.0
occ:1.00
 OD1 B:ASN985 2.5 12.0 1.0
OD2 B:ASP983 2.8 17.6 1.0
O B:PHE1059 2.9 21.7 1.0
O B:ALA1056 2.9 13.5 1.0
O B:GLY1061 3.1 9.2 1.0
O B:HOH2378 3.3 21.6 1.0
OG B:SER1063 3.4 25.1 1.0
O B:GLU1057 3.4 22.7 1.0
CG B:ASN985 3.4 16.4 1.0
O B:VAL984 3.6 19.3 1.0
ND2 B:ASN985 3.8 19.1 1.0
CB B:SER1063 3.9 18.7 1.0
C B:PHE1059 3.9 14.6 1.0
C B:GLU1057 4.0 20.2 1.0
C B:ALA1056 4.0 14.3 1.0
CG B:ASP983 4.0 18.5 1.0
C B:VAL984 4.1 17.7 1.0
CA B:GLU1057 4.1 17.4 1.0
N B:VAL984 4.2 19.6 1.0
CB B:PHE1059 4.3 13.7 1.0
C B:GLY1061 4.3 12.2 1.0
N B:PHE1059 4.3 16.5 1.0
CA B:PHE1059 4.4 15.2 1.0
N B:SER1063 4.5 12.8 1.0
C B:ASP983 4.5 19.9 1.0
N B:GLY1061 4.5 17.3 1.0
O B:HOH2377 4.5 21.7 1.0
N B:GLU1057 4.6 14.1 1.0
CA B:ASP983 4.7 18.5 1.0
CB B:ASN985 4.7 9.8 1.0
N B:ASN985 4.7 17.6 1.0
CA B:VAL984 4.7 18.2 1.0
OD1 B:ASP983 4.8 26.0 1.0
CA B:ASN985 4.8 15.5 1.0
CA B:SER1063 4.8 15.2 1.0
C B:PRO1062 4.9 16.6 1.0
CD2 B:PHE1059 4.9 8.9 1.0
N B:SER1058 5.0 16.9 1.0
CB B:ASP983 5.0 16.8 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: Fri Jul 12 09:21:27 2024

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