Iron in PDB 2iv2: Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli

All present enzymatic activity of Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli:
1.17.1.9; 1.17.99.7;

The structure of Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli, PDB code: 2iv2 was solved by H.C.A.Raaijmakers, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.50 / 2.27
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.400, 146.400, 81.270, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.6

The structure of Reinterpretation of Reduced 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 Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli (pdb code 2iv2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli, PDB code: 2iv2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Reinterpretation of Reduced 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 Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe800 b:23.0 occ:1.00 FE1 X:SF4800 0.0 23.0 1.0 SG X:CYS42 2.2 19.4 1.0 S2 X:SF4800 2.2 21.8 1.0 S4 X:SF4800 2.4 21.4 1.0 S3 X:SF4800 2.4 20.0 1.0 FE3 X:SF4800 2.7 22.1 1.0 FE4 X:SF4800 2.7 21.6 1.0 FE2 X:SF4800 2.7 22.5 1.0 CB X:CYS42 3.2 20.1 1.0 N X:CYS42 3.7 20.4 1.0 S1 X:SF4800 3.9 20.9 1.0 CA X:CYS42 4.0 20.5 1.0 N X:GLY45 4.4 21.3 1.0 NZ X:LYS44 4.4 22.2 1.0 CD X:PRO182 4.4 21.0 1.0 CG X:PRO182 4.6 21.2 1.0 C X:CYS42 4.6 20.4 1.0 SG X:CYS11 4.7 20.6 1.0 O X:HOH2084 4.7 16.1 1.0 O X:CYS42 4.7 19.9 1.0 CB X:LYS44 4.7 21.4 1.0 SG X:CYS15 4.7 22.3 1.0 CD1 X:ILE183 4.8 18.8 1.0 CB X:PRO182 4.8 21.1 1.0 SG X:CYS8 4.8 21.9 1.0 C X:LEU41 4.9 20.3 1.0 CE X:LYS44 4.9 23.1 1.0

Iron binding site 2 out of 4 in the Reinterpretation of Reduced 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 Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe800 b:22.5 occ:1.00 FE2 X:SF4800 0.0 22.5 1.0 SG X:CYS8 2.2 21.9 1.0 S1 X:SF4800 2.3 20.9 1.0 S3 X:SF4800 2.3 20.0 1.0 S4 X:SF4800 2.4 21.4 1.0 FE3 X:SF4800 2.6 22.1 1.0 FE4 X:SF4800 2.7 21.6 1.0 FE1 X:SF4800 2.7 23.0 1.0 CB X:CYS8 3.0 22.0 1.0 S2 X:SF4800 3.8 21.8 1.0 N X:GLY45 4.2 21.3 1.0 CB X:TYR10 4.2 23.0 1.0 CA X:GLY45 4.3 21.2 1.0 CA X:CYS8 4.5 22.0 1.0 N X:CYS11 4.5 22.0 1.0 SG X:CYS42 4.5 19.4 1.0 SG X:CYS15 4.6 22.3 1.0 CB X:CYS15 4.7 22.1 1.0 CD2 X:TYR10 4.8 24.0 1.0 SG X:CYS11 4.8 20.6 1.0 N X:TYR10 4.8 22.1 1.0 C X:CYS8 4.9 21.6 1.0 O X:CYS11 5.0 20.6 1.0 CA X:TYR10 5.0 22.5 1.0

Iron binding site 3 out of 4 in the Reinterpretation of Reduced 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 Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe800 b:22.1 occ:1.00 FE3 X:SF4800 0.0 22.1 1.0 SG X:CYS15 2.2 22.3 1.0 S1 X:SF4800 2.3 20.9 1.0 S2 X:SF4800 2.3 21.8 1.0 S4 X:SF4800 2.3 21.4 1.0 FE2 X:SF4800 2.6 22.5 1.0 FE1 X:SF4800 2.7 23.0 1.0 FE4 X:SF4800 2.8 21.6 1.0 CB X:CYS15 3.2 22.1 1.0 S3 X:SF4800 3.9 20.0 1.0 CB X:SER13 4.0 21.3 1.0 CD1 X:ILE183 4.1 18.8 1.0 N X:CYS15 4.3 22.4 1.0 CA X:CYS15 4.3 22.1 1.0 CB X:ILE183 4.4 20.3 1.0 CG1 X:ILE183 4.4 20.4 1.0 CB X:CYS8 4.5 22.0 1.0 SG X:CYS8 4.6 21.9 1.0 OG X:SER13 4.6 20.9 1.0 SG X:CYS11 4.8 20.6 1.0 N X:CYS42 4.8 20.4 1.0 SG X:CYS42 4.8 19.4 1.0 CD2 X:LEU41 4.8 16.4 1.0

Iron binding site 4 out of 4 in the Reinterpretation of Reduced 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 Reinterpretation of Reduced Form of Formate Dehydrogenase H From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe800 b:21.6 occ:1.00 FE4 X:SF4800 0.0 21.6 1.0 S3 X:SF4800 2.2 20.0 1.0 SG X:CYS11 2.2 20.6 1.0 S1 X:SF4800 2.3 20.9 1.0 S2 X:SF4800 2.4 21.8 1.0 FE2 X:SF4800 2.7 22.5 1.0 FE1 X:SF4800 2.7 23.0 1.0 FE3 X:SF4800 2.8 22.1 1.0 CB X:CYS11 3.5 21.4 1.0 CB X:SER13 3.8 21.3 1.0 N X:CYS11 3.8 22.0 1.0 OG X:SER13 3.9 20.9 1.0 CA X:CYS11 4.0 21.7 1.0 S4 X:SF4800 4.0 21.4 1.0 O X:HOH2084 4.1 16.1 1.0 O X:CYS11 4.1 20.6 1.0 C X:CYS11 4.2 21.7 1.0 N X:SER13 4.5 22.1 1.0 CD X:PRO182 4.6 21.0 1.0 SG X:CYS42 4.6 19.4 1.0 SG X:CYS8 4.6 21.9 1.0 CA X:SER13 4.7 21.8 1.0 SG X:CYS15 4.8 22.3 1.0 CB X:TYR10 4.9 23.0 1.0 N X:ALA12 5.0 22.2 1.0

H.C.A.Raaijmakers, M.J.Romao. Formate-Reduced E. Coli Formate Dehydrogenase H: the Reinterpretation of the Crystal Structure Suggests A New Reaction Mechanism. J.Biol.Inorg.Chem. V. 11 849 2006.
ISSN: ISSN 0949-8257
PubMed: 16830149
DOI: 10.1007/S00775-006-0129-2