Iron in PDB 1fdo: Oxidized Form of Formate Dehydrogenase H From E. Coli

All present enzymatic activity of Oxidized Form of Formate Dehydrogenase H From E. Coli:
1.2.1.2;

The structure of Oxidized Form of Formate Dehydrogenase H From E. Coli, PDB code: 1fdo was solved by P.D.Sun, J.C.Boyington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.600, 146.600, 81.100, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 28.1

The structure of Oxidized Form of Formate Dehydrogenase H From E. Coli also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

The binding sites of Iron atom in the Oxidized Form of Formate Dehydrogenase H From E. Coli (pdb code 1fdo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Oxidized Form of Formate Dehydrogenase H From E. Coli, PDB code: 1fdo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:11.2 occ:1.00 FE1 A:SF4800 0.0 11.2 1.0 S2 A:SF4800 2.3 13.9 1.0 S4 A:SF4800 2.3 14.9 1.0 S3 A:SF4800 2.3 14.6 1.0 SG A:CYS42 2.4 15.3 1.0 FE4 A:SF4800 2.5 13.3 1.0 FE2 A:SF4800 2.7 14.2 1.0 FE3 A:SF4800 2.8 12.9 1.0 CB A:CYS42 3.5 12.8 1.0 S1 A:SF4800 3.9 14.3 1.0 N A:CYS42 3.9 12.3 1.0 CA A:CYS42 4.2 13.2 1.0 N A:GLY45 4.3 18.8 1.0 SG A:CYS11 4.6 10.7 1.0 CD A:PRO182 4.6 14.3 1.0 CE A:LYS44 4.6 20.6 1.0 O A:CYS42 4.7 14.2 1.0 C A:CYS42 4.7 13.1 1.0 CG A:PRO182 4.8 13.7 1.0 CA A:GLY45 4.8 18.2 1.0 O A:HOH831 4.8 19.7 1.0 CB A:PRO182 4.8 13.1 1.0 SG A:CYS8 4.9 15.4 1.0 SG A:CYS15 4.9 9.6 1.0

Iron binding site 2 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:14.2 occ:1.00 FE2 A:SF4800 0.0 14.2 1.0 S3 A:SF4800 2.3 14.6 1.0 S1 A:SF4800 2.3 14.3 1.0 S4 A:SF4800 2.3 14.9 1.0 SG A:CYS8 2.3 15.4 1.0 FE4 A:SF4800 2.6 13.3 1.0 FE3 A:SF4800 2.7 12.9 1.0 FE1 A:SF4800 2.7 11.2 1.0 CB A:CYS8 3.0 13.1 1.0 S2 A:SF4800 3.9 13.9 1.0 CB A:TYR10 4.1 9.1 1.0 CA A:GLY45 4.2 18.2 1.0 N A:CYS11 4.3 7.5 1.0 N A:GLY45 4.4 18.8 1.0 CA A:CYS8 4.5 13.6 1.0 CB A:CYS15 4.6 10.5 1.0 SG A:CYS11 4.7 10.7 1.0 N A:TYR10 4.7 10.4 1.0 SG A:CYS42 4.7 15.3 1.0 SG A:CYS15 4.7 9.6 1.0 CD2 A:TYR10 4.8 10.9 1.0 C A:CYS8 4.8 13.3 1.0 CA A:TYR10 4.8 8.2 1.0 CG A:TYR10 5.0 7.6 1.0

Iron binding site 3 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:12.9 occ:1.00 FE3 A:SF4800 0.0 12.9 1.0 S1 A:SF4800 2.2 14.3 1.0 SG A:CYS15 2.2 9.6 1.0 S4 A:SF4800 2.3 14.9 1.0 S2 A:SF4800 2.4 13.9 1.0 FE4 A:SF4800 2.7 13.3 1.0 FE2 A:SF4800 2.7 14.2 1.0 FE1 A:SF4800 2.8 11.2 1.0 CB A:CYS15 2.9 10.5 1.0 CB A:SER13 3.9 8.2 1.0 S3 A:SF4800 4.0 14.6 1.0 CA A:CYS15 4.2 11.9 1.0 N A:CYS15 4.2 11.4 1.0 CD1 A:ILE183 4.2 11.3 1.0 OG A:SER13 4.4 11.9 1.0 CG1 A:ILE183 4.5 13.5 1.0 CB A:CYS8 4.5 13.1 1.0 CD2 A:LEU41 4.6 12.9 1.0 CB A:ILE183 4.6 14.3 1.0 SG A:CYS11 4.7 10.7 1.0 SG A:CYS8 4.7 15.4 1.0

Iron binding site 4 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe800 b:13.3 occ:1.00 FE4 A:SF4800 0.0 13.3 1.0 S2 A:SF4800 2.2 13.9 1.0 S3 A:SF4800 2.3 14.6 1.0 S1 A:SF4800 2.3 14.3 1.0 SG A:CYS11 2.3 10.7 1.0 FE1 A:SF4800 2.5 11.2 1.0 FE2 A:SF4800 2.6 14.2 1.0 FE3 A:SF4800 2.7 12.9 1.0 CB A:CYS11 3.5 8.8 1.0 OG A:SER13 3.7 11.9 1.0 S4 A:SF4800 3.7 14.9 1.0 N A:CYS11 3.8 7.5 1.0 CB A:SER13 3.9 8.2 1.0 CA A:CYS11 4.0 6.6 1.0 O A:HOH831 4.3 19.7 1.0 C A:CYS11 4.4 5.8 1.0 O A:CYS11 4.5 4.8 1.0 CD A:PRO182 4.6 14.3 1.0 SG A:CYS42 4.6 15.3 1.0 N A:SER13 4.6 6.3 1.0 SG A:CYS15 4.7 9.6 1.0 SG A:CYS8 4.7 15.4 1.0 CA A:SER13 4.9 7.0 1.0 CB A:TYR10 4.9 9.1 1.0 C A:TYR10 5.0 8.7 1.0

J.C.Boyington, V.N.Gladyshev, S.V.Khangulov, T.C.Stadtman, P.D.Sun. Crystal Structure of Formate Dehydrogenase H: Catalysis Involving Mo, Molybdopterin, Selenocysteine, and An FE4S4 Cluster. Science V. 275 1305 1997.
ISSN: ISSN 0036-8075
PubMed: 9036855
DOI: 10.1126/SCIENCE.275.5304.1305