Zinc in PDB 5vj5: Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline:
1.1.1.1;

The structure of Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline, PDB code: 5vj5 was solved by B.V.Plapp, S.Baskar Raj, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.280, 73.410, 180.800, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 29.5

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline (pdb code 5vj5). 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 Complexed with 1,10-Phenanthroline, PDB code: 5vj5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline


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 Complexed with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:29.8 occ:1.00 SG A:CYS174 2.2 26.5 1.0 NE2 A:HIS67 2.3 27.4 1.0 N1 A:PHN403 2.3 25.0 1.0 N10 A:PHN403 2.4 22.8 1.0 SG A:CYS46 2.5 40.3 1.0 C1A A:PHN403 3.1 24.9 1.0 C10 A:PHN403 3.1 23.0 1.0 CE1 A:HIS67 3.2 24.7 1.0 CD2 A:HIS67 3.3 27.1 1.0 C2 A:PHN403 3.3 26.4 1.0 C9 A:PHN403 3.4 22.1 1.0 CB A:CYS174 3.4 31.2 1.0 CB A:CYS46 3.7 34.9 1.0 CB A:SER48 4.2 28.9 1.0 OG A:SER48 4.3 29.8 1.0 ND1 A:HIS67 4.4 23.3 1.0 CG A:HIS67 4.4 24.2 1.0 C4A A:PHN403 4.5 24.2 1.0 C6A A:PHN403 4.5 24.4 1.0 C3 A:PHN403 4.6 23.6 1.0 CE2 A:PHE93 4.7 27.4 1.0 O A:HOH523 4.7 35.6 1.0 CZ A:PHE93 4.7 25.4 1.0 C8 A:PHN403 4.7 22.1 1.0 CA A:CYS174 4.7 29.0 1.0 N A:SER48 4.9 28.1 1.0

Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline


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 Complexed with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:32.3 occ:1.00 SG A:CYS103 2.1 28.1 1.0 SG A:CYS97 2.3 31.9 1.0 SG A:CYS100 2.4 34.1 1.0 SG A:CYS111 2.4 31.4 1.0 CB A:CYS111 3.3 30.8 1.0 CB A:CYS103 3.4 30.7 1.0 CB A:CYS97 3.5 31.9 1.0 CB A:CYS100 3.5 37.7 1.0 N A:CYS97 3.6 32.6 1.0 CA A:CYS111 3.8 26.4 1.0 N A:CYS100 3.8 39.8 1.0 CA A:CYS97 4.0 32.7 1.0 N A:LEU112 4.0 29.6 1.0 N A:GLY98 4.1 36.3 1.0 N A:CYS103 4.2 28.0 1.0 CA A:CYS100 4.2 39.5 1.0 C A:CYS111 4.3 26.5 1.0 CA A:CYS103 4.4 27.6 1.0 C A:CYS97 4.4 34.1 1.0 N A:LYS99 4.4 38.9 1.0 CG A:LYS113 4.4 37.9 1.0 C A:GLN96 4.6 29.1 1.0 N A:LYS113 4.8 28.6 1.0 CA A:GLN96 4.9 32.3 1.0 C A:CYS100 4.9 34.9 1.0 C A:LYS99 5.0 46.3 1.0

Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline


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 Complexed with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:30.9 occ:1.00 SG B:CYS174 2.2 28.6 1.0 N1 B:PHN403 2.2 27.6 1.0 NE2 B:HIS67 2.3 30.2 1.0 SG B:CYS46 2.5 34.6 1.0 N10 B:PHN403 2.5 24.9 1.0 C1A B:PHN403 3.0 25.4 1.0 C10 B:PHN403 3.1 25.5 1.0 CD2 B:HIS67 3.2 29.1 1.0 C2 B:PHN403 3.2 26.7 1.0 CE1 B:HIS67 3.4 29.6 1.0 CB B:CYS174 3.4 29.1 1.0 C9 B:PHN403 3.5 27.3 1.0 CB B:CYS46 3.7 33.1 1.0 CB B:SER48 4.3 25.6 1.0 OG B:SER48 4.4 26.2 1.0 CG B:HIS67 4.4 26.9 1.0 ND1 B:HIS67 4.4 29.3 1.0 C4A B:PHN403 4.4 25.5 1.0 CE2 B:PHE93 4.5 24.8 1.0 C3 B:PHN403 4.5 24.0 1.0 C6A B:PHN403 4.6 25.7 1.0 CZ B:PHE93 4.6 22.4 1.0 CA B:CYS174 4.7 27.4 1.0 C8 B:PHN403 4.8 26.4 1.0 O B:HOH598 4.9 42.0 1.0 N B:SER48 5.0 29.0 1.0 C B:CYS174 5.0 29.1 1.0

Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase Complexed with 1,10-Phenanthroline


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 Complexed with 1,10-Phenanthroline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:33.5 occ:1.00 SG B:CYS103 2.0 29.3 1.0 SG B:CYS97 2.3 36.0 1.0 SG B:CYS100 2.4 37.1 1.0 SG B:CYS111 2.5 33.1 1.0 CB B:CYS103 3.3 33.7 1.0 CB B:CYS111 3.4 30.8 1.0 CB B:CYS100 3.5 37.7 1.0 CB B:CYS97 3.5 32.4 1.0 N B:CYS97 3.7 28.9 1.0 CA B:CYS111 3.8 29.4 1.0 N B:CYS100 3.8 40.2 1.0 N B:LEU112 4.0 28.6 1.0 N B:GLY98 4.0 34.6 1.0 CA B:CYS97 4.0 32.3 1.0 N B:CYS103 4.1 30.2 1.0 CA B:CYS100 4.2 39.4 1.0 C B:CYS111 4.3 29.9 1.0 CA B:CYS103 4.3 29.4 1.0 N B:LYS99 4.3 39.2 1.0 C B:CYS97 4.4 36.8 1.0 C B:GLN96 4.6 30.2 1.0 CG B:LYS113 4.7 39.5 1.0 N B:LYS113 4.8 29.4 1.0 C B:CYS100 4.8 32.5 1.0 C B:LYS99 4.9 49.9 1.0 O B:CYS100 4.9 25.5 1.0 CA B:GLY98 4.9 35.3 1.0 CA B:GLN96 5.0 33.5 1.0

B.V.Plapp, B.R.Savarimuthu, D.J.Ferraro, J.K.Rubach, E.N.Brown, S.Ramaswamy. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry V. 56 3632 2017.
ISSN: ISSN 1520-4995
PubMed: 28640600
DOI: 10.1021/ACS.BIOCHEM.7B00446