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Calcium 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:

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

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus, Oxygen Inhibited Form, PDB code: 2c3u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2c3u

Go back to Calcium Binding Sites List in 2c3u
Calcium 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 Calcium with other atoms in the Ca 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:Ca2239

b:34.6
occ:1.00
 O A:PHE1059 2.7 18.1 1.0
OD2 A:ASP983 2.7 14.9 1.0
OD1 A:ASN985 2.8 17.6 1.0
O A:GLY1061 2.8 16.3 1.0
O A:ALA1056 3.0 11.9 1.0
OG A:SER1063 3.2 27.2 1.0
O A:GLU1057 3.6 20.1 1.0
O A:VAL984 3.6 9.7 1.0
CG A:ASN985 3.7 13.0 1.0
C A:PHE1059 3.8 19.6 1.0
O A:HOH2268 3.8 7.7 1.0
CG A:ASP983 3.8 20.8 1.0
CB A:SER1063 3.9 15.9 1.0
C A:GLY1061 4.0 20.2 1.0
C A:GLU1057 4.1 18.1 1.0
C A:ALA1056 4.1 12.9 1.0
ND2 A:ASN985 4.2 11.7 1.0
C A:VAL984 4.2 12.7 1.0
CB A:PHE1059 4.3 12.8 1.0
N A:VAL984 4.3 14.9 1.0
CA A:GLU1057 4.3 16.6 1.0
N A:GLY1061 4.3 26.5 1.0
N A:PHE1059 4.3 15.4 1.0
CA A:PHE1059 4.4 18.9 1.0
N A:SER1063 4.4 13.0 1.0
C A:ASP983 4.5 16.6 1.0
CA A:ASP983 4.5 16.5 1.0
OD1 A:ASP983 4.6 21.9 1.0
O A:HOH2269 4.7 20.2 1.0
N A:GLU1057 4.7 14.1 1.0
CD2 A:PHE1059 4.7 10.6 1.0
C A:PRO1062 4.7 16.0 1.0
CB A:ASP983 4.7 16.9 1.0
CA A:SER1063 4.8 15.9 1.0
CA A:VAL984 4.9 14.7 1.0
N A:ASN985 4.9 10.9 1.0
CA A:GLY1061 4.9 20.9 1.0
N A:PRO1060 4.9 21.2 1.0
CB A:ASN985 4.9 10.2 1.0
CA A:PRO1062 4.9 14.6 1.0
N A:PRO1062 4.9 17.0 1.0
CA A:ASN985 5.0 12.9 1.0
CG A:PHE1059 5.0 15.1 1.0

Calcium binding site 2 out of 2 in 2c3u

Go back to Calcium Binding Sites List in 2c3u
Calcium 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 Calcium with other atoms in the Ca 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:Ca2239

b:30.5
occ:1.00
 OD1 B:ASN985 2.7 12.0 1.0
O B:PHE1059 2.7 15.2 1.0
O B:GLY1061 2.8 14.2 1.0
OD2 B:ASP983 2.8 19.7 1.0
O B:ALA1056 2.9 12.7 1.0
OG B:SER1063 3.4 20.9 1.0
O B:HOH2357 3.4 32.2 1.0
O B:GLU1057 3.5 14.9 1.0
CG B:ASN985 3.6 10.8 1.0
O B:VAL984 3.7 13.0 1.0
C B:PHE1059 3.8 12.9 1.0
CB B:SER1063 4.0 7.2 1.0
CG B:ASP983 4.0 20.4 1.0
C B:GLY1061 4.0 14.4 1.0
ND2 B:ASN985 4.0 14.4 1.0
C B:GLU1057 4.0 13.9 1.0
C B:ALA1056 4.0 13.2 1.0
C B:VAL984 4.2 14.2 1.0
N B:GLY1061 4.2 18.1 1.0
CA B:GLU1057 4.2 13.1 1.0
N B:VAL984 4.3 16.6 1.0
CB B:PHE1059 4.3 7.1 1.0
N B:PHE1059 4.3 12.5 1.0
O B:HOH2387 4.4 12.5 1.0
CA B:PHE1059 4.4 10.9 1.0
N B:SER1063 4.5 10.8 1.0
C B:ASP983 4.6 17.0 1.0
N B:GLU1057 4.6 12.7 1.0
CA B:ASP983 4.6 16.6 1.0
CD2 B:PHE1059 4.7 8.4 1.0
N B:ASN985 4.7 12.7 1.0
C B:PRO1062 4.7 13.2 1.0
OD1 B:ASP983 4.8 18.7 1.0
CA B:VAL984 4.8 15.1 1.0
CB B:ASN985 4.8 7.5 1.0
CA B:GLY1061 4.8 14.9 1.0
CA B:SER1063 4.9 10.9 1.0
CB B:ASP983 4.9 17.6 1.0
CA B:ASN985 4.9 7.8 1.0
CA B:PRO1062 4.9 14.2 1.0
N B:PRO1060 4.9 16.1 1.0
N B:PRO1062 4.9 14.3 1.0
CG B:PHE1059 5.0 12.0 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: Sat Dec 12 03:33:32 2020

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