Iron in PDB 1kek: 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;

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

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase 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 (pdb code 1kek). 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, PDB code: 1kek:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2233 b:30.4 occ:1.00 FE1 A:SF42233 0.0 30.4 1.0 S3 A:SF42233 2.2 29.4 1.0 S2 A:SF42233 2.3 30.4 1.0 S4 A:SF42233 2.3 30.1 1.0 SG A:CYS689 2.3 32.9 1.0 FE4 A:SF42233 2.7 32.1 1.0 FE2 A:SF42233 2.7 30.8 1.0 FE3 A:SF42233 2.8 29.9 1.0 CB A:CYS689 3.4 36.9 1.0 CA A:CYS689 3.7 37.4 1.0 N A:GLN691 3.9 33.1 1.0 N A:ILE690 3.9 35.6 1.0 S1 A:SF42233 3.9 30.8 1.0 NE1 A:TRP684 4.0 29.8 1.0 CB A:ALA761 4.2 33.0 1.0 C A:CYS689 4.2 37.1 1.0 CG1 A:ILE738 4.4 29.8 1.0 CA A:GLN691 4.4 33.6 1.0 N A:CYS692 4.6 31.5 1.0 SG A:CYS755 4.7 33.5 1.0 CD1 A:TRP684 4.8 30.7 1.0 C A:ILE690 4.8 34.8 1.0 SG A:CYS692 4.9 29.4 1.0 CA A:ILE690 4.9 35.5 1.0 N A:CYS689 5.0 37.8 1.0 SG A:CYS695 5.0 29.2 1.0

Iron binding site 2 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2233 b:30.8 occ:1.00 FE2 A:SF42233 0.0 30.8 1.0 SG A:CYS692 2.3 29.4 1.0 S3 A:SF42233 2.3 29.4 1.0 S1 A:SF42233 2.3 30.8 1.0 S4 A:SF42233 2.3 30.1 1.0 FE1 A:SF42233 2.7 30.4 1.0 FE3 A:SF42233 2.8 29.9 1.0 FE4 A:SF42233 2.8 32.1 1.0 N A:CYS692 3.5 31.5 1.0 CB A:CYS692 3.6 28.2 1.0 N A:ASN693 3.9 29.1 1.0 S2 A:SF42233 4.0 30.4 1.0 CA A:CYS692 4.0 31.8 1.0 CD A:PRO756 4.0 33.3 1.0 N A:GLN694 4.3 26.2 1.0 CG1 A:ILE690 4.3 35.8 1.0 C A:CYS692 4.3 30.1 1.0 N A:GLN691 4.4 33.1 1.0 C A:GLN691 4.5 32.9 1.0 SG A:CYS689 4.7 32.9 1.0 CG A:PRO756 4.7 34.4 1.0 SG A:CYS755 4.8 33.5 1.0 CA A:GLN691 4.8 33.6 1.0 SG A:CYS695 4.8 29.2 1.0 CA A:ASN693 4.8 28.7 1.0 CB A:GLN694 4.8 27.6 1.0 N A:CYS695 4.8 28.0 1.0 N A:ILE690 4.9 35.6 1.0 C A:ASN693 5.0 28.9 1.0

Iron binding site 3 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2233 b:29.9 occ:1.00 FE3 A:SF42233 0.0 29.9 1.0 S1 A:SF42233 2.3 30.8 1.0 S4 A:SF42233 2.3 30.1 1.0 SG A:CYS695 2.3 29.2 1.0 S2 A:SF42233 2.4 30.4 1.0 FE4 A:SF42233 2.7 32.1 1.0 FE2 A:SF42233 2.8 30.8 1.0 FE1 A:SF42233 2.8 30.4 1.0 CB A:CYS695 3.3 27.5 1.0 S3 A:SF42233 3.9 29.4 1.0 N A:CYS695 3.9 28.0 1.0 CG1 A:ILE738 4.1 29.8 1.0 CA A:CYS695 4.3 28.4 1.0 CD1 A:LEU762 4.4 27.9 1.0 CD1 A:ILE738 4.4 30.9 1.0 SG A:CYS692 4.6 29.4 1.0 N A:GLN694 4.6 26.2 1.0 N A:ASN693 4.7 29.1 1.0 SG A:CYS689 4.7 32.9 1.0 CG2 A:ILE738 4.8 31.3 1.0 SG A:CYS755 4.8 33.5 1.0 CA A:ASN693 4.8 28.7 1.0 CG A:LEU762 4.9 29.1 1.0 C A:ASN693 5.0 28.9 1.0

Iron binding site 4 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2233 b:32.1 occ:1.00 FE4 A:SF42233 0.0 32.1 1.0 SG A:CYS755 2.3 33.5 1.0 S2 A:SF42233 2.3 30.4 1.0 S3 A:SF42233 2.3 29.4 1.0 S1 A:SF42233 2.3 30.8 1.0 FE1 A:SF42233 2.7 30.4 1.0 FE3 A:SF42233 2.7 29.9 1.0 FE2 A:SF42233 2.8 30.8 1.0 CB A:CYS755 3.6 32.9 1.0 CA A:CYS755 3.8 31.3 1.0 S4 A:SF42233 3.9 30.1 1.0 CB A:ALA761 4.0 33.0 1.0 CD A:PRO756 4.1 33.3 1.0 CD1 A:LEU762 4.4 27.9 1.0 C A:CYS755 4.5 32.5 1.0 CD A:PRO757 4.5 38.7 1.0 CG A:LEU762 4.6 29.1 1.0 N A:PRO756 4.6 32.2 1.0 SG A:CYS692 4.7 29.4 1.0 CA A:ALA761 4.7 33.1 1.0 SG A:CYS695 4.8 29.2 1.0 N A:ALA761 4.8 33.6 1.0 CG A:PRO757 4.8 41.5 1.0 SG A:CYS689 4.9 32.9 1.0 CB A:CYS695 4.9 27.5 1.0 C A:ALA761 4.9 33.2 1.0

Iron binding site 5 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 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 S2 A:SF42234 2.3 25.1 1.0 S3 A:SF42234 2.3 25.0 1.0 SG A:CYS699 2.3 23.1 1.0 S4 A:SF42234 2.3 25.3 1.0 FE3 A:SF42234 2.7 26.0 1.0 FE4 A:SF42234 2.7 25.1 1.0 FE2 A:SF42234 2.7 26.3 1.0 CB A:CYS699 3.3 20.4 1.0 S1 A:SF42234 3.9 24.0 1.0 CA A:CYS699 3.9 23.2 1.0 CD A:PRO700 4.1 24.1 1.0 CB A:ALA703 4.2 25.1 1.0 N A:PRO700 4.6 22.8 1.0 C A:CYS699 4.6 21.1 1.0 SG A:CYS748 4.7 27.3 1.0 N A:ALA703 4.8 25.8 1.0 SG A:CYS751 4.8 30.4 1.0 CG1 A:ILE704 4.8 23.3 1.0 SG A:CYS745 4.9 24.2 1.0 CA A:ALA703 4.9 27.6 1.0 N A:HIS701 4.9 22.0 1.0 CD1 A:ILE704 4.9 24.6 1.0 O A:HOH2332 5.0 24.3 1.0

Iron binding site 6 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2234 b:26.3 occ:1.00 FE2 A:SF42234 0.0 26.3 1.0 SG A:CYS745 2.3 24.2 1.0 S1 A:SF42234 2.3 24.0 1.0 S4 A:SF42234 2.3 25.3 1.0 S3 A:SF42234 2.3 25.0 1.0 FE3 A:SF42234 2.7 26.0 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE4 A:SF42234 2.8 25.1 1.0 CB A:CYS745 3.3 23.3 1.0 CA A:CYS745 3.8 23.7 1.0 N A:MET746 3.8 23.6 1.0 N A:GLY747 3.9 27.3 1.0 S2 A:SF42234 3.9 25.1 1.0 CD A:PRO682 4.0 29.9 1.0 C A:CYS745 4.2 23.9 1.0 CB A:ALA703 4.5 25.1 1.0 CG A:PRO682 4.5 29.2 1.0 CA A:GLY747 4.5 23.5 1.0 N A:CYS748 4.7 24.4 1.0 SG A:CYS699 4.7 23.1 1.0 C A:MET746 4.9 24.1 1.0 SG A:CYS751 4.9 30.4 1.0 CA A:MET746 4.9 24.2 1.0

Iron binding site 7 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2234 b:26.0 occ:1.00 FE3 A:SF42234 0.0 26.0 1.0 S1 A:SF42234 2.3 24.0 1.0 S4 A:SF42234 2.3 25.3 1.0 S2 A:SF42234 2.3 25.1 1.0 SG A:CYS751 2.3 30.4 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE2 A:SF42234 2.7 26.3 1.0 FE4 A:SF42234 2.8 25.1 1.0 CB A:CYS751 3.4 26.8 1.0 S3 A:SF42234 3.9 25.0 1.0 CG A:PRO682 4.1 29.2 1.0 N A:CYS751 4.1 26.8 1.0 CD A:PRO682 4.2 29.9 1.0 CA A:CYS751 4.4 28.1 1.0 CD1 A:ILE704 4.4 24.6 1.0 N A:GLY749 4.7 28.2 1.0 SG A:CYS748 4.7 27.3 1.0 SG A:CYS745 4.7 24.2 1.0 N A:ASN750 4.7 25.8 1.0 CB A:PRO682 4.8 29.9 1.0 SG A:CYS699 4.8 23.1 1.0 CG1 A:ILE704 4.8 23.3 1.0 CA A:GLY749 4.9 27.5 1.0 C A:GLY749 5.0 27.8 1.0

Iron binding site 8 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2234 b:25.1 occ:1.00 FE4 A:SF42234 0.0 25.1 1.0 S3 A:SF42234 2.3 25.0 1.0 S2 A:SF42234 2.3 25.1 1.0 SG A:CYS748 2.3 27.3 1.0 S1 A:SF42234 2.4 24.0 1.0 FE1 A:SF42234 2.7 25.2 1.0 FE2 A:SF42234 2.8 26.3 1.0 FE3 A:SF42234 2.8 26.0 1.0 N A:CYS748 3.5 24.4 1.0 CB A:CYS748 3.6 23.8 1.0 N A:GLY749 3.6 28.2 1.0 CA A:CYS748 3.9 26.3 1.0 S4 A:SF42234 4.0 25.3 1.0 O A:HOH2332 4.0 24.3 1.0 CD A:PRO700 4.2 24.1 1.0 C A:CYS748 4.3 27.2 1.0 N A:ASN750 4.3 25.8 1.0 N A:GLY747 4.5 27.3 1.0 C A:GLY747 4.5 26.4 1.0 CA A:GLY749 4.6 27.5 1.0 SG A:CYS745 4.7 24.2 1.0 SG A:CYS699 4.7 23.1 1.0 C A:GLY749 4.8 27.8 1.0 SG A:CYS751 4.8 30.4 1.0 CA A:GLY747 4.9 23.5 1.0 N A:MET746 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2235 b:21.5 occ:1.00 FE1 A:SF42235 0.0 21.5 1.0 S2 A:SF42235 2.3 20.0 1.0 SG A:CYS812 2.3 20.1 1.0 S3 A:SF42235 2.3 21.4 1.0 S4 A:SF42235 2.3 22.2 1.0 FE2 A:SF42235 2.7 20.3 1.0 FE3 A:SF42235 2.7 19.9 1.0 FE4 A:SF42235 2.7 20.5 1.0 CB A:CYS812 3.1 20.4 1.0 N A:CYS812 3.9 18.5 1.0 S1 A:SF42235 3.9 20.1 1.0 CA A:CYS812 4.2 22.4 1.0 CG1 A:ILE1072 4.3 22.7 1.0 NZ A:LYS459 4.4 24.0 1.0 CD1 A:ILE1072 4.4 25.6 1.0 CD A:LYS459 4.5 24.2 1.0 CG2 A:ILE1072 4.7 23.6 1.0 SG A:CYS815 4.7 19.9 1.0 CB A:CYS815 4.7 19.9 1.0 SG A:CYS1071 4.7 19.6 1.0 SG A:CYS840 4.8 17.6 1.0 N A:ILE1072 4.9 20.0 1.0 CE A:LYS459 4.9 24.9 1.0

Iron binding site 10 out of 24 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2235 b:20.3 occ:1.00 FE2 A:SF42235 0.0 20.3 1.0 S1 A:SF42235 2.3 20.1 1.0 S4 A:SF42235 2.3 22.2 1.0 S3 A:SF42235 2.3 21.4 1.0 SG A:CYS815 2.4 19.9 1.0 FE1 A:SF42235 2.7 21.5 1.0 FE3 A:SF42235 2.7 19.9 1.0 FE4 A:SF42235 2.8 20.5 1.0 CB A:CYS815 3.2 19.9 1.0 CA A:CYS815 3.9 20.7 1.0 S2 A:SF42235 4.0 20.0 1.0 N A:GLY816 4.5 22.7 1.0 CG A:GLU817 4.5 19.9 1.0 C A:CYS815 4.6 20.4 1.0 CB A:CYS812 4.6 20.4 1.0 CD A:GLU817 4.7 20.7 1.0 OE1 A:GLU817 4.7 17.5 1.0 SG A:CYS812 4.7 20.1 1.0 N A:CYS812 4.7 18.5 1.0 CB A:ALA811 4.9 19.7 1.0 SG A:CYS840 4.9 17.6 1.0 CB A:CYS840 4.9 17.4 1.0 O A:THR1070 4.9 23.1 1.0 SG A:CYS1071 4.9 19.6 1.0 CB A:GLU817 4.9 20.5 1.0 N A:GLU817 5.0 21.0 1.0 CD1 A:TRP844 5.0 19.3 1.0

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