Zinc in PDB 4xd2: Horse Liver Alcohol Dehydrogenase-Nadh Complex

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase-Nadh Complex:
1.1.1.1;

The structure of Horse Liver Alcohol Dehydrogenase-Nadh Complex, PDB code: 4xd2 was solved by B.V.Plapp, S.Baskar Raj, D.J.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.158, 50.911, 92.660, 92.05, 103.05, 109.60
R / Rfree (%)	17.7 / 19.8

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase-Nadh Complex (pdb code 4xd2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase-Nadh Complex, PDB code: 4xd2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.9 occ:0.80 ZN A:ZN401 0.0 13.9 0.8 ZN A:ZN401 1.3 16.4 0.2 O A:HOH920 2.0 17.0 0.8 NE2 A:HIS67 2.1 14.6 1.0 SG A:CYS174 2.3 13.0 1.0 SG A:CYS46 2.3 14.1 1.0 CE1 A:HIS67 3.0 13.2 1.0 CD2 A:HIS67 3.1 13.1 1.0 CB A:CYS46 3.4 15.2 1.0 CB A:CYS174 3.4 12.1 1.0 C5N A:NAI403 3.4 11.7 1.0 C6N A:NAI403 3.8 11.9 1.0 OG A:SER48 3.9 13.6 1.0 C4N A:NAI403 4.0 11.9 1.0 CB A:SER48 4.1 11.2 1.0 ND1 A:HIS67 4.2 11.5 1.0 CG A:HIS67 4.2 11.4 1.0 NH2 A:ARG369 4.6 18.2 1.0 CA A:CYS174 4.7 11.0 1.0 CA A:CYS46 4.8 14.1 1.0 OE2 A:GLU68 4.8 19.1 1.0 N A:SER48 4.8 10.9 1.0 CE2 A:PHE93 4.9 13.7 1.0 N1N A:NAI403 4.9 10.4 1.0

Zinc binding site 2 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.4 occ:0.20 ZN A:ZN401 0.0 16.4 0.2 ZN A:ZN401 1.3 13.9 0.8 SG A:CYS46 2.2 14.1 1.0 NE2 A:HIS67 2.2 14.6 1.0 SG A:CYS174 2.6 13.0 1.0 CB A:CYS46 2.6 15.2 1.0 CB A:CYS174 3.0 12.1 1.0 CE1 A:HIS67 3.0 13.2 1.0 CD2 A:HIS67 3.2 13.1 1.0 O A:HOH920 3.3 17.0 0.8 OE2 A:GLU68 3.7 19.1 1.0 NH2 A:ARG369 3.8 18.2 1.0 CA A:CYS46 4.1 14.1 1.0 ND1 A:HIS67 4.1 11.5 1.0 CD A:GLU68 4.2 15.9 1.0 CG A:HIS67 4.2 11.4 1.0 CB A:GLU68 4.2 12.4 1.0 C5N A:NAI403 4.3 11.7 1.0 CA A:CYS174 4.4 11.0 1.0 N A:GLY175 4.5 10.6 1.0 C6N A:NAI403 4.7 11.9 1.0 CG A:GLU68 4.7 15.4 1.0 OE1 A:GLU68 4.7 19.4 1.0 C A:CYS174 4.7 10.2 1.0 CB A:SER48 4.9 11.2 1.0 N A:CYS46 4.9 16.2 1.0 OG A:SER48 4.9 13.6 1.0 CZ A:ARG369 4.9 15.0 1.0 C A:CYS46 4.9 12.4 1.0

Zinc binding site 3 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:12.9 occ:1.00 SG A:CYS100 2.3 13.4 1.0 SG A:CYS97 2.3 14.8 1.0 SG A:CYS111 2.3 12.4 1.0 SG A:CYS103 2.3 12.6 1.0 CB A:CYS111 3.3 12.1 1.0 CB A:CYS103 3.4 13.1 1.0 CB A:CYS100 3.4 15.3 1.0 CB A:CYS97 3.4 16.9 1.0 N A:CYS97 3.6 12.3 1.0 CA A:CYS111 3.7 10.6 1.0 N A:CYS100 3.9 16.3 1.0 N A:LEU112 3.9 12.4 1.0 CA A:CYS97 4.0 14.5 1.0 N A:GLY98 4.0 13.3 1.0 N A:CYS103 4.2 12.3 1.0 CA A:CYS100 4.2 15.7 1.0 C A:CYS111 4.3 11.7 1.0 C A:CYS97 4.4 14.2 1.0 CA A:CYS103 4.4 12.9 1.0 N A:LYS99 4.5 16.4 1.0 C A:GLN96 4.6 12.0 1.0 N A:LYS113 4.8 12.9 1.0 C A:CYS100 4.9 14.5 1.0 CG A:LYS113 4.9 19.3 1.0 O A:CYS100 4.9 15.1 1.0 CA A:GLN96 5.0 10.0 1.0 O A:HOH708 5.0 38.9 1.0 CA A:GLY98 5.0 14.5 1.0

Zinc binding site 4 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.6 occ:0.80 ZN B:ZN401 0.0 17.6 0.8 ZN B:ZN401 1.4 20.0 0.2 NE2 B:HIS67 2.0 18.4 1.0 O B:HOH862 2.1 22.8 0.8 SG B:CYS174 2.2 16.9 1.0 SG B:CYS46 2.3 17.6 1.0 CE1 B:HIS67 3.0 15.3 1.0 CD2 B:HIS67 3.1 16.8 1.0 CB B:CYS174 3.3 16.1 1.0 CB B:CYS46 3.4 18.5 1.0 C5N B:NAI403 3.5 13.8 1.0 C6N B:NAI403 3.9 15.1 1.0 OG B:SER48 4.0 16.9 1.0 C4N B:NAI403 4.1 14.8 1.0 CB B:SER48 4.1 14.8 1.0 ND1 B:HIS67 4.1 15.9 1.0 CG B:HIS67 4.2 14.8 1.0 NH2 B:ARG369 4.6 23.8 1.0 CA B:CYS174 4.7 13.3 1.0 OE2 B:GLU68 4.8 26.6 1.0 CA B:CYS46 4.8 18.9 1.0 N B:SER48 4.9 14.8 1.0 CE2 B:PHE93 4.9 17.5 1.0 N1N B:NAI403 5.0 14.1 1.0 N B:GLY175 5.0 13.6 1.0 C B:CYS174 5.0 13.6 1.0

Zinc binding site 5 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Horse Liver Alcohol Dehydrogenase-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:20.0 occ:0.20 ZN B:ZN401 0.0 20.0 0.2 ZN B:ZN401 1.4 17.6 0.8 SG B:CYS46 2.2 17.6 1.0 NE2 B:HIS67 2.3 18.4 1.0 SG B:CYS174 2.5 16.9 1.0 CB B:CYS46 2.6 18.5 1.0 CB B:CYS174 2.9 16.1 1.0 CE1 B:HIS67 3.0 15.3 1.0 CD2 B:HIS67 3.2 16.8 1.0 O B:HOH862 3.4 22.8 0.8 OE2 B:GLU68 3.6 26.6 1.0 NH2 B:ARG369 3.8 23.8 1.0 ND1 B:HIS67 4.1 15.9 1.0 CD B:GLU68 4.1 21.5 1.0 CA B:CYS46 4.1 18.9 1.0 CB B:GLU68 4.1 17.1 1.0 CG B:HIS67 4.2 14.8 1.0 CA B:CYS174 4.4 13.3 1.0 C5N B:NAI403 4.4 13.8 1.0 N B:GLY175 4.5 13.6 1.0 CG B:GLU68 4.6 19.6 1.0 OE1 B:GLU68 4.7 24.2 1.0 C B:CYS174 4.7 13.6 1.0 C6N B:NAI403 4.8 15.1 1.0 CZ B:ARG369 4.8 18.9 1.0 N B:CYS46 4.8 18.4 1.0 O B:HOH573 4.9 16.6 1.0 CB B:SER48 4.9 14.8 1.0 OD2 B:ASP49 4.9 18.8 1.0 C B:CYS46 4.9 17.5 1.0

Zinc binding site 6 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Horse Liver Alcohol Dehydrogenase-Nadh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:17.4 occ:1.00 SG B:CYS111 2.3 16.3 1.0 SG B:CYS97 2.3 20.3 1.0 SG B:CYS100 2.3 17.5 1.0 SG B:CYS103 2.4 16.0 1.0 CB B:CYS111 3.3 15.8 1.0 CB B:CYS100 3.4 19.4 1.0 CB B:CYS97 3.4 19.2 1.0 CB B:CYS103 3.4 16.2 1.0 N B:CYS97 3.5 16.9 1.0 CA B:CYS111 3.8 15.4 1.0 CA B:CYS97 3.9 17.6 1.0 N B:LEU112 3.9 16.3 1.0 N B:CYS100 4.0 18.2 1.0 N B:GLY98 4.0 18.4 1.0 N B:CYS103 4.2 15.4 1.0 CA B:CYS100 4.2 21.0 1.0 C B:CYS111 4.3 16.1 1.0 C B:CYS97 4.3 19.4 1.0 CA B:CYS103 4.4 15.8 1.0 N B:LYS99 4.6 19.9 1.0 C B:GLN96 4.6 14.4 1.0 N B:LYS113 4.8 17.0 1.0 C B:CYS100 4.9 18.8 1.0 CG B:LYS113 4.9 25.3 1.0 CA B:GLN96 4.9 14.2 1.0 O B:CYS100 5.0 18.4 1.0

B.V.Plapp, S.Baskar Raj, D.J.Ferraro. Structure of Horse Liver Alcohol Dehydrogenase Complexed with Nadh To Be Published.