Iron in PDB 9qm0: W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris

All present enzymatic activity of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris:
1.2.1.2;

The structure of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris, PDB code: 9qm0 was solved by G.Vilela-Alves, A.R.Oliveira, I.C.Pereira, M.J.Romao, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.17 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.396, 123.099, 147.189, 90, 90, 90
R / Rfree (%)	17.2 / 21.4

The structure of W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Tungsten

(W)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris (pdb code 9qm0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris, PDB code: 9qm0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1123 b:16.5 occ:1.00 FE1 A:SF41123 0.0 16.5 1.0 SG A:CYS53 2.2 16.3 1.0 S2 A:SF41123 2.3 16.9 1.0 S4 A:SF41123 2.3 17.5 1.0 S3 A:SF41123 2.3 15.8 1.0 FE2 A:SF41123 2.7 16.6 1.0 FE3 A:SF41123 2.7 16.1 1.0 FE4 A:SF41123 2.7 17.3 1.0 CB A:CYS53 3.4 14.6 1.0 N A:CYS53 3.6 12.3 1.0 CA A:CYS53 3.8 14.1 1.0 O A:HOH1378 3.8 14.6 1.0 S1 A:SF41123 3.9 17.4 1.0 O A:CYS53 4.0 13.9 1.0 C A:CYS53 4.1 15.9 1.0 CB A:VAL55 4.1 14.8 1.0 CG2 A:VAL55 4.3 17.5 1.0 CD A:PRO234 4.6 16.4 1.0 SG A:CYS57 4.6 18.1 1.0 N A:VAL55 4.7 15.6 1.0 SG A:CYS88 4.7 17.2 1.0 SG A:CYS50 4.7 20.9 1.0 C A:TYR52 4.8 15.2 1.0 CA A:VAL55 4.9 14.4 1.0 CG1 A:VAL55 5.0 14.6 1.0 N A:ALA54 5.0 16.7 1.0

Iron binding site 2 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1123 b:16.6 occ:1.00 FE2 A:SF41123 0.0 16.6 1.0 SG A:CYS57 2.1 18.1 1.0 S3 A:SF41123 2.3 15.8 1.0 S4 A:SF41123 2.3 17.5 1.0 S1 A:SF41123 2.3 17.4 1.0 FE3 A:SF41123 2.7 16.1 1.0 FE1 A:SF41123 2.7 16.5 1.0 FE4 A:SF41123 2.7 17.3 1.0 CB A:CYS57 3.1 19.0 1.0 S2 A:SF41123 3.9 16.9 1.0 CD1 A:ILE235 4.1 18.5 1.0 N A:CYS57 4.3 16.7 1.0 CG1 A:ILE235 4.3 17.4 1.0 CB A:VAL55 4.3 14.8 1.0 CA A:CYS57 4.3 18.0 1.0 CG1 A:VAL55 4.3 14.6 1.0 CB A:ILE235 4.3 17.9 1.0 CB A:CYS50 4.7 17.5 1.0 SG A:CYS50 4.7 20.9 1.0 SG A:CYS53 4.7 16.3 1.0 CD2 A:LEU87 4.9 20.3 1.0 SG A:CYS88 4.9 17.2 1.0 CG2 A:VAL55 4.9 17.5 1.0

Iron binding site 3 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1123 b:16.1 occ:1.00 FE3 A:SF41123 0.0 16.1 1.0 S2 A:SF41123 2.3 16.9 1.0 SG A:CYS50 2.3 20.9 1.0 S4 A:SF41123 2.3 17.5 1.0 S1 A:SF41123 2.3 17.4 1.0 FE2 A:SF41123 2.7 16.6 1.0 FE4 A:SF41123 2.7 17.3 1.0 FE1 A:SF41123 2.7 16.5 1.0 CB A:CYS50 3.1 17.5 1.0 S3 A:SF41123 3.9 15.8 1.0 CB A:TYR52 4.1 15.6 1.0 N A:CYS53 4.2 12.3 1.0 CA A:GLY91 4.3 19.2 1.0 N A:GLY91 4.4 15.1 1.0 SG A:CYS57 4.6 18.1 1.0 CA A:CYS50 4.6 15.1 1.0 SG A:CYS88 4.6 17.2 1.0 CB A:CYS57 4.6 19.0 1.0 N A:TYR52 4.8 15.4 1.0 CA A:TYR52 4.8 16.4 1.0 SG A:CYS53 4.8 16.3 1.0 C A:TYR52 4.9 15.2 1.0 O A:CYS53 4.9 13.9 1.0 CD2 A:TYR52 4.9 16.4 1.0

Iron binding site 4 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1123 b:17.3 occ:1.00 FE4 A:SF41123 0.0 17.3 1.0 S1 A:SF41123 2.3 17.4 1.0 S3 A:SF41123 2.3 15.8 1.0 SG A:CYS88 2.3 17.2 1.0 S2 A:SF41123 2.3 16.9 1.0 FE3 A:SF41123 2.7 16.1 1.0 FE1 A:SF41123 2.7 16.5 1.0 FE2 A:SF41123 2.7 16.6 1.0 CB A:CYS88 3.3 16.2 1.0 N A:CYS88 3.9 15.3 1.0 S4 A:SF41123 3.9 17.5 1.0 CA A:CYS88 4.1 16.9 1.0 CD A:PRO234 4.3 16.4 1.0 O A:HOH1378 4.4 14.6 1.0 CD1 A:ILE235 4.5 18.5 1.0 NZ A:LYS90 4.5 21.5 1.0 N A:GLY91 4.5 15.1 1.0 CG A:PRO234 4.5 19.8 1.0 SG A:CYS53 4.7 16.3 1.0 C A:CYS88 4.7 15.4 1.0 SG A:CYS57 4.8 18.1 1.0 SG A:CYS50 4.9 20.9 1.0 O A:CYS88 4.9 15.4 1.0 CB A:PRO234 4.9 17.1 1.0 CA A:GLY91 5.0 19.2 1.0

Iron binding site 5 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1706 b:17.8 occ:1.00 FE1 B:SF41706 0.0 17.8 1.0 S3 B:SF41706 2.3 18.5 1.0 SG B:CYS157 2.3 17.2 1.0 S4 B:SF41706 2.3 18.1 1.0 S2 B:SF41706 2.3 20.2 1.0 FE2 B:SF41706 2.7 16.9 1.0 FE4 B:SF41706 2.8 17.2 1.0 FE3 B:SF41706 2.8 16.6 1.0 CB B:CYS157 3.2 20.6 1.0 CA B:CYS157 3.8 18.4 1.0 S1 B:SF41706 3.9 16.0 1.0 OG1 B:THR159 4.0 16.8 1.0 CB B:THR161 4.1 17.4 1.0 CG B:MET162 4.2 16.6 1.0 CD B:PRO158 4.3 19.4 1.0 OG1 B:THR161 4.5 14.3 1.0 CG2 B:THR161 4.5 18.0 1.0 C B:CYS157 4.6 17.2 1.0 SG B:CYS15 4.6 15.0 1.0 N B:PRO158 4.7 17.7 1.0 SG B:CYS18 4.8 19.1 1.0 N B:MET162 5.0 17.3 1.0 N B:CYS157 5.0 16.9 1.0

Iron binding site 6 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1706 b:16.9 occ:1.00 FE2 B:SF41706 0.0 16.9 1.0 S4 B:SF41706 2.3 18.1 1.0 SG B:CYS18 2.3 19.1 1.0 S1 B:SF41706 2.3 16.0 1.0 S3 B:SF41706 2.3 18.5 1.0 FE1 B:SF41706 2.7 17.8 1.0 FE3 B:SF41706 2.7 16.6 1.0 FE4 B:SF41706 2.8 17.2 1.0 CB B:CYS18 3.2 20.1 1.0 O B:HOH1843 3.8 18.0 1.0 N B:CYS18 3.8 18.2 1.0 S2 B:SF41706 3.9 20.2 1.0 CA B:CYS18 4.1 18.9 1.0 CG B:PRO71 4.4 22.6 1.0 SG B:CYS15 4.6 15.0 1.0 CB B:PRO71 4.6 19.7 1.0 N B:ARG16 4.6 14.3 1.0 N B:GLY17 4.7 14.0 1.0 CA B:ARG16 4.8 16.2 1.0 SG B:CYS157 4.8 17.2 1.0 CG2 B:VAL53 4.8 13.8 1.0 SG B:CYS12 4.9 16.4 1.0 C B:GLY17 5.0 17.5 1.0 C B:ARG16 5.0 17.1 1.0

Iron binding site 7 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1706 b:16.6 occ:1.00 FE3 B:SF41706 0.0 16.6 1.0 SG B:CYS15 2.3 15.0 1.0 S1 B:SF41706 2.3 16.0 1.0 S2 B:SF41706 2.3 20.2 1.0 S4 B:SF41706 2.3 18.1 1.0 FE2 B:SF41706 2.7 16.9 1.0 FE1 B:SF41706 2.8 17.8 1.0 FE4 B:SF41706 2.8 17.2 1.0 CB B:CYS15 3.5 13.9 1.0 N B:CYS15 3.5 15.9 1.0 N B:ARG16 3.7 14.3 1.0 CA B:CYS15 3.9 16.1 1.0 S3 B:SF41706 3.9 18.5 1.0 N B:GLY17 4.1 14.0 1.0 C B:CYS15 4.2 14.6 1.0 OG1 B:THR13 4.3 17.1 1.0 CD B:PRO158 4.4 19.4 1.0 C B:ALA14 4.5 17.1 1.0 N B:ALA14 4.6 16.3 1.0 CA B:ARG16 4.6 16.2 1.0 SG B:CYS18 4.7 19.1 1.0 SG B:CYS157 4.7 17.2 1.0 CA B:ALA14 4.8 16.4 1.0 SG B:CYS12 4.8 16.4 1.0 N B:CYS18 4.8 18.2 1.0 CA B:GLY17 4.9 17.6 1.0 C B:ARG16 4.9 17.1 1.0 N B:THR13 5.0 16.0 1.0

Iron binding site 8 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1706 b:17.2 occ:1.00 FE4 B:SF41706 0.0 17.2 1.0 S2 B:SF41706 2.3 20.2 1.0 S1 B:SF41706 2.3 16.0 1.0 S3 B:SF41706 2.3 18.5 1.0 SG B:CYS12 2.4 16.4 1.0 FE1 B:SF41706 2.8 17.8 1.0 FE2 B:SF41706 2.8 16.9 1.0 FE3 B:SF41706 2.8 16.6 1.0 CB B:CYS12 3.5 15.4 1.0 CA B:CYS12 3.8 16.2 1.0 S4 B:SF41706 3.9 18.1 1.0 N B:ALA14 4.1 16.3 1.0 N B:THR13 4.1 16.0 1.0 CG B:PRO71 4.3 22.6 1.0 C B:CYS12 4.4 14.2 1.0 OG1 B:THR161 4.4 14.3 1.0 CG2 B:THR161 4.4 18.0 1.0 CA B:ALA14 4.5 16.4 1.0 CB B:THR161 4.5 17.4 1.0 N B:CYS15 4.7 15.9 1.0 SG B:CYS157 4.8 17.2 1.0 SG B:CYS18 4.8 19.1 1.0 OG1 B:THR159 4.9 16.8 1.0 SG B:CYS15 5.0 15.0 1.0

Iron binding site 9 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1707 b:21.5 occ:1.00 FE1 B:SF41707 0.0 21.5 1.0 SG B:CYS77 2.2 23.6 1.0 S3 B:SF41707 2.3 23.3 1.0 S2 B:SF41707 2.3 22.6 1.0 S4 B:SF41707 2.3 20.4 1.0 FE4 B:SF41707 2.7 21.8 1.0 FE2 B:SF41707 2.7 22.2 1.0 FE3 B:SF41707 2.8 19.9 1.0 CB B:CYS77 3.5 22.7 1.0 N B:CYS77 3.8 17.8 1.0 S1 B:SF41707 3.9 21.4 1.0 CA B:CYS77 4.2 24.0 1.0 SG B:CYS121 4.5 22.8 1.0 N B:HIS76 4.5 21.5 1.0 CD2 B:TYR123 4.5 24.7 1.0 SG B:CYS74 4.6 20.3 1.0 CB B:PRO80 4.6 31.8 1.0 CD B:PRO81 4.7 24.3 1.0 SG B:CYS82 4.8 24.6 1.0 CB B:ARG75 4.8 18.9 1.0 N B:ARG75 4.8 20.8 1.0 CE2 B:TYR123 4.8 25.8 1.0 C B:HIS76 4.9 22.5 1.0 CA B:PRO80 4.9 27.5 1.0 CA B:HIS76 4.9 20.6 1.0 C B:ARG75 5.0 18.7 1.0

Iron binding site 10 out of 16 in the W-Formate Dehydrogenase U192C From Desulfovibrio Vulgaris


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 U192C From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1707 b:22.2 occ:1.00 FE2 B:SF41707 0.0 22.2 1.0 S4 B:SF41707 2.3 20.4 1.0 S1 B:SF41707 2.3 21.4 1.0 S3 B:SF41707 2.3 23.3 1.0 SG B:CYS82 2.3 24.6 1.0 FE4 B:SF41707 2.7 21.8 1.0 FE1 B:SF41707 2.7 21.5 1.0 FE3 B:SF41707 2.8 19.9 1.0 CB B:CYS82 3.2 21.7 1.0 S2 B:SF41707 3.9 22.6 1.0 CB B:PRO80 4.2 31.8 1.0 N B:CYS82 4.3 24.2 1.0 CA B:CYS82 4.3 22.1 1.0 CG1 B:VAL103 4.4 20.6 1.0 SG B:CYS74 4.6 20.3 1.0 CE B:LYS137 4.7 23.5 1.0 SG B:CYS77 4.8 23.6 1.0 SG B:CYS121 4.8 22.8 1.0 CZ B:PHE105 4.8 24.1 1.0 CE1 B:PHE105 4.9 24.8 1.0 CA B:PRO80 5.0 27.5 1.0

A.R.Oliveira, G.Vilela-Alves, C.Mota, V.Fourmond, C.Leger, F.Biaso, B.Guigliarelli, M.J.Romao, I.C.Pereira. The Role of Selenocysteine in Catalysis and Oxygen Tolerance of A W‐Dependent Formate Dehydrogenase Acs Catalysis 2025.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.5C02382