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Magnesium 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:

Iron (Fe) 24 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate., PDB code: 2pda:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2pda

Go back to Magnesium Binding Sites List in 2pda
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1237

b:12.5
occ:1.00
 O2A A:TPP1236 1.7 13.9 1.0
O1B A:TPP1236 1.8 13.9 1.0
O A:VAL993 2.4 12.9 1.0
OD1 A:ASP963 2.4 2.0 1.0
OG1 A:THR991 2.5 7.8 1.0
O A:HOH2004 2.5 26.3 1.0
PA A:TPP1236 2.7 13.0 1.0
PB A:TPP1236 2.9 13.2 1.0
O3A A:TPP1236 3.0 13.8 1.0
CG A:ASP963 3.3 2.7 1.0
O2B A:TPP1236 3.4 13.4 1.0
C A:VAL993 3.6 12.4 1.0
N A:SER995 3.7 11.3 1.0
O1A A:TPP1236 3.7 13.7 1.0
OD2 A:ASP963 3.8 2.3 1.0
N A:ASP963 3.9 2.6 1.0
CB A:THR991 3.9 8.1 1.0
O7 A:TPP1236 4.0 14.3 1.0
O3B A:TPP1236 4.0 13.5 1.0
CA A:TYR994 4.1 11.3 1.0
N A:GLY964 4.1 2.8 1.0
OG A:SER995 4.2 12.9 1.0
N A:TYR994 4.3 12.1 1.0
CB A:SER995 4.4 12.4 1.0
C A:TYR994 4.4 11.6 1.0
CG2 A:THR991 4.5 7.8 1.0
CB A:ASP963 4.5 2.0 1.0
N A:VAL993 4.5 12.4 1.0
N A:THR991 4.5 7.9 1.0
CA A:GLY962 4.6 2.0 1.0
CA A:ASP963 4.6 2.3 1.0
C A:GLY962 4.6 2.3 1.0
CA A:SER995 4.7 11.5 1.0
CA A:THR991 4.7 8.7 1.0
CA A:VAL993 4.7 12.4 1.0
O A:MET989 4.8 3.7 1.0
C A:ASP963 4.9 2.5 1.0
C7 A:TPP1236 4.9 15.0 1.0
CA A:GLY964 5.0 2.9 1.0

Magnesium binding site 2 out of 2 in 2pda

Go back to Magnesium Binding Sites List in 2pda
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1244

b:12.5
occ:1.00
 O2A B:TPP1243 1.7 13.9 1.0
O1B B:TPP1243 1.8 13.9 1.0
O B:VAL993 2.4 12.9 1.0
OD1 B:ASP963 2.4 2.0 1.0
OG1 B:THR991 2.5 7.8 1.0
O B:HOH2104 2.5 26.3 1.0
PA B:TPP1243 2.7 13.0 1.0
PB B:TPP1243 2.9 13.2 1.0
O3A B:TPP1243 3.0 13.8 1.0
CG B:ASP963 3.3 2.7 1.0
O2B B:TPP1243 3.4 13.4 1.0
C B:VAL993 3.6 12.4 1.0
N B:SER995 3.7 11.3 1.0
O1A B:TPP1243 3.7 13.7 1.0
OD2 B:ASP963 3.8 2.3 1.0
N B:ASP963 3.9 2.6 1.0
CB B:THR991 3.9 8.1 1.0
O7 B:TPP1243 4.0 14.3 1.0
O3B B:TPP1243 4.0 13.5 1.0
CA B:TYR994 4.1 11.3 1.0
N B:GLY964 4.1 2.8 1.0
OG B:SER995 4.2 12.9 1.0
N B:TYR994 4.3 12.1 1.0
CB B:SER995 4.4 12.4 1.0
C B:TYR994 4.4 11.6 1.0
CG2 B:THR991 4.5 7.8 1.0
CB B:ASP963 4.5 2.0 1.0
N B:VAL993 4.5 12.4 1.0
N B:THR991 4.5 7.9 1.0
CA B:GLY962 4.6 2.0 1.0
CA B:ASP963 4.6 2.3 1.0
C B:GLY962 4.6 2.3 1.0
CA B:SER995 4.7 11.5 1.0
CA B:THR991 4.7 8.7 1.0
CA B:VAL993 4.7 12.4 1.0
O B:MET989 4.8 3.7 1.0
C B:ASP963 4.9 2.5 1.0
C7 B:TPP1243 4.9 15.0 1.0
CA B:GLY964 5.0 2.9 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: Wed Aug 14 02:06:41 2024

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