Chlorine in PDB 6d4c: Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide

All present enzymatic activity of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide:
1.17.1.9;

The structure of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide, PDB code: 6d4c was solved by Q.Guo, H.Ye, L.Gakhar, C.M.Cheatum, A.Kohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.99 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.188, 115.899, 65.469, 90.00, 108.56, 90.00
R / Rfree (%)	15.9 / 18.5

The binding sites of Chlorine atom in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide (pdb code 6d4c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide, PDB code: 6d4c:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:27.4 occ:1.00 HE1 A:HIS232 2.6 14.3 1.0 H62A A:NAD501 2.6 14.4 1.0 O A:HOH1066 2.9 38.3 1.0 O A:HOH993 2.9 24.6 1.0 HA3 A:GLY234 3.1 15.6 1.0 HE2 A:TYR196 3.4 15.4 1.0 N6A A:NAD501 3.4 12.0 1.0 CE1 A:HIS232 3.5 11.9 1.0 HA2 A:GLY359 3.7 18.1 1.0 HD2 A:TYR196 3.7 14.0 1.0 H61A A:NAD501 3.9 14.4 1.0 CE2 A:TYR196 4.0 12.9 1.0 CA A:GLY234 4.1 13.0 1.0 HE2 A:HIS232 4.1 14.1 1.0 O A:HOH759 4.1 38.1 1.0 CD2 A:TYR196 4.2 11.7 1.0 NE2 A:HIS232 4.2 11.7 1.0 C6A A:NAD501 4.3 10.8 1.0 HA3 A:GLY359 4.3 18.1 1.0 N7A A:NAD501 4.4 10.3 1.0 HA2 A:GLY234 4.4 15.6 1.0 CA A:GLY359 4.4 15.1 1.0 C A:GLY234 4.5 13.4 1.0 O A:GLY234 4.5 14.5 1.0 ND1 A:HIS232 4.6 11.3 1.0 HG23 A:THR235 4.6 12.8 1.0 C5A A:NAD501 4.6 10.0 1.0 O A:HOH708 4.7 26.5 1.0 H A:GLY234 4.7 12.7 1.0 H A:LYS360 4.8 29.6 1.0 O A:HOH933 4.9 21.9 1.0 N A:GLY234 5.0 10.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123G Mutant Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:28.6 occ:1.00 HE1 B:HIS232 2.6 20.1 1.0 H61A B:NAD501 2.7 24.6 1.0 O B:HOH990 3.0 27.9 1.0 HA3 B:GLY234 3.1 16.8 1.0 HE2 B:TYR196 3.3 17.5 1.0 CE1 B:HIS232 3.5 16.7 1.0 HD2 B:TYR196 3.5 17.2 1.0 N6A B:NAD501 3.5 20.5 1.0 HA2 B:GLY359 3.7 25.4 1.0 CE2 B:TYR196 3.9 14.6 1.0 CD2 B:TYR196 4.0 14.3 1.0 CA B:GLY234 4.0 14.0 1.0 H62A B:NAD501 4.0 24.6 1.0 HE2 B:HIS232 4.1 17.6 1.0 NE2 B:HIS232 4.2 14.7 1.0 HA2 B:GLY234 4.3 16.8 1.0 C6A B:NAD501 4.4 17.0 1.0 N7A B:NAD501 4.4 15.3 1.0 O B:HOH932 4.5 29.7 1.0 C B:GLY234 4.5 18.4 1.0 O B:HOH629 4.5 34.8 1.0 ND1 B:HIS232 4.5 17.6 1.0 CA B:GLY359 4.5 21.1 1.0 HA3 B:GLY359 4.5 25.4 1.0 O B:GLY234 4.6 19.1 1.0 HG23 B:THR235 4.6 14.9 1.0 C5A B:NAD501 4.7 13.8 1.0 H B:GLY234 4.8 15.5 1.0 O B:HOH950 4.8 23.8 1.0 HG2 B:LYS360 4.8 52.3 1.0 O B:HOH1011 4.9 34.7 1.0 H B:LYS360 4.9 39.5 1.0 N B:GLY234 5.0 12.9 1.0

P.L.Pagano, Q.Guo, C.Ranasinghe, E.Schroeder, K.Robben, F.Hase, H.Ye, K.Wickersham, A.Aspuru-Guzik, D.T.Major, L.Gakhar, A.Kohen, C.M.Cheatum. Oscillatory Active-Site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B03345