Chlorine in PDB 8bqh: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min, PDB code: 8bqh 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)	90.65 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.361, 127.456, 128.952, 90, 90, 90
R / Rfree (%)	15.1 / 17.5

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min also contains other interesting chemical elements:

Iron	(Fe)	16 atoms
Tungsten	(W)	1 atom

The binding sites of Chlorine atom in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min (pdb code 8bqh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min, PDB code: 8bqh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1122 b:34.7 occ:1.00 N A:ARG70 3.3 17.9 1.0 O A:HOH1399 3.4 29.7 1.0 CD A:LYS65 3.6 49.5 1.0 CB A:ALA64 3.8 18.4 1.0 CA A:GLY69 3.8 30.8 1.0 CG A:ARG70 3.8 18.5 1.0 CB A:ARG70 3.9 16.9 1.0 C A:GLY69 4.0 20.5 1.0 CA A:ARG70 4.2 17.2 1.0 NZ A:LYS65 4.4 53.4 1.0 CG A:LYS65 4.5 41.7 1.0 CE A:LYS65 4.5 44.0 1.0 O A:ARG70 4.7 14.7 1.0 CD A:ARG70 4.9 19.0 1.0 C A:ARG70 4.9 15.5 1.0 CA A:ALA64 5.0 19.5 1.0

Chlorine binding site 2 out of 5 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1123 b:26.7 occ:1.00 O A:HOH1628 2.8 34.1 1.0 N A:ALA673 3.4 18.6 1.0 O A:HOH1282 3.4 23.3 1.0 N A:ILE672 3.4 14.8 1.0 NH1 A:ARG653 3.5 26.4 1.0 O A:LEU670 3.5 14.4 1.0 CB A:ALA673 3.7 17.4 1.0 CG1 A:ILE672 3.9 16.9 1.0 CA A:ALA673 4.1 18.5 1.0 CA A:ASN671 4.1 18.1 1.0 C A:ASN671 4.2 18.3 1.0 C A:ILE672 4.2 15.9 1.0 CA A:ILE672 4.3 15.2 1.0 CZ A:ARG653 4.4 25.4 1.0 NH2 A:ARG653 4.4 17.6 1.0 C A:LEU670 4.5 17.5 1.0 OD1 A:ASN671 4.7 23.7 1.0 CB A:ILE672 4.7 16.6 1.0 N A:ASN671 4.8 15.4 1.0 CD1 A:ILE672 5.0 21.6 1.0

Chlorine binding site 3 out of 5 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1124 b:43.9 occ:1.00 N A:SER984 3.5 25.1 1.0 CD A:ARG934 3.7 28.5 1.0 CA A:PRO983 3.7 19.5 1.0 CB A:PRO983 3.8 19.0 1.0 ND2 A:ASN561 3.9 14.2 1.0 N A:ALA985 4.0 67.6 1.0 CG A:ARG934 4.1 20.1 1.0 C A:PRO983 4.1 21.2 1.0 OG A:SER984 4.2 33.1 1.0 CA A:SER984 4.6 38.9 1.0 CB A:ALA985 4.6 74.5 1.0 CA A:ALA985 4.6 74.3 1.0 NE A:ARG934 4.7 29.5 1.0 O A:HOH1562 4.7 32.9 1.0 C A:SER984 4.7 38.9 1.0 NH1 A:ARG934 4.9 28.6 1.0 CG A:ASN561 4.9 12.7 1.0 CB A:SER984 5.0 36.2 1.0

Chlorine binding site 4 out of 5 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1125 b:42.6 occ:1.00 N A:LYS746 3.2 15.8 1.0 CB A:LYS746 3.8 20.1 1.0 OD1 A:ASP745 3.8 17.7 1.0 CA A:LYS746 3.9 16.3 1.0 C A:ASP745 4.1 18.2 1.0 CA A:ASP745 4.2 15.0 1.0 N A:THR747 4.2 12.0 1.0 C A:LYS746 4.2 15.3 1.0 CG A:LYS746 4.4 26.6 1.0 O A:ARG744 4.6 12.6 1.0 CG A:ASP745 4.8 16.8 1.0 OG1 A:THR747 4.9 14.5 1.0

Chlorine binding site 5 out of 5 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1126 b:44.7 occ:1.00 CD A:LYS118 3.7 36.3 1.0 CE2 A:PHE124 3.9 30.7 1.0 NZ A:LYS118 4.0 53.6 1.0 CZ A:PHE124 4.0 22.2 1.0 CE A:LYS118 4.1 46.6 1.0 CD2 A:TYR109 4.3 14.9 1.0 CG1 A:VAL120 4.3 14.2 1.0 CE2 A:TYR109 4.7 14.4 1.0 CD2 A:PHE124 4.8 27.5 1.0 CG A:LYS118 4.9 27.4 1.0

G.Vilela-Alves, R.R.Manuel, A.R.Oliveira, I.C.Pereira, M.J.Romao, C.Mota. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci V. 24 2022.
ISSN: ESSN 1422-0067
PubMed: 36613918
DOI: 10.3390/IJMS24010476