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Calcium in PDB 2pda: Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.

Enzymatic activity of Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.

All present enzymatic activity of Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.:
1.2.7.1;

Protein crystallography data

The structure of Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate., PDB code: 2pda was solved by E.Chabriere, M.H.Charon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.000, 146.300, 211.900, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 29.7

Other elements in 2pda:

The structure of Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. 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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. (pdb code 2pda). 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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate., PDB code: 2pda:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2pda

Go back to Calcium Binding Sites List in 2pda
Calcium binding site 1 out of 2 in the Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.


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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1238

b:2.8
occ:1.00
 OD1 A:ASN985 2.4 3.0 1.0
O A:GLY1061 2.7 5.7 1.0
O A:PHE1059 2.8 7.3 1.0
O A:ALA1056 2.8 12.3 1.0
OG A:SER1063 2.9 6.2 1.0
OD1 A:ASP983 3.0 12.0 1.0
O A:GLU1057 3.3 12.2 1.0
CG A:ASN985 3.5 3.4 1.0
C A:GLU1057 3.8 11.4 1.0
O A:VAL984 3.8 3.6 1.0
CG A:ASP983 3.9 10.6 1.0
C A:GLY1061 3.9 5.8 1.0
C A:ALA1056 3.9 12.2 1.0
C A:PHE1059 4.0 7.2 1.0
ND2 A:ASN985 4.0 4.0 1.0
CA A:GLU1057 4.1 11.6 1.0
CB A:SER1063 4.2 4.4 1.0
N A:PHE1059 4.3 8.1 1.0
N A:GLY1061 4.3 6.5 1.0
C A:VAL984 4.3 3.3 1.0
N A:GLU1057 4.5 12.0 1.0
N A:VAL984 4.5 4.8 1.0
OD2 A:ASP983 4.6 11.2 1.0
N A:SER1058 4.6 10.6 1.0
CA A:PHE1059 4.6 7.2 1.0
CB A:PHE1059 4.7 7.5 1.0
C A:PRO1062 4.7 5.5 1.0
CB A:ASN985 4.7 3.0 1.0
C A:ASP983 4.7 5.7 1.0
N A:SER1063 4.8 5.2 1.0
CA A:ASP983 4.8 6.5 1.0
CA A:GLY1061 4.8 5.6 1.0
N A:PRO1062 4.8 5.4 1.0
C A:SER1058 4.9 8.9 1.0
CB A:ASP983 4.9 8.5 1.0
N A:ASN985 4.9 2.7 1.0
CA A:ASN985 4.9 2.8 1.0
CA A:PRO1062 5.0 5.1 1.0

Calcium binding site 2 out of 2 in 2pda

Go back to Calcium Binding Sites List in 2pda
Calcium binding site 2 out of 2 in the Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.


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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1245

b:2.8
occ:1.00
 OD1 B:ASN985 2.4 3.0 1.0
O B:GLY1061 2.7 5.7 1.0
O B:PHE1059 2.8 7.3 1.0
O B:ALA1056 2.8 12.3 1.0
OG B:SER1063 2.9 6.2 1.0
OD1 B:ASP983 3.0 12.0 1.0
O B:GLU1057 3.3 12.2 1.0
CG B:ASN985 3.5 3.4 1.0
C B:GLU1057 3.8 11.4 1.0
O B:VAL984 3.8 3.6 1.0
CG B:ASP983 3.9 10.6 1.0
C B:GLY1061 3.9 5.8 1.0
C B:ALA1056 3.9 12.2 1.0
C B:PHE1059 4.0 7.2 1.0
ND2 B:ASN985 4.0 4.0 1.0
CA B:GLU1057 4.1 11.6 1.0
CB B:SER1063 4.2 4.4 1.0
N B:PHE1059 4.3 8.1 1.0
N B:GLY1061 4.3 6.5 1.0
C B:VAL984 4.3 3.3 1.0
N B:GLU1057 4.5 12.0 1.0
N B:VAL984 4.5 4.8 1.0
OD2 B:ASP983 4.6 11.2 1.0
N B:SER1058 4.6 10.6 1.0
CA B:PHE1059 4.6 7.2 1.0
CB B:PHE1059 4.7 7.5 1.0
C B:PRO1062 4.7 5.5 1.0
CB B:ASN985 4.7 3.0 1.0
C B:ASP983 4.7 5.7 1.0
N B:SER1063 4.8 5.2 1.0
CA B:ASP983 4.8 6.5 1.0
CA B:GLY1061 4.8 5.6 1.0
N B:PRO1062 4.8 5.4 1.0
C B:SER1058 4.9 8.9 1.0
CB B:ASP983 4.9 8.5 1.0
N B:ASN985 4.9 2.7 1.0
CA B:ASN985 4.9 2.8 1.0
CA B:PRO1062 5.0 5.1 1.0

Reference:

E.Chabriere, M.H.Charon, A.Volbeda, L.Pieulle, E.C.Hatchikian, J.C.Fontecilla-Camps. Crystal Structures of the Key Anaerobic Enzyme Pyruvate:Ferredoxin Oxidoreductase, Free and in Complex with Pyruvate. Nat.Struct.Biol. V. 6 182 1999.
ISSN: ISSN 1072-8368
PubMed: 10048931
DOI: 10.1038/5870
Page generated: Fri Jul 12 15:08:17 2024

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