Iron in PDB 2c3p: 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;

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

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
Calcium	(Ca)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3p:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 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 Iron with other atoms in the Fe 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:Fe2233 b:30.7 occ:1.00 FE1 A:SF42233 0.0 30.7 1.0 S2 A:SF42233 2.3 31.7 1.0 S3 A:SF42233 2.3 30.5 1.0 SG A:CYS689 2.3 30.8 1.0 S4 A:SF42233 2.3 27.9 1.0 FE4 A:SF42233 2.7 32.7 1.0 FE2 A:SF42233 2.7 31.5 1.0 FE3 A:SF42233 2.7 33.3 1.0 CB A:CYS689 3.4 29.8 1.0 CA A:CYS689 3.8 35.0 1.0 S1 A:SF42233 3.9 32.4 1.0 NE1 A:TRP684 3.9 29.8 1.0 N A:GLN691 4.0 31.5 1.0 N A:ILE690 4.1 32.0 1.0 CB A:ALA761 4.2 22.4 1.0 C A:CYS689 4.3 33.2 1.0 CA A:GLN691 4.4 34.2 1.0 N A:CYS692 4.5 31.1 1.0 CG1 A:ILE738 4.5 24.5 1.0 CD1 A:TRP684 4.7 30.6 1.0 SG A:CYS755 4.7 33.0 1.0 SG A:CYS695 4.8 35.9 1.0 SG A:CYS692 4.9 30.9 1.0 CE2 A:TRP684 4.9 29.9 1.0 C A:ILE690 5.0 29.9 1.0

Iron binding site 2 out of 24 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 Iron with other atoms in the Fe 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 A:Fe2233 b:31.5 occ:1.00 FE2 A:SF42233 0.0 31.5 1.0 S4 A:SF42233 2.3 27.9 1.0 S1 A:SF42233 2.3 32.4 1.0 SG A:CYS695 2.3 35.9 1.0 S3 A:SF42233 2.3 30.5 1.0 FE4 A:SF42233 2.7 32.7 1.0 FE3 A:SF42233 2.7 33.3 1.0 FE1 A:SF42233 2.7 30.7 1.0 CB A:CYS695 3.3 30.1 1.0 S2 A:SF42233 3.9 31.7 1.0 N A:CYS695 4.0 29.8 1.0 CD1 A:LEU762 4.2 18.3 1.0 CG1 A:ILE738 4.3 24.5 1.0 CA A:CYS695 4.3 30.6 1.0 CD1 A:ILE738 4.6 21.1 1.0 N A:ASN693 4.6 27.6 1.0 SG A:CYS692 4.7 30.9 1.0 N A:GLN694 4.7 31.9 1.0 SG A:CYS689 4.7 30.8 1.0 SG A:CYS755 4.8 33.0 1.0 CG A:LEU762 4.8 23.1 1.0 CA A:ASN693 4.9 30.2 1.0 CG2 A:ILE738 4.9 26.1 1.0

Iron binding site 3 out of 24 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 Iron with other atoms in the Fe binding site number 3 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:Fe2233 b:33.3 occ:1.00 FE3 A:SF42233 0.0 33.3 1.0 S1 A:SF42233 2.3 32.4 1.0 S4 A:SF42233 2.3 27.9 1.0 SG A:CYS692 2.3 30.9 1.0 S2 A:SF42233 2.3 31.7 1.0 FE2 A:SF42233 2.7 31.5 1.0 FE1 A:SF42233 2.7 30.7 1.0 FE4 A:SF42233 2.7 32.7 1.0 N A:CYS692 3.5 31.1 1.0 CB A:CYS692 3.6 28.7 1.0 N A:ASN693 3.9 27.6 1.0 S3 A:SF42233 3.9 30.5 1.0 CA A:CYS692 3.9 30.8 1.0 CD A:PRO756 4.0 30.6 1.0 N A:GLN694 4.3 31.9 1.0 C A:CYS692 4.3 28.8 1.0 CG1 A:ILE690 4.6 29.6 1.0 C A:GLN691 4.7 33.3 1.0 N A:GLN691 4.7 31.5 1.0 SG A:CYS695 4.7 35.9 1.0 SG A:CYS689 4.7 30.8 1.0 CG A:PRO756 4.7 26.5 1.0 SG A:CYS755 4.7 33.0 1.0 N A:CYS695 4.9 29.8 1.0 CB A:GLN694 4.9 30.6 1.0 CA A:ASN693 4.9 30.2 1.0 CA A:GLN691 4.9 34.2 1.0 N A:ILE690 5.0 32.0 1.0

Iron binding site 4 out of 24 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 Iron with other atoms in the Fe binding site number 4 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:Fe2233 b:32.7 occ:1.00 FE4 A:SF42233 0.0 32.7 1.0 S3 A:SF42233 2.3 30.5 1.0 SG A:CYS755 2.3 33.0 1.0 S1 A:SF42233 2.3 32.4 1.0 S2 A:SF42233 2.3 31.7 1.0 FE1 A:SF42233 2.7 30.7 1.0 FE2 A:SF42233 2.7 31.5 1.0 FE3 A:SF42233 2.7 33.3 1.0 CB A:CYS755 3.5 30.0 1.0 CB A:ALA761 3.7 22.4 1.0 S4 A:SF42233 3.9 27.9 1.0 CA A:CYS755 3.9 27.8 1.0 CD1 A:LEU762 4.2 18.3 1.0 CD A:PRO756 4.3 30.6 1.0 CG A:LEU762 4.4 23.1 1.0 CD A:PRO757 4.6 38.0 1.0 C A:CYS755 4.7 30.5 1.0 SG A:CYS695 4.7 35.9 1.0 CA A:ALA761 4.7 27.9 1.0 SG A:CYS692 4.7 30.9 1.0 N A:PRO756 4.8 30.8 1.0 SG A:CYS689 4.8 30.8 1.0 N A:ALA761 4.8 30.8 1.0 CG A:PRO757 4.8 41.1 1.0 C A:ALA761 4.9 27.7 1.0 CB A:CYS695 5.0 30.1 1.0

Iron binding site 5 out of 24 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 Iron with other atoms in the Fe binding site number 5 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:Fe2234 b:25.2 occ:1.00 FE1 A:SF42234 0.0 25.2 1.0 S3 A:SF42234 2.3 25.8 1.0 S2 A:SF42234 2.3 24.4 1.0 SG A:CYS699 2.3 25.0 1.0 S4 A:SF42234 2.3 25.5 1.0 FE2 A:SF42234 2.7 25.4 1.0 FE4 A:SF42234 2.7 22.5 1.0 FE3 A:SF42234 2.7 25.0 1.0 CB A:CYS699 3.3 24.5 1.0 S1 A:SF42234 3.9 27.6 1.0 CA A:CYS699 3.9 22.9 1.0 CD A:PRO700 3.9 25.5 1.0 CB A:ALA703 4.1 28.4 1.0 N A:PRO700 4.5 26.0 1.0 C A:CYS699 4.6 25.9 1.0 SG A:CYS748 4.7 24.5 1.0 SG A:CYS751 4.8 29.1 1.0 N A:ALA703 4.8 28.2 1.0 SG A:CYS745 4.8 24.2 1.0 CG1 A:ILE704 4.8 21.8 1.0 O A:HOH2218 4.9 20.0 1.0 CA A:ALA703 4.9 27.6 1.0 CD1 A:ILE704 4.9 22.7 1.0 N A:HIS701 4.9 20.7 1.0

Iron binding site 6 out of 24 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 Iron with other atoms in the Fe binding site number 6 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:Fe2234 b:25.4 occ:1.00 FE2 A:SF42234 0.0 25.4 1.0 S4 A:SF42234 2.3 25.5 1.0 S3 A:SF42234 2.3 25.8 1.0 S1 A:SF42234 2.3 27.6 1.0 SG A:CYS751 2.3 29.1 1.0 FE3 A:SF42234 2.6 25.0 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE4 A:SF42234 2.7 22.5 1.0 CB A:CYS751 3.4 27.3 1.0 S2 A:SF42234 3.9 24.4 1.0 N A:CYS751 4.0 23.6 1.0 CG A:PRO682 4.0 26.4 1.0 CD A:PRO682 4.2 23.8 1.0 CD1 A:ILE704 4.3 22.7 1.0 CA A:CYS751 4.3 23.8 1.0 N A:GLY749 4.6 25.8 1.0 N A:ASN750 4.7 20.1 1.0 SG A:CYS745 4.7 24.2 1.0 SG A:CYS748 4.7 24.5 1.0 CB A:PRO682 4.7 26.1 1.0 SG A:CYS699 4.8 25.0 1.0 CG1 A:ILE704 4.8 21.8 1.0 CA A:GLY749 4.8 23.5 1.0 C A:GLY749 4.9 26.5 1.0 N A:ALA752 5.0 23.7 1.0

Iron binding site 7 out of 24 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 Iron with other atoms in the Fe binding site number 7 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:Fe2234 b:25.0 occ:1.00 FE3 A:SF42234 0.0 25.0 1.0 SG A:CYS745 2.3 24.2 1.0 S1 A:SF42234 2.3 27.6 1.0 S2 A:SF42234 2.3 24.4 1.0 S4 A:SF42234 2.3 25.5 1.0 FE2 A:SF42234 2.6 25.4 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE4 A:SF42234 2.7 22.5 1.0 CB A:CYS745 3.4 26.4 1.0 N A:GLY747 3.8 25.4 1.0 S3 A:SF42234 3.9 25.8 1.0 CD A:PRO682 3.9 23.8 1.0 CA A:CYS745 4.0 25.9 1.0 N A:MET746 4.0 26.4 1.0 CA A:GLY747 4.2 26.4 1.0 CG A:PRO682 4.4 26.4 1.0 C A:CYS745 4.4 25.4 1.0 N A:CYS748 4.4 25.1 1.0 CB A:ALA703 4.5 28.4 1.0 SG A:CYS699 4.8 25.0 1.0 SG A:CYS751 4.8 29.1 1.0 C A:GLY747 4.8 24.0 1.0 C A:MET746 4.8 27.1 1.0 SG A:CYS748 4.9 24.5 1.0

Iron binding site 8 out of 24 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 Iron with other atoms in the Fe binding site number 8 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:Fe2234 b:22.5 occ:1.00 FE4 A:SF42234 0.0 22.5 1.0 S3 A:SF42234 2.3 25.8 1.0 S1 A:SF42234 2.3 27.6 1.0 S2 A:SF42234 2.3 24.4 1.0 SG A:CYS748 2.3 24.5 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE2 A:SF42234 2.7 25.4 1.0 FE3 A:SF42234 2.7 25.0 1.0 N A:CYS748 3.5 25.1 1.0 CB A:CYS748 3.6 24.6 1.0 N A:GLY749 3.6 25.8 1.0 S4 A:SF42234 3.9 25.5 1.0 CA A:CYS748 3.9 22.1 1.0 O A:HOH2218 4.0 20.0 1.0 CD A:PRO700 4.1 25.5 1.0 N A:ASN750 4.2 20.1 1.0 C A:CYS748 4.2 25.9 1.0 CA A:GLY749 4.5 23.5 1.0 C A:GLY747 4.5 24.0 1.0 N A:GLY747 4.6 25.4 1.0 SG A:CYS745 4.7 24.2 1.0 SG A:CYS699 4.7 25.0 1.0 SG A:CYS751 4.7 29.1 1.0 C A:GLY749 4.8 26.5 1.0 CA A:GLY747 4.8 26.4 1.0 CB A:ASN750 4.9 24.4 1.0 CG A:PRO700 4.9 27.6 1.0 N A:CYS751 4.9 23.6 1.0

Iron binding site 9 out of 24 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 Iron with other atoms in the Fe binding site number 9 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:Fe2235 b:18.2 occ:1.00 FE1 A:SF42235 0.0 18.2 1.0 SG A:CYS812 2.3 18.1 1.0 S3 A:SF42235 2.3 15.4 1.0 S2 A:SF42235 2.3 19.0 1.0 S4 A:SF42235 2.3 16.1 1.0 FE2 A:SF42235 2.6 15.7 1.0 FE3 A:SF42235 2.7 18.7 1.0 FE4 A:SF42235 2.7 18.4 1.0 CB A:CYS812 3.3 14.3 1.0 N A:CYS812 3.9 18.6 1.0 S1 A:SF42235 3.9 20.5 1.0 CD A:LYS459 4.1 23.7 1.0 CA A:CYS812 4.2 18.4 1.0 CG1 A:ILE1072 4.2 19.0 1.0 CD1 A:ILE1072 4.3 14.3 1.0 SG A:CYS815 4.7 16.8 1.0 CE A:LYS459 4.7 24.8 1.0 SG A:CYS840 4.7 21.2 1.0 CG2 A:ILE1072 4.7 12.0 1.0 SG A:CYS1071 4.7 19.4 1.0 NZ A:LYS459 4.8 27.3 1.0 CB A:CYS815 4.9 18.4 1.0

Iron binding site 10 out of 24 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 Iron with other atoms in the Fe binding site number 10 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:Fe2235 b:15.7 occ:1.00 FE2 A:SF42235 0.0 15.7 1.0 S3 A:SF42235 2.3 15.4 1.0 S4 A:SF42235 2.3 16.1 1.0 S1 A:SF42235 2.3 20.5 1.0 SG A:CYS840 2.3 21.2 1.0 FE4 A:SF42235 2.5 18.4 1.0 FE1 A:SF42235 2.6 18.2 1.0 FE3 A:SF42235 2.7 18.7 1.0 CB A:CYS840 3.3 15.5 1.0 S2 A:SF42235 3.8 19.0 1.0 CB A:SER995 4.1 13.1 1.0 NZ A:LYS459 4.2 27.3 1.0 CE A:LYS459 4.2 24.8 1.0 SG A:CYS1071 4.5 19.4 1.0 CD A:LYS459 4.6 23.7 1.0 CA A:CYS840 4.6 18.0 1.0 SG A:CYS812 4.7 18.1 1.0 SG A:CYS815 4.8 16.8 1.0 OG A:SER995 4.8 14.8 1.0 OE1 A:GLU817 4.8 13.9 1.0 CD A:GLU817 5.0 16.7 1.0

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