Zinc in PDB 5cdu: I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole

All present enzymatic activity of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole:
1.1.1.1;

The structure of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole, PDB code: 5cdu was solved by B.V.Plapp, K.Shanmuganatham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.230, 51.260, 92.410, 91.88, 103.12, 109.95
R / Rfree (%)	16.1 / 20.1

The binding sites of Zinc atom in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole (pdb code 5cdu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole, PDB code: 5cdu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.0 occ:1.00 N1 A:PZO404 2.1 16.9 1.0 NE2 A:HIS67 2.1 15.2 1.0 SG A:CYS174 2.3 17.4 1.0 SG A:CYS46 2.3 18.8 1.0 N2 A:PZO404 3.1 19.8 1.0 CD2 A:HIS67 3.1 16.2 1.0 CE1 A:HIS67 3.1 15.0 1.0 C5 A:PZO404 3.1 19.5 1.0 C5N A:NAJ403 3.2 15.1 1.0 CB A:CYS46 3.3 17.3 1.0 CB A:CYS174 3.3 15.5 1.0 C4N A:NAJ403 3.7 14.8 1.0 C6N A:NAJ403 4.0 14.0 1.0 OG A:SER48 4.1 16.8 1.0 CB A:SER48 4.1 17.2 1.0 ND1 A:HIS67 4.2 16.1 1.0 CG A:HIS67 4.2 16.7 1.0 C3 A:PZO404 4.3 18.9 1.0 C4 A:PZO404 4.3 19.4 1.0 NH2 A:ARG369 4.5 21.7 1.0 CE2 A:PHE93 4.6 15.4 1.0 CA A:CYS174 4.7 15.2 1.0 CA A:CYS46 4.8 15.8 1.0 OE2 A:GLU68 4.8 20.0 1.0 CZ A:PHE93 4.9 14.7 1.0 N A:SER48 5.0 17.0 1.0

Zinc binding site 2 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.5 occ:1.00 SG A:CYS97 2.3 19.2 1.0 SG A:CYS100 2.3 18.2 1.0 SG A:CYS103 2.4 17.3 1.0 SG A:CYS111 2.4 17.4 1.0 CB A:CYS111 3.3 16.6 1.0 CB A:CYS103 3.3 18.2 1.0 CB A:CYS97 3.4 20.4 1.0 CB A:CYS100 3.4 19.3 1.0 N A:CYS97 3.5 17.6 1.0 CA A:CYS111 3.8 15.2 1.0 N A:CYS100 3.9 20.1 1.0 CA A:CYS97 3.9 19.8 1.0 N A:GLY98 3.9 19.3 1.0 N A:LEU112 4.0 17.0 1.0 CA A:CYS100 4.2 19.7 1.0 N A:CYS103 4.2 18.4 1.0 C A:CYS111 4.3 17.2 1.0 C A:CYS97 4.3 21.2 1.0 CA A:CYS103 4.3 18.1 1.0 N A:LYS99 4.4 21.7 1.0 C A:GLN96 4.6 16.6 1.0 N A:LYS113 4.8 16.7 1.0 C A:CYS100 4.8 19.8 1.0 CG A:LYS113 4.9 24.6 1.0 O A:CYS100 4.9 20.1 1.0 CA A:GLN96 4.9 17.1 1.0 CA A:GLY98 5.0 20.6 1.0

Zinc binding site 3 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:19.9 occ:1.00 NE2 B:HIS67 2.1 17.0 1.0 N1 B:PZO404 2.1 19.0 1.0 SG B:CYS174 2.3 20.9 1.0 SG B:CYS46 2.3 19.6 1.0 CD2 B:HIS67 3.0 18.6 1.0 C5 B:PZO404 3.1 20.1 1.0 CE1 B:HIS67 3.1 19.5 1.0 N2 B:PZO404 3.1 22.6 1.0 C5N B:NAJ403 3.2 16.9 1.0 CB B:CYS46 3.3 21.8 1.0 CB B:CYS174 3.3 17.3 1.0 C4N B:NAJ403 3.7 17.7 1.0 C6N B:NAJ403 4.0 16.1 1.0 OG B:SER48 4.1 19.2 1.0 CB B:SER48 4.1 18.9 1.0 ND1 B:HIS67 4.2 18.8 1.0 CG B:HIS67 4.2 19.4 1.0 C4 B:PZO404 4.3 21.4 1.0 C3 B:PZO404 4.3 21.5 1.0 NH2 B:ARG369 4.4 26.6 1.0 CE2 B:PHE93 4.6 18.3 1.0 CA B:CYS174 4.7 17.0 1.0 CA B:CYS46 4.8 20.6 1.0 OE2 B:GLU68 4.9 21.7 1.0 CZ B:PHE93 4.9 18.8 1.0 N B:SER48 4.9 17.5 1.0

Zinc binding site 4 out of 4 in the I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of I220V Horse Liver Alcohol Dehydrogenase Complexed with Nad and Pyrazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.0 occ:1.00 SG B:CYS103 2.3 18.6 1.0 SG B:CYS111 2.3 18.9 1.0 SG B:CYS100 2.3 20.1 1.0 SG B:CYS97 2.4 22.3 1.0 CB B:CYS111 3.3 19.9 1.0 CB B:CYS103 3.3 19.0 1.0 CB B:CYS100 3.4 23.0 1.0 CB B:CYS97 3.4 19.1 1.0 N B:CYS97 3.5 20.1 1.0 CA B:CYS111 3.7 18.1 1.0 N B:GLY98 3.8 23.6 1.0 N B:CYS100 3.8 22.8 1.0 CA B:CYS97 3.9 21.1 1.0 N B:LEU112 3.9 20.6 1.0 N B:CYS103 4.1 17.6 1.0 CA B:CYS100 4.2 22.8 1.0 C B:CYS97 4.3 22.9 1.0 C B:CYS111 4.3 18.8 1.0 CA B:CYS103 4.3 18.3 1.0 N B:LYS99 4.5 23.2 1.0 C B:GLN96 4.6 17.2 1.0 CA B:GLY98 4.8 22.6 1.0 CG B:LYS113 4.8 24.5 1.0 N B:LYS113 4.8 19.4 1.0 C B:CYS100 4.9 23.0 1.0 CA B:GLN96 4.9 16.5 1.0 O B:HOH777 4.9 33.2 1.0 O B:CYS100 5.0 21.7 1.0 C B:LYS99 5.0 28.5 1.0

K.K.Shanmuganatham, R.S.Wallace, A.T.Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. 2017.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370