Tungsten in PDB 8cm5: W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris

The structure of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris, PDB code: 8cm5 was solved by G.Vilela-Alves, C.Mota, K.Klymanska, 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)	48.83 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.44, 261.055, 126.209, 90, 90.58, 90
R / Rfree (%)	18.4 / 24

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

Iron

(Fe)

64 atoms

The binding sites of Tungsten atom in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris (pdb code 8cm5). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 4 binding sites of Tungsten where determined in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris, PDB code: 8cm5:
Jump to Tungsten binding site number: 1; 2; 3; 4;

Tungsten binding site 1 out of 4 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ A:W1103 b:20.5 occ:1.00 S13 A:MGD1105 2.3 16.8 1.0 S A:H2S1102 2.3 38.7 1.0 S13 A:MGD1104 2.3 18.3 1.0 S12 A:MGD1104 2.4 16.9 1.0 S12 A:MGD1105 2.4 15.3 1.0 SE A:SEC192 2.6 24.0 1.0 C13 A:MGD1104 3.2 15.6 1.0 C12 A:MGD1104 3.3 16.9 1.0 CB A:SEC192 3.3 24.6 1.0 C13 A:MGD1105 3.4 19.4 1.0 C12 A:MGD1105 3.4 16.0 1.0 NH2 A:ARG884 3.9 23.5 1.0 CA A:GLY442 4.1 18.4 1.0 NE2 A:GLN890 4.4 26.3 1.0 CA A:SEC192 4.4 26.1 1.0 N A:GLU443 4.6 21.4 1.0 N A:GLY442 4.6 22.1 1.0 C14 A:MGD1104 4.7 16.9 1.0 SD A:MET405 4.7 22.3 1.0 C11 A:MGD1104 4.7 16.1 1.0 C14 A:MGD1105 4.8 20.6 1.0 C A:GLY442 4.8 19.1 1.0 C11 A:MGD1105 4.9 18.4 1.0 OE1 A:GLN890 5.0 23.6 1.0 CZ A:ARG884 5.0 21.3 1.0

Tungsten binding site 2 out of 4 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ C:W1103 b:22.6 occ:1.00 S13 C:MGD1105 2.0 21.8 1.0 S13 C:MGD1104 2.3 22.6 1.0 S C:H2S1102 2.3 23.7 1.0 S12 C:MGD1105 2.4 22.1 1.0 S12 C:MGD1104 2.5 23.1 1.0 SE C:SEC192 2.6 26.0 1.0 C13 C:MGD1104 3.3 20.1 1.0 C13 C:MGD1105 3.3 23.3 1.0 C12 C:MGD1104 3.4 22.2 1.0 CB C:SEC192 3.4 22.7 1.0 C12 C:MGD1105 3.4 23.5 1.0 NH2 C:ARG884 4.0 25.0 1.0 CA C:GLY442 4.1 22.3 1.0 CA C:SEC192 4.5 25.6 1.0 NE2 C:GLN890 4.5 28.0 1.0 N C:GLU443 4.5 23.0 1.0 N C:GLY442 4.6 21.0 1.0 C14 C:MGD1104 4.7 19.7 1.0 SD C:MET405 4.7 24.9 1.0 C14 C:MGD1105 4.7 23.5 1.0 C11 C:MGD1104 4.8 20.9 1.0 C C:GLY442 4.8 20.9 1.0 C11 C:MGD1105 4.9 22.1 1.0 CG C:GLU443 4.9 31.1 1.0

Tungsten binding site 3 out of 4 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ K:W1102 b:24.2 occ:1.00 S13 K:MGD1104 1.9 16.7 1.0 S K:H2S1101 2.1 20.9 1.0 S13 K:MGD1103 2.2 22.9 1.0 S12 K:MGD1103 2.4 20.0 1.0 S12 K:MGD1104 2.5 21.9 1.0 SE K:SEC192 2.7 31.6 1.0 C13 K:MGD1104 3.2 22.2 1.0 C13 K:MGD1103 3.3 21.9 1.0 C12 K:MGD1104 3.4 20.7 1.0 C12 K:MGD1103 3.4 21.1 1.0 CB K:SEC192 3.5 28.7 1.0 NH2 K:ARG884 3.9 21.6 1.0 CA K:GLY442 4.2 23.5 1.0 CA K:SEC192 4.6 31.8 1.0 N K:GLU443 4.6 25.5 1.0 N K:GLY442 4.7 29.6 1.0 C14 K:MGD1104 4.7 19.6 1.0 NE2 K:GLN890 4.7 31.4 1.0 C11 K:MGD1104 4.8 22.6 1.0 C14 K:MGD1103 4.8 22.4 1.0 C11 K:MGD1103 4.8 21.1 1.0 SD K:MET405 4.8 27.7 1.0 OE1 K:GLN890 4.9 27.3 1.0 C K:GLY442 4.9 23.6 1.0

Tungsten binding site 4 out of 4 in the W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris within 5.0Å range: probe atom residue distance (Å) B Occ R:W1102 b:22.4 occ:1.00 S13 R:MGD1104 2.1 16.0 1.0 S R:H2S1101 2.3 31.8 1.0 S12 R:MGD1104 2.4 18.0 1.0 S13 R:MGD1103 2.4 20.6 1.0 S12 R:MGD1103 2.5 23.9 1.0 SE R:SEC192 2.7 29.8 1.0 C13 R:MGD1104 3.2 16.5 1.0 C12 R:MGD1104 3.3 16.8 1.0 CB R:SEC192 3.4 31.1 1.0 C13 R:MGD1103 3.4 22.6 1.0 C12 R:MGD1103 3.4 21.4 1.0 NH2 R:ARG884 4.1 20.5 1.0 CA R:GLY442 4.1 27.7 1.0 NE2 R:GLN890 4.4 24.0 1.0 CA R:SEC192 4.5 28.9 1.0 C14 R:MGD1104 4.7 17.2 1.0 N R:GLU443 4.7 26.7 1.0 N R:GLY442 4.7 26.1 1.0 C11 R:MGD1104 4.8 18.4 1.0 C14 R:MGD1103 4.8 20.9 1.0 SD R:MET405 4.8 26.0 1.0 C11 R:MGD1103 4.8 22.1 1.0 C R:GLY442 4.9 26.5 1.0 OE1 R:GLN890 4.9 24.1 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