Zinc in PDB 7ude: Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K:
1.1.1.1;

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude was solved by B.V.Plapp, L.Gakhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.28, 51.18, 92.59, 91.9, 103.02, 109.89
R / Rfree (%)	13.3 / 16

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K (pdb code 7ude). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:10.4 occ:1.00 O A:ETF404 1.9 10.4 1.0 NE2 A:HIS67 2.0 10.2 1.0 SG A:CYS174 2.3 10.1 1.0 SG A:CYS46 2.3 9.8 1.0 C2 A:ETF404 2.9 11.9 1.0 CE1 A:HIS67 3.0 9.2 1.0 CD2 A:HIS67 3.1 9.9 1.0 CB A:CYS46 3.3 9.8 1.0 C5N A:NAJ403 3.3 9.2 1.0 CB A:CYS174 3.4 9.5 1.0 OG A:SER48 3.7 9.8 1.0 C4N A:NAJ403 4.0 9.3 1.0 C6N A:NAJ403 4.0 9.0 1.0 CB A:SER48 4.0 8.9 1.0 ND1 A:HIS67 4.2 9.2 1.0 CG A:HIS67 4.2 8.8 1.0 C1 A:ETF404 4.2 14.2 1.0 F3 A:ETF404 4.6 17.0 1.0 NH2 A:ARG369 4.6 10.6 1.0 CA A:CYS174 4.7 8.9 1.0 CA A:CYS46 4.8 10.0 1.0 F1 A:ETF404 4.8 17.1 1.0 OE2 A:GLU68 4.8 11.8 1.0 N A:SER48 4.8 8.9 1.0 CE2 A:PHE93 4.9 10.4 1.0 N1N A:NAJ403 5.0 8.3 1.0

Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.3 occ:1.00 SG A:CYS111 2.3 11.0 1.0 SG A:CYS97 2.3 13.3 1.0 SG A:CYS100 2.3 11.9 1.0 SG A:CYS103 2.4 11.1 1.0 CB A:CYS111 3.3 10.6 1.0 CB A:CYS97 3.4 13.0 1.0 CB A:CYS100 3.4 13.5 1.0 CB A:CYS103 3.4 11.4 1.0 N A:CYS97 3.5 10.9 1.0 CA A:CYS111 3.7 10.4 1.0 N A:CYS100 3.9 14.5 1.0 CA A:CYS97 3.9 11.9 1.0 N A:GLY98 4.0 12.8 1.0 N A:LEU112 4.0 10.6 1.0 N A:CYS103 4.2 10.8 1.0 CA A:CYS100 4.2 14.4 1.0 C A:CYS97 4.3 12.8 1.0 C A:CYS111 4.3 10.8 1.0 CA A:CYS103 4.4 10.8 1.0 N A:LYS99 4.5 14.9 1.0 C A:GLN96 4.6 10.7 1.0 C A:CYS100 4.9 13.2 1.0 N A:LYS113 4.9 11.2 1.0 CG A:LYS113 4.9 16.3 1.0 O A:CYS100 4.9 12.4 1.0 CA A:GLN96 4.9 10.4 1.0 O A:HOH886 4.9 32.0 1.0

Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:13.2 occ:1.00 O B:ETF404 2.0 13.4 1.0 NE2 B:HIS67 2.0 13.1 1.0 SG B:CYS174 2.3 12.8 1.0 SG B:CYS46 2.3 12.8 1.0 C2 B:ETF404 2.9 14.5 1.0 CE1 B:HIS67 3.0 12.0 1.0 CD2 B:HIS67 3.1 13.0 1.0 CB B:CYS46 3.3 13.0 1.0 C5N B:NAJ403 3.4 11.0 1.0 CB B:CYS174 3.4 11.8 1.0 OG B:SER48 3.8 12.1 1.0 C4N B:NAJ403 3.9 11.8 1.0 C6N B:NAJ403 4.0 10.5 1.0 CB B:SER48 4.0 11.2 1.0 ND1 B:HIS67 4.2 12.6 1.0 CG B:HIS67 4.2 11.9 1.0 C1 B:ETF404 4.3 17.4 1.0 F3 B:ETF404 4.6 19.8 1.0 NH2 B:ARG369 4.6 13.8 1.0 CA B:CYS174 4.7 11.4 1.0 CA B:CYS46 4.8 12.8 1.0 F1 B:ETF404 4.8 21.4 1.0 N B:SER48 4.9 11.5 1.0 OE2 B:GLU68 4.9 14.3 1.0 CE2 B:PHE93 4.9 12.2 1.0 N1N B:NAJ403 5.0 10.7 1.0

Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.1 occ:1.00 SG B:CYS111 2.3 13.7 1.0 SG B:CYS97 2.3 17.1 1.0 SG B:CYS100 2.3 14.9 1.0 SG B:CYS103 2.4 13.0 1.0 CB B:CYS111 3.3 13.1 1.0 CB B:CYS100 3.4 17.0 1.0 CB B:CYS103 3.4 14.1 1.0 CB B:CYS97 3.4 17.4 1.0 N B:CYS97 3.5 14.5 1.0 CA B:CYS111 3.7 12.1 1.0 N B:CYS100 3.9 16.5 1.0 CA B:CYS97 3.9 15.9 1.0 N B:LEU112 4.0 13.7 1.0 N B:GLY98 4.0 16.5 1.0 CA B:CYS100 4.2 17.0 1.0 N B:CYS103 4.2 12.8 1.0 C B:CYS111 4.3 12.5 1.0 C B:CYS97 4.3 17.3 1.0 CA B:CYS103 4.4 12.8 1.0 N B:LYS99 4.5 17.5 1.0 C B:GLN96 4.6 13.2 1.0 C B:CYS100 4.8 15.1 1.0 N B:LYS113 4.9 13.6 1.0 CG B:LYS113 4.9 18.7 1.0 O B:CYS100 4.9 15.5 1.0 CA B:GLN96 4.9 12.5 1.0

B.V.Plapp, L.Gakhar, R.Subramanian. Dependence of Crystallographic Atomic Displacement Factors on Temperature (25-150 K) For Complexes of Horse Liver Alcohol Dehydrogenases Acta Crystallogr.,Sect.D V. D78 1221 2022.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322008361