Zinc in PDB 7rm6: Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide:
1.1.1.1;

The structure of Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide, PDB code: 7rm6 was solved by C.Zheng, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.94 / 1.43
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.142, 50.979, 92.864, 92.41, 103.03, 108.94
R / Rfree (%)	19 / 20.8

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide (pdb code 7rm6). 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 in Complex with Nadh and N- Cylcohexyl Formamide, PDB code: 7rm6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.3 occ:1.00 NE2 A:HIS67 2.2 19.8 1.0 O9 A:CXF404 2.2 20.4 1.0 SG A:CYS46 2.2 19.9 1.0 SG A:CYS174 2.3 19.3 1.0 C7 A:CXF404 2.8 20.6 1.0 CD2 A:HIS67 3.1 20.4 1.0 CE1 A:HIS67 3.2 17.5 1.0 CB A:CYS46 3.3 19.1 1.0 CB A:CYS174 3.3 17.2 1.0 C5N A:NAI403 3.4 17.8 1.0 OG A:SER48 3.9 18.5 1.0 CB A:SER48 4.0 17.5 1.0 C6N A:NAI403 4.1 17.3 1.0 C4N A:NAI403 4.2 17.9 1.0 N8 A:CXF404 4.2 23.5 1.0 ND1 A:HIS67 4.3 21.3 1.0 CG A:HIS67 4.3 18.2 1.0 NH2 A:ARG369 4.6 21.6 1.0 CA A:CYS174 4.7 16.8 1.0 CA A:CYS46 4.7 17.9 1.0 N A:GLY175 4.9 21.1 1.0 N A:SER48 4.9 19.5 1.0 OE2 A:GLU68 4.9 20.5 1.0

Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.7 occ:1.00 SG A:CYS111 2.3 21.0 1.0 SG A:CYS100 2.3 23.2 1.0 SG A:CYS103 2.3 23.0 1.0 SG A:CYS97 2.3 24.9 1.0 CB A:CYS111 3.3 20.8 1.0 CB A:CYS97 3.4 22.8 1.0 CB A:CYS100 3.4 26.8 1.0 CB A:CYS103 3.4 27.0 1.0 N A:CYS97 3.6 21.4 1.0 CA A:CYS111 3.7 19.5 1.0 N A:CYS100 3.9 24.9 1.0 CA A:CYS97 3.9 24.9 1.0 N A:GLY98 4.0 24.9 1.0 N A:LEU112 4.0 21.7 1.0 CA A:CYS100 4.2 26.0 1.0 N A:CYS103 4.3 23.3 1.0 C A:CYS111 4.3 20.5 1.0 C A:CYS97 4.3 26.5 1.0 CA A:CYS103 4.4 25.9 1.0 N A:LYS99 4.6 29.1 1.0 C A:GLN96 4.7 23.9 1.0 CG A:LYS113 4.8 27.4 1.0 C A:CYS100 4.8 25.1 1.0 N A:LYS113 4.9 22.5 1.0 O A:CYS100 4.9 25.8 1.0 CA A:GLY98 5.0 27.9 1.0 CA A:GLN96 5.0 22.6 1.0 C A:LYS99 5.0 27.9 1.0

Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.1 occ:1.00 NE2 B:HIS67 2.2 23.2 1.0 O9 B:CXF404 2.2 23.9 1.0 SG B:CYS174 2.3 22.6 1.0 SG B:CYS46 2.3 23.9 1.0 C7 B:CXF404 2.9 22.8 1.0 CD2 B:HIS67 3.1 22.5 1.0 CE1 B:HIS67 3.2 24.6 1.0 CB B:CYS46 3.3 20.1 1.0 CB B:CYS174 3.3 20.5 1.0 C5N B:NAI403 3.6 21.5 1.0 CB B:SER48 3.9 25.1 1.0 OG B:SER48 4.0 22.4 1.0 C4N B:NAI403 4.1 21.7 1.0 C6N B:NAI403 4.1 21.5 1.0 N8 B:CXF404 4.2 24.6 1.0 ND1 B:HIS67 4.2 25.7 1.0 CG B:HIS67 4.3 22.4 1.0 NH2 B:ARG369 4.5 23.7 1.0 CA B:CYS174 4.7 22.4 1.0 CA B:CYS46 4.7 21.4 1.0 N B:GLY175 4.9 22.1 1.0 N B:SER48 4.9 23.1 1.0 CE2 B:PHE93 4.9 25.4 1.0 OE2 B:GLU68 5.0 22.6 1.0

Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cylcohexyl Formamide


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 in Complex with Nadh and N- Cylcohexyl Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:25.1 occ:1.00 SG B:CYS103 2.3 23.5 1.0 SG B:CYS111 2.3 24.4 1.0 SG B:CYS97 2.3 27.2 1.0 SG B:CYS100 2.4 27.4 1.0 CB B:CYS111 3.2 23.0 1.0 CB B:CYS103 3.4 23.5 1.0 CB B:CYS100 3.4 25.7 1.0 CB B:CYS97 3.5 24.2 1.0 N B:CYS97 3.6 24.6 1.0 CA B:CYS111 3.8 22.4 1.0 N B:CYS100 3.9 27.7 1.0 N B:GLY98 3.9 26.1 1.0 CA B:CYS97 3.9 28.5 1.0 N B:LEU112 4.0 23.5 1.0 CA B:CYS100 4.2 29.1 1.0 N B:CYS103 4.3 23.6 1.0 C B:CYS111 4.3 23.3 1.0 CA B:CYS103 4.4 25.2 1.0 C B:CYS97 4.4 23.5 1.0 N B:LYS99 4.5 28.0 1.0 C B:GLN96 4.6 25.0 1.0 C B:CYS100 4.8 27.1 1.0 CA B:GLY98 4.9 27.1 1.0 O B:CYS100 4.9 27.1 1.0 N B:LYS113 4.9 25.1 1.0 CA B:GLN96 4.9 22.6 1.0 CG B:LYS113 5.0 31.7 1.0

C.Zheng, Y.Mao, J.Kozuch, A.O.Atsango, Z.Ji, T.E.Markland, S.G.Boxer. A Two-Directional Vibrational Probe Reveals Different Electric Field Orientations in Solution and An Enzyme Active Site. Nat.Chem. V. 14 891 2022.
ISSN: ESSN 1755-4349
PubMed: 35513508
DOI: 10.1038/S41557-022-00937-W