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Calcium in PDB 1kek: Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase

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

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

Protein crystallography data

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase, PDB code: 1kek was solved by E.Chabriere, X.Vernede, B.Guigliarelli, M.-H.Charon, 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) 27.38 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.110, 145.760, 210.260, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.7

Other elements in 1kek:

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase 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 (pdb code 1kek). 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, PDB code: 1kek:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1kek

Go back to Calcium Binding Sites List in 1kek
Calcium binding site 1 out of 2 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2238

b:35.6
occ:1.00
O A:PHE1059 2.6 19.5 1.0
OD1 A:ASN985 2.7 15.3 1.0
OD2 A:ASP983 2.8 18.5 1.0
O A:ALA1056 2.9 17.6 1.0
O A:GLY1061 3.0 17.4 1.0
OG A:SER1063 3.3 25.1 1.0
O A:GLU1057 3.3 16.6 1.0
CG A:ASN985 3.7 16.2 1.0
C A:PHE1059 3.8 21.0 1.0
C A:GLU1057 3.9 18.8 1.0
O A:HOH2284 3.9 21.9 1.0
CG A:ASP983 3.9 19.6 1.0
O A:VAL984 3.9 17.4 1.0
C A:ALA1056 4.0 16.9 1.0
N A:PHE1059 4.1 16.7 1.0
CA A:GLU1057 4.1 19.3 1.0
ND2 A:ASN985 4.1 13.9 1.0
CB A:SER1063 4.1 18.2 1.0
CB A:PHE1059 4.2 18.9 1.0
CA A:PHE1059 4.2 18.7 1.0
C A:GLY1061 4.2 18.9 1.0
C A:VAL984 4.4 16.1 1.0
N A:GLY1061 4.5 26.3 1.0
O A:HOH2642 4.5 27.4 1.0
N A:VAL984 4.5 17.2 1.0
N A:GLU1057 4.6 20.1 1.0
N A:SER1063 4.6 16.2 1.0
CA A:ASP983 4.6 17.4 1.0
OD1 A:ASP983 4.7 21.6 1.0
C A:ASP983 4.7 17.7 1.0
CD2 A:PHE1059 4.8 18.4 1.0
CB A:ASP983 4.8 19.6 1.0
N A:SER1058 4.8 18.0 1.0
C A:SER1058 4.8 18.9 1.0
N A:PRO1060 4.8 22.5 1.0
C A:PRO1062 4.8 15.1 1.0
CB A:ASN985 4.9 15.0 1.0
N A:ASN985 5.0 14.8 1.0
CG A:PHE1059 5.0 21.4 1.0

Calcium binding site 2 out of 2 in 1kek

Go back to Calcium Binding Sites List in 1kek
Calcium binding site 2 out of 2 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3238

b:32.1
occ:1.00
O B:PHE1059 2.7 18.5 1.0
OD1 B:ASN985 2.7 16.4 1.0
OD2 B:ASP983 2.8 26.7 1.0
O B:ALA1056 2.9 17.9 1.0
O B:GLY1061 3.0 16.2 1.0
OG B:SER1063 3.4 22.9 1.0
O B:GLU1057 3.5 15.5 1.0
CG B:ASN985 3.6 16.0 1.0
C B:PHE1059 3.8 18.3 1.0
O B:VAL984 3.8 16.0 1.0
CG B:ASP983 3.9 23.4 1.0
CB B:SER1063 4.0 13.5 1.0
C B:GLU1057 4.0 16.5 1.0
C B:ALA1056 4.0 15.5 1.0
ND2 B:ASN985 4.1 15.7 1.0
O B:HOH3365 4.1 21.9 1.0
CA B:GLU1057 4.2 15.5 1.0
C B:GLY1061 4.2 17.4 1.0
N B:PHE1059 4.2 16.2 1.0
CB B:PHE1059 4.3 15.7 1.0
C B:VAL984 4.3 16.7 1.0
CA B:PHE1059 4.3 15.9 1.0
N B:GLY1061 4.4 22.2 1.0
N B:VAL984 4.5 18.1 1.0
N B:SER1063 4.5 13.7 1.0
O B:HOH3464 4.5 21.0 1.0
N B:GLU1057 4.6 15.0 1.0
CA B:ASP983 4.7 19.1 1.0
OD1 B:ASP983 4.7 23.3 1.0
CD2 B:PHE1059 4.7 15.1 1.0
C B:ASP983 4.7 15.7 1.0
CB B:ASP983 4.8 20.8 1.0
C B:PRO1062 4.8 14.7 1.0
CB B:ASN985 4.8 14.3 1.0
N B:PRO1060 4.8 19.3 1.0
N B:ASN985 4.9 14.4 1.0
CA B:SER1063 4.9 13.4 1.0
C B:SER1058 4.9 17.4 1.0
N B:SER1058 4.9 16.7 1.0
CA B:PRO1062 4.9 15.9 1.0
CA B:ASN985 4.9 13.5 1.0

Reference:

E.Chabriere, X.Vernede, B.Guigliarelli, M.H.Charon, E.C.Hatchikian, J.C.Fontecilla-Camps. Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase. Science V. 294 2559 2001.
ISSN: ISSN 0036-8075
PubMed: 11752578
DOI: 10.1126/SCIENCE.1066198
Page generated: Sat Dec 12 03:03:43 2020

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