Iron in PDB 2pda: 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;

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

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
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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. (pdb code 2pda). 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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate., PDB code: 2pda:
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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate.


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 Complex Between Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio Africanus and Pyruvate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1233 b:22.8 occ:1.00 FE1 A:SF41233 0.0 22.8 1.0 SG A:CYS689 2.3 23.0 1.0 S3 A:SF41233 2.3 23.9 1.0 S2 A:SF41233 2.3 24.0 1.0 S4 A:SF41233 2.3 23.4 1.0 FE4 A:SF41233 2.7 23.1 1.0 FE2 A:SF41233 2.7 23.4 1.0 FE3 A:SF41233 2.7 22.7 1.0 CB A:CYS689 3.3 22.0 1.0 CA A:CYS689 3.6 21.0 1.0 CB A:ALA761 3.8 21.0 1.0 S1 A:SF41233 3.9 23.2 1.0 NE1 A:TRP684 4.0 15.4 1.0 N A:ILE690 4.1 19.4 1.0 N A:GLN691 4.2 20.1 1.0 CG1 A:ILE738 4.2 20.7 1.0 C A:CYS689 4.2 20.1 1.0 N A:CYS692 4.6 21.6 1.0 CA A:GLN691 4.6 21.1 1.0 CD1 A:ILE738 4.7 21.0 1.0 SG A:CYS755 4.7 22.9 1.0 CE2 A:TRP684 4.8 15.6 1.0 SG A:CYS695 4.8 22.7 1.0 N A:CYS689 4.8 21.1 1.0 CZ2 A:TRP684 4.8 15.6 1.0 SG A:CYS692 4.8 22.9 1.0 CD1 A:TRP684 5.0 15.9 1.0

Iron binding site 2 out of 24 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 Iron with other atoms in the Fe 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 A:Fe1233 b:23.4 occ:1.00 FE2 A:SF41233 0.0 23.4 1.0 S4 A:SF41233 2.3 23.4 1.0 S3 A:SF41233 2.3 23.9 1.0 S1 A:SF41233 2.3 23.2 1.0 SG A:CYS692 2.3 22.9 1.0 FE4 A:SF41233 2.7 23.1 1.0 FE1 A:SF41233 2.7 22.8 1.0 FE3 A:SF41233 2.7 22.7 1.0 CB A:CYS692 3.7 21.8 1.0 N A:CYS692 3.7 21.6 1.0 CD A:PRO756 3.9 21.2 1.0 S2 A:SF41233 3.9 24.0 1.0 CA A:CYS692 4.0 21.5 1.0 N A:ASN693 4.1 20.4 1.0 CG1 A:ILE690 4.3 16.2 1.0 C A:CYS692 4.4 21.1 1.0 CG A:PRO756 4.4 21.8 1.0 SG A:CYS689 4.6 23.0 1.0 N A:GLN694 4.6 19.3 1.0 SG A:CYS755 4.7 22.9 1.0 N A:GLN691 4.7 20.1 1.0 C A:GLN691 4.7 21.4 1.0 SG A:CYS695 4.7 22.7 1.0 N A:ILE690 4.8 19.4 1.0 CA A:GLN691 5.0 21.1 1.0

Iron binding site 3 out of 24 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 Iron with other atoms in the Fe binding site number 3 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:Fe1233 b:22.7 occ:1.00 FE3 A:SF41233 0.0 22.7 1.0 S1 A:SF41233 2.3 23.2 1.0 S2 A:SF41233 2.3 24.0 1.0 SG A:CYS695 2.3 22.7 1.0 S4 A:SF41233 2.3 23.4 1.0 FE4 A:SF41233 2.6 23.1 1.0 FE1 A:SF41233 2.7 22.8 1.0 FE2 A:SF41233 2.7 23.4 1.0 CB A:CYS695 3.3 20.7 1.0 CD1 A:LEU762 3.9 15.8 1.0 S3 A:SF41233 3.9 23.9 1.0 CD1 A:ILE738 3.9 21.0 1.0 N A:CYS695 4.1 18.9 1.0 CG1 A:ILE738 4.2 20.7 1.0 CA A:CYS695 4.3 19.3 1.0 SG A:CYS689 4.7 23.0 1.0 SG A:CYS755 4.7 22.9 1.0 N A:ASN693 4.8 20.4 1.0 SG A:CYS692 4.8 22.9 1.0 N A:GLN694 4.9 19.3 1.0 CG A:LEU762 4.9 16.1 1.0

Iron binding site 4 out of 24 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 Iron with other atoms in the Fe binding site number 4 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:Fe1233 b:23.1 occ:1.00 FE4 A:SF41233 0.0 23.1 1.0 S1 A:SF41233 2.3 23.2 1.0 SG A:CYS755 2.3 22.9 1.0 S3 A:SF41233 2.3 23.9 1.0 S2 A:SF41233 2.3 24.0 1.0 FE3 A:SF41233 2.6 22.7 1.0 FE2 A:SF41233 2.7 23.4 1.0 FE1 A:SF41233 2.7 22.8 1.0 CB A:ALA761 3.2 21.0 1.0 CB A:CYS755 3.4 21.4 1.0 S4 A:SF41233 3.8 23.4 1.0 CA A:CYS755 3.9 20.9 1.0 CD A:PRO756 3.9 21.2 1.0 CD1 A:LEU762 4.3 15.8 1.0 CA A:ALA761 4.4 20.6 1.0 CD A:PRO757 4.4 21.2 1.0 C A:CYS755 4.6 20.9 1.0 N A:PRO756 4.7 21.1 1.0 N A:ALA761 4.7 21.0 1.0 SG A:CYS692 4.7 22.9 1.0 SG A:CYS695 4.7 22.7 1.0 SG A:CYS689 4.8 23.0 1.0 N A:LEU762 4.8 19.4 1.0 CG A:LEU762 4.8 16.1 1.0 C A:ALA761 4.9 20.3 1.0 CG A:PRO757 4.9 21.1 1.0 CA A:CYS689 5.0 21.0 1.0

Iron binding site 5 out of 24 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 Iron with other atoms in the Fe binding site number 5 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:Fe1234 b:15.9 occ:1.00 FE1 A:SF41234 0.0 15.9 1.0 S4 A:SF41234 2.2 16.8 1.0 S2 A:SF41234 2.3 16.0 1.0 SG A:CYS699 2.3 15.5 1.0 S3 A:SF41234 2.3 16.0 1.0 FE3 A:SF41234 2.5 15.2 1.0 FE2 A:SF41234 2.5 15.6 1.0 FE4 A:SF41234 2.6 15.5 1.0 CB A:CYS699 3.3 15.2 1.0 CB A:ALA703 3.5 14.9 1.0 CA A:CYS699 3.8 15.1 1.0 S1 A:SF41234 3.8 16.1 1.0 C A:CYS699 4.4 15.2 1.0 CD A:PRO700 4.5 15.3 1.0 CA A:ALA703 4.6 15.1 1.0 N A:ALA703 4.6 15.2 1.0 SG A:CYS748 4.6 15.9 1.0 N A:PRO700 4.6 15.2 1.0 SG A:CYS751 4.6 16.3 1.0 SG A:CYS745 4.7 14.8 1.0 CD1 A:ILE704 4.8 15.1 1.0 CG1 A:ILE704 4.8 15.8 1.0 N A:CYS699 4.9 15.3 1.0

Iron binding site 6 out of 24 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 Iron with other atoms in the Fe binding site number 6 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:Fe1234 b:15.6 occ:1.00 FE2 A:SF41234 0.0 15.6 1.0 S3 A:SF41234 2.3 16.0 1.0 S4 A:SF41234 2.3 16.8 1.0 S1 A:SF41234 2.3 16.1 1.0 SG A:CYS745 2.3 14.8 1.0 FE1 A:SF41234 2.5 15.9 1.0 FE3 A:SF41234 2.6 15.2 1.0 FE4 A:SF41234 2.7 15.5 1.0 CB A:CYS745 3.5 15.3 1.0 N A:GLY747 3.7 14.4 1.0 S2 A:SF41234 3.9 16.0 1.0 CD A:PRO682 3.9 18.7 1.0 N A:MET746 4.0 15.2 1.0 CA A:CYS745 4.0 15.6 1.0 CB A:ALA703 4.0 14.9 1.0 CA A:GLY747 4.1 14.2 1.0 N A:CYS748 4.2 14.9 1.0 CG A:PRO682 4.3 18.6 1.0 C A:CYS745 4.4 15.4 1.0 SG A:CYS699 4.6 15.5 1.0 C A:GLY747 4.7 14.5 1.0 SG A:CYS751 4.7 16.3 1.0 C A:MET746 4.8 14.7 1.0 SG A:CYS748 4.8 15.9 1.0 CA A:MET746 5.0 15.3 1.0

Iron binding site 7 out of 24 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 Iron with other atoms in the Fe binding site number 7 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:Fe1234 b:15.2 occ:1.00 FE3 A:SF41234 0.0 15.2 1.0 S2 A:SF41234 2.2 16.0 1.0 S4 A:SF41234 2.2 16.8 1.0 SG A:CYS751 2.3 16.3 1.0 S1 A:SF41234 2.3 16.1 1.0 FE1 A:SF41234 2.5 15.9 1.0 FE4 A:SF41234 2.5 15.5 1.0 FE2 A:SF41234 2.6 15.6 1.0 CB A:CYS751 3.4 15.7 1.0 S3 A:SF41234 3.8 16.0 1.0 N A:CYS751 3.8 16.3 1.0 CG A:PRO682 3.8 18.6 1.0 CD1 A:ILE704 4.1 15.1 1.0 CD A:PRO682 4.3 18.7 1.0 CA A:CYS751 4.3 15.8 1.0 SG A:CYS748 4.5 15.9 1.0 N A:ASN750 4.5 16.2 1.0 SG A:CYS699 4.5 15.5 1.0 N A:GLY749 4.6 15.7 1.0 CB A:PRO682 4.7 18.6 1.0 SG A:CYS745 4.7 14.8 1.0 CG1 A:ILE704 4.7 15.8 1.0 C A:GLY749 4.9 15.9 1.0 CB A:CYS699 4.9 15.2 1.0 C A:ASN750 4.9 16.4 1.0 CA A:GLY749 5.0 15.9 1.0

Iron binding site 8 out of 24 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 Iron with other atoms in the Fe binding site number 8 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:Fe1234 b:15.5 occ:1.00 FE4 A:SF41234 0.0 15.5 1.0 S1 A:SF41234 2.2 16.1 1.0 S2 A:SF41234 2.3 16.0 1.0 SG A:CYS748 2.3 15.9 1.0 S3 A:SF41234 2.3 16.0 1.0 FE3 A:SF41234 2.5 15.2 1.0 FE1 A:SF41234 2.6 15.9 1.0 FE2 A:SF41234 2.7 15.6 1.0 CB A:CYS748 3.4 15.9 1.0 N A:CYS748 3.5 14.9 1.0 N A:GLY749 3.7 15.7 1.0 S4 A:SF41234 3.8 16.8 1.0 CA A:CYS748 3.9 15.2 1.0 N A:ASN750 4.1 16.2 1.0 C A:CYS748 4.3 15.6 1.0 CD A:PRO700 4.4 15.3 1.0 CB A:ASN750 4.4 15.9 1.0 SG A:CYS699 4.6 15.5 1.0 SG A:CYS751 4.6 16.3 1.0 C A:GLY747 4.6 14.5 1.0 N A:GLY747 4.6 14.4 1.0 CA A:GLY749 4.7 15.9 1.0 CG A:PRO700 4.7 15.2 1.0 SG A:CYS745 4.8 14.8 1.0 CA A:ASN750 4.8 16.2 1.0 N A:CYS751 4.8 16.3 1.0 C A:GLY749 4.9 15.9 1.0 CA A:GLY747 4.9 14.2 1.0

Iron binding site 9 out of 24 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 Iron with other atoms in the Fe binding site number 9 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:Fe1235 b:13.0 occ:1.00 FE1 A:SF41235 0.0 13.0 1.0 S4 A:SF41235 2.2 11.9 1.0 SG A:CYS812 2.3 13.6 1.0 S3 A:SF41235 2.3 13.2 1.0 S2 A:SF41235 2.3 13.1 1.0 FE2 A:SF41235 2.5 12.9 1.0 FE3 A:SF41235 2.6 13.8 1.0 FE4 A:SF41235 2.6 12.0 1.0 CB A:CYS812 3.2 13.9 1.0 S1 A:SF41235 3.8 12.1 1.0 N A:CYS812 4.1 13.6 1.0 CA A:CYS812 4.3 13.7 1.0 CG1 A:ILE1072 4.3 8.8 1.0 CG2 A:ILE1072 4.4 8.9 1.0 CD1 A:ILE1072 4.4 7.9 1.0 SG A:CYS815 4.5 13.8 1.0 CD A:LYS459 4.6 15.2 1.0 NZ A:LYS459 4.6 13.7 1.0 SG A:CYS1071 4.7 11.3 1.0 SG A:CYS840 4.7 11.6 1.0 N A:ILE1072 4.7 9.4 1.0 CB A:CYS815 4.8 13.3 1.0 CB A:ILE1072 4.9 8.7 1.0

Iron binding site 10 out of 24 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 Iron with other atoms in the Fe binding site number 10 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:Fe1235 b:12.9 occ:1.00 FE2 A:SF41235 0.0 12.9 1.0 S1 A:SF41235 2.3 12.1 1.0 S4 A:SF41235 2.3 11.9 1.0 S3 A:SF41235 2.3 13.2 1.0 SG A:CYS815 2.3 13.8 1.0 FE1 A:SF41235 2.5 13.0 1.0 FE3 A:SF41235 2.6 13.8 1.0 FE4 A:SF41235 2.7 12.0 1.0 CB A:CYS815 3.4 13.3 1.0 S2 A:SF41235 3.9 13.1 1.0 CA A:CYS815 4.0 13.2 1.0 CG A:GLU817 4.1 7.2 1.0 N A:GLY816 4.4 12.2 1.0 SG A:CYS812 4.4 13.6 1.0 CD A:GLU817 4.5 7.2 1.0 CB A:CYS812 4.6 13.9 1.0 O A:THR1070 4.6 8.1 1.0 C A:CYS815 4.6 12.7 1.0 SG A:CYS840 4.7 11.6 1.0 OE1 A:GLU817 4.8 5.6 1.0 SG A:CYS1071 4.9 11.3 1.0 N A:CYS812 4.9 13.6 1.0 CB A:CYS840 4.9 11.2 1.0 N A:GLU817 5.0 10.0 1.0 CB A:GLU817 5.0 8.4 1.0 CD1 A:TRP844 5.0 7.2 1.0

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