Iron in PDB 8cm6: W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide

The structure of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide, PDB code: 8cm6 was solved by G.Vilela-Alves, C.Mota, A.R.Oliveira, R.R.Manuel, I.C.Pereira, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.57 / 1.42
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.467, 74.949, 122.806, 73.87, 89.14, 71.12
R / Rfree (%)	14.9 / 17.6

The structure of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide also contains other interesting chemical elements:

Tungsten	(W)	2 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide (pdb code 8cm6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide, PDB code: 8cm6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1105 b:10.4 occ:1.00 FE1 A:SF41105 0.0 10.4 1.0 SG A:CYS53 2.2 10.5 1.0 S4 A:SF41105 2.3 10.1 1.0 S2 A:SF41105 2.3 9.6 1.0 S3 A:SF41105 2.3 10.1 1.0 FE2 A:SF41105 2.7 10.7 1.0 FE3 A:SF41105 2.7 9.8 1.0 FE4 A:SF41105 2.7 9.8 1.0 CB A:CYS53 3.4 10.3 1.0 N A:CYS53 3.7 9.5 1.0 CA A:CYS53 3.8 10.4 1.0 S1 A:SF41105 3.9 10.0 1.0 O A:HOH1379 3.9 9.9 1.0 O A:CYS53 4.0 10.3 1.0 C A:CYS53 4.0 9.4 1.0 CB A:VAL55 4.1 10.5 1.0 CG2 A:VAL55 4.3 11.5 1.0 N A:VAL55 4.5 9.7 1.0 CD A:PRO234 4.7 9.6 1.0 SG A:CYS50 4.7 10.5 1.0 SG A:CYS57 4.7 10.6 1.0 SG A:CYS88 4.7 10.7 1.0 CA A:VAL55 4.9 9.7 1.0 C A:TYR52 4.9 9.3 1.0 N A:ALA54 4.9 9.3 1.0

Iron binding site 2 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1105 b:10.7 occ:1.00 FE2 A:SF41105 0.0 10.7 1.0 S3 A:SF41105 2.3 10.1 1.0 S4 A:SF41105 2.3 10.1 1.0 SG A:CYS57 2.3 10.6 1.0 S1 A:SF41105 2.3 10.0 1.0 FE3 A:SF41105 2.7 9.8 1.0 FE1 A:SF41105 2.7 10.4 1.0 FE4 A:SF41105 2.8 9.8 1.0 CB A:CYS57 3.2 10.1 1.0 S2 A:SF41105 3.8 9.6 1.0 CD1 A:ILE235 4.1 12.4 1.0 N A:CYS57 4.2 9.3 1.0 CB A:VAL55 4.3 10.5 1.0 CA A:CYS57 4.3 10.0 1.0 CB A:ILE235 4.4 11.1 1.0 CG1 A:ILE235 4.4 11.2 1.0 CG1 A:VAL55 4.4 11.4 1.0 SG A:CYS50 4.6 10.5 1.0 CB A:CYS50 4.7 9.9 1.0 SG A:CYS53 4.7 10.5 1.0 CD2 A:LEU87 4.9 11.0 1.0 SG A:CYS88 5.0 10.7 1.0

Iron binding site 3 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1105 b:9.8 occ:1.00 FE3 A:SF41105 0.0 9.8 1.0 S2 A:SF41105 2.2 9.6 1.0 S4 A:SF41105 2.3 10.1 1.0 SG A:CYS50 2.3 10.5 1.0 S1 A:SF41105 2.3 10.0 1.0 FE2 A:SF41105 2.7 10.7 1.0 FE4 A:SF41105 2.7 9.8 1.0 FE1 A:SF41105 2.7 10.4 1.0 CB A:CYS50 3.2 9.9 1.0 S3 A:SF41105 3.9 10.1 1.0 N A:GLY91 4.2 10.5 1.0 CB A:TYR52 4.2 9.0 1.0 CA A:GLY91 4.2 10.7 1.0 N A:CYS53 4.3 9.5 1.0 CA A:CYS50 4.6 9.8 1.0 SG A:CYS57 4.6 10.6 1.0 SG A:CYS88 4.6 10.7 1.0 CB A:CYS57 4.6 10.1 1.0 N A:TYR52 4.8 9.8 1.0 SG A:CYS53 4.8 10.5 1.0 CA A:TYR52 4.8 9.3 1.0 O A:CYS53 4.9 10.3 1.0 C A:TYR52 4.9 9.3 1.0

Iron binding site 4 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1105 b:9.8 occ:1.00 FE4 A:SF41105 0.0 9.8 1.0 S1 A:SF41105 2.2 10.0 1.0 S2 A:SF41105 2.3 9.6 1.0 SG A:CYS88 2.3 10.7 1.0 S3 A:SF41105 2.3 10.1 1.0 FE3 A:SF41105 2.7 9.8 1.0 FE1 A:SF41105 2.7 10.4 1.0 FE2 A:SF41105 2.8 10.7 1.0 CB A:CYS88 3.3 8.8 1.0 N A:CYS88 3.9 10.2 1.0 S4 A:SF41105 3.9 10.1 1.0 CA A:CYS88 4.1 9.6 1.0 N A:GLY91 4.3 10.5 1.0 CD A:PRO234 4.4 9.6 1.0 O A:HOH1379 4.4 9.9 1.0 CD1 A:ILE235 4.5 12.4 1.0 NZ A:LYS90 4.5 10.1 1.0 SG A:CYS53 4.7 10.5 1.0 C A:CYS88 4.7 9.5 1.0 CG A:PRO234 4.7 9.8 1.0 SG A:CYS50 4.8 10.5 1.0 SG A:CYS57 4.9 10.6 1.0 CA A:GLY91 4.9 10.7 1.0 O A:CYS88 4.9 10.7 1.0 CB A:PRO234 4.9 9.8 1.0 CB A:LYS90 5.0 9.7 1.0

Iron binding site 5 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:11.1 occ:1.00 FE1 B:SF4301 0.0 11.1 1.0 S3 B:SF4301 2.3 11.2 1.0 S4 B:SF4301 2.3 11.7 1.0 S2 B:SF4301 2.3 11.1 1.0 SG B:CYS157 2.4 11.5 1.0 FE2 B:SF4301 2.7 10.9 1.0 FE3 B:SF4301 2.7 10.7 1.0 FE4 B:SF4301 2.8 11.2 1.0 CB B:CYS157 3.3 11.2 1.0 CA B:CYS157 3.8 10.3 1.0 S1 B:SF4301 3.9 11.5 1.0 OG1 B:THR159 3.9 11.5 1.0 CB B:THR161 4.0 10.8 1.0 CD B:PRO158 4.0 12.8 1.0 CG B:MET162 4.3 12.6 1.0 OG1 B:THR161 4.4 11.3 1.0 N B:PRO158 4.5 11.2 1.0 C B:CYS157 4.5 10.9 1.0 CG2 B:THR161 4.6 10.9 1.0 SG B:CYS15 4.7 11.0 1.0 SG B:CYS18 4.9 11.1 1.0 N B:MET162 4.9 11.6 1.0 SG B:CYS12 5.0 12.0 1.0 N B:THR159 5.0 11.2 1.0

Iron binding site 6 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:10.9 occ:1.00 FE2 B:SF4301 0.0 10.9 1.0 S4 B:SF4301 2.2 11.7 1.0 S1 B:SF4301 2.3 11.5 1.0 S3 B:SF4301 2.3 11.2 1.0 SG B:CYS18 2.3 11.1 1.0 FE3 B:SF4301 2.7 10.7 1.0 FE1 B:SF4301 2.7 11.1 1.0 FE4 B:SF4301 2.8 11.2 1.0 CB B:CYS18 3.2 10.4 1.0 O B:HOH475 3.9 14.2 1.0 S2 B:SF4301 3.9 11.1 1.0 N B:CYS18 3.9 10.7 1.0 CA B:CYS18 4.2 10.5 1.0 CG B:PRO71 4.4 13.5 1.0 SG B:CYS15 4.6 11.0 1.0 CB B:PRO71 4.7 11.8 1.0 N B:GLY17 4.7 10.3 1.0 N B:ARG16 4.7 10.2 1.0 SG B:CYS12 4.8 12.0 1.0 CA B:ARG16 4.9 11.0 1.0 SG B:CYS157 4.9 11.5 1.0 CG2 B:VAL53 4.9 11.9 1.0

Iron binding site 7 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:10.7 occ:1.00 FE3 B:SF4301 0.0 10.7 1.0 S1 B:SF4301 2.3 11.5 1.0 S2 B:SF4301 2.3 11.1 1.0 SG B:CYS15 2.3 11.0 1.0 S4 B:SF4301 2.3 11.7 1.0 FE2 B:SF4301 2.7 10.9 1.0 FE1 B:SF4301 2.7 11.1 1.0 FE4 B:SF4301 2.8 11.2 1.0 N B:CYS15 3.5 10.1 1.0 CB B:CYS15 3.6 10.2 1.0 N B:ARG16 3.8 10.2 1.0 S3 B:SF4301 3.9 11.2 1.0 CA B:CYS15 3.9 9.7 1.0 CD B:PRO158 4.1 12.8 1.0 N B:GLY17 4.2 10.3 1.0 C B:CYS15 4.2 10.1 1.0 OG1 B:THR13 4.4 11.1 1.0 C B:ALA14 4.5 10.8 1.0 N B:ALA14 4.5 10.3 1.0 CG B:PRO158 4.6 14.6 1.0 SG B:CYS18 4.6 11.1 1.0 CA B:ARG16 4.7 11.0 1.0 SG B:CYS12 4.8 12.0 1.0 CA B:ALA14 4.8 10.5 1.0 SG B:CYS157 4.8 11.5 1.0 N B:CYS18 4.9 10.7 1.0 CA B:GLY17 4.9 10.9 1.0 C B:ARG16 4.9 10.9 1.0 N B:THR13 5.0 10.3 1.0

Iron binding site 8 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:11.2 occ:1.00 FE4 B:SF4301 0.0 11.2 1.0 S1 B:SF4301 2.3 11.5 1.0 S2 B:SF4301 2.3 11.1 1.0 SG B:CYS12 2.3 12.0 1.0 S3 B:SF4301 2.3 11.2 1.0 FE1 B:SF4301 2.8 11.1 1.0 FE2 B:SF4301 2.8 10.9 1.0 FE3 B:SF4301 2.8 10.7 1.0 CB B:CYS12 3.5 11.4 1.0 CA B:CYS12 3.8 10.3 1.0 S4 B:SF4301 3.9 11.7 1.0 N B:ALA14 4.0 10.3 1.0 N B:THR13 4.1 10.3 1.0 CG B:PRO71 4.3 13.5 1.0 OG1 B:THR161 4.3 11.3 1.0 CG2 B:THR161 4.4 10.9 1.0 C B:CYS12 4.4 10.2 1.0 CB B:THR161 4.4 10.8 1.0 CA B:ALA14 4.5 10.5 1.0 N B:CYS15 4.7 10.1 1.0 SG B:CYS18 4.8 11.1 1.0 OG1 B:THR159 4.8 11.5 1.0 SG B:CYS157 4.9 11.5 1.0 C B:THR13 5.0 10.6 1.0

Iron binding site 9 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:14.2 occ:1.00 FE1 B:SF4302 0.0 14.2 1.0 S4 B:SF4302 2.3 14.3 1.0 SG B:CYS77 2.3 15.2 1.0 S2 B:SF4302 2.3 13.6 1.0 S3 B:SF4302 2.3 14.4 1.0 FE4 B:SF4302 2.7 13.4 1.0 FE2 B:SF4302 2.7 13.7 1.0 FE3 B:SF4302 2.8 13.7 1.0 CB B:CYS77 3.3 14.6 1.0 N B:CYS77 3.8 14.7 1.0 S1 B:SF4302 3.9 12.8 1.0 CA B:CYS77 4.1 16.1 1.0 CD2 B:TYR123 4.5 14.5 1.0 CB B:PRO80 4.5 15.2 1.0 N B:HIS76 4.6 12.5 1.0 SG B:CYS121 4.6 14.1 1.0 CD B:PRO81 4.7 17.8 1.0 SG B:CYS74 4.7 13.0 1.0 CA B:PRO80 4.7 16.9 1.0 CE2 B:TYR123 4.8 14.7 1.0 CB B:ARG75 4.8 11.8 1.0 N B:ARG75 4.8 12.6 1.0 SG B:CYS82 4.8 15.1 1.0 C B:HIS76 4.9 14.2 1.0 O B:HOH579 5.0 24.1 1.0

Iron binding site 10 out of 32 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:13.7 occ:1.00 FE2 B:SF4302 0.0 13.7 1.0 S4 B:SF4302 2.3 14.3 1.0 S3 B:SF4302 2.3 14.4 1.0 S1 B:SF4302 2.3 12.8 1.0 SG B:CYS82 2.3 15.1 1.0 FE4 B:SF4302 2.7 13.4 1.0 FE1 B:SF4302 2.7 14.2 1.0 FE3 B:SF4302 2.8 13.7 1.0 CB B:CYS82 3.2 14.8 1.0 S2 B:SF4302 3.9 13.6 1.0 CB B:PRO80 4.1 15.2 1.0 N B:CYS82 4.2 16.0 1.0 CA B:CYS82 4.3 16.4 1.0 CG1 B:VAL103 4.5 13.6 1.0 SG B:CYS74 4.7 13.0 1.0 SG B:CYS121 4.8 14.1 1.0 CA B:PRO80 4.8 16.9 1.0 CE B:LYS137 4.8 12.0 1.0 SG B:CYS77 4.9 15.2 1.0

A.R.Oliveira, C.Mota, R.R.Manuel, G.Vilela-Alves, N.Pedrosa, V.Fourmond, K.Klymanska, C.Leger, B.Guigliarelli, M.J.Romao, I.C.Pereira. W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469