Chlorine in PDB 6d4b: Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A Mutant Complexed with Nad+ and Azide

All present enzymatic activity of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A Mutant Complexed with Nad+ and Azide:
1.17.1.9;

The structure of Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A Mutant Complexed with Nad+ and Azide, PDB code: 6d4b 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)	44.94 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.171, 116.098, 63.088, 90.00, 106.84, 90.00
R / Rfree (%)	15.4 / 18

The binding sites of Chlorine atom in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A Mutant Complexed with Nad+ and Azide (pdb code 6d4b). 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 V123A Mutant Complexed with Nad+ and Azide, PDB code: 6d4b:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A 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 V123A Mutant Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:19.3 occ:1.00 HE1 A:HIS232 2.5 11.1 1.0 H62A A:NAD501 2.6 11.6 1.0 O A:HOH1069 2.9 17.5 1.0 HA3 A:GLY234 3.0 10.9 1.0 O A:HOH978 3.3 36.1 1.0 CE1 A:HIS232 3.4 9.2 1.0 N6A A:NAD501 3.4 9.7 1.0 HE2 A:TYR196 3.5 9.0 1.0 HA2 A:GLY359 3.7 11.2 1.0 HD2 A:TYR196 3.8 11.4 1.0 H61A A:NAD501 4.0 11.6 1.0 CA A:GLY234 4.0 9.1 1.0 HE2 A:HIS232 4.0 10.0 1.0 HZ2 A:LYS360 4.0 47.9 1.0 CE2 A:TYR196 4.1 7.5 1.0 NE2 A:HIS232 4.1 8.3 1.0 CD2 A:TYR196 4.2 9.5 1.0 C6A A:NAD501 4.3 7.3 1.0 HZ1 A:LYS360 4.3 47.9 1.0 HA2 A:GLY234 4.3 10.9 1.0 N7A A:NAD501 4.4 7.8 1.0 C A:GLY234 4.4 8.9 1.0 HA3 A:GLY359 4.5 11.2 1.0 HZ3 A:LYS360 4.5 47.9 1.0 O A:GLY234 4.5 10.0 1.0 NZ A:LYS360 4.5 39.9 1.0 ND1 A:HIS232 4.5 8.7 1.0 CA A:GLY359 4.5 9.3 1.0 HG23 A:THR235 4.5 10.1 1.0 O A:HOH679 4.6 23.3 1.0 O A:HOH662 4.6 36.0 1.0 C5A A:NAD501 4.7 7.3 1.0 H A:GLY234 4.7 7.4 1.0 H A:LYS360 4.8 28.3 1.0 O A:HOH1104 4.9 38.3 1.0 N A:GLY234 4.9 6.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Candida Boidinii Formate Dehydrogenase V123A 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 V123A Mutant Complexed with Nad+ and Azide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:23.8 occ:1.00 HE1 B:HIS232 2.5 17.6 1.0 H61A B:NAD501 2.6 16.7 1.0 HA3 B:GLY234 2.9 12.4 1.0 O B:HOH1037 3.0 27.1 1.0 O B:HOH856 3.3 29.4 1.0 HE2 B:TYR196 3.4 13.3 1.0 CE1 B:HIS232 3.4 14.7 1.0 N6A B:NAD501 3.5 13.9 1.0 HD2 B:TYR196 3.6 10.4 1.0 HA2 B:GLY359 3.7 17.4 1.0 CA B:GLY234 3.9 10.3 1.0 HZ1 B:LYS360 3.9 50.5 1.0 CE2 B:TYR196 3.9 11.1 1.0 HZ2 B:LYS360 3.9 50.5 1.0 HE2 B:HIS232 4.0 11.7 1.0 H62A B:NAD501 4.0 16.7 1.0 O B:HOH761 4.0 28.9 1.0 HZ3 B:LYS360 4.0 50.5 1.0 CD2 B:TYR196 4.1 8.6 1.0 NE2 B:HIS232 4.1 9.7 1.0 HA2 B:GLY234 4.2 12.4 1.0 NZ B:LYS360 4.2 42.0 1.0 C6A B:NAD501 4.4 12.0 1.0 C B:GLY234 4.4 14.8 1.0 N7A B:NAD501 4.4 10.5 1.0 O B:GLY234 4.4 15.3 1.0 ND1 B:HIS232 4.5 14.3 1.0 O B:HOH908 4.5 24.6 1.0 HG23 B:THR235 4.5 9.9 1.0 HA3 B:GLY359 4.6 17.4 1.0 CA B:GLY359 4.6 14.4 1.0 H B:GLY234 4.6 12.8 1.0 C5A B:NAD501 4.7 9.8 1.0 O B:HOH975 4.8 23.1 1.0 N B:GLY234 4.8 10.7 1.0 H B:LYS360 5.0 24.9 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