Zinc in PDB 1het: Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh

All present enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh:
1.1.1.1;

The structure of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh, PDB code: 1het was solved by R.Meijers, R.J.Morris, H.W.Adolph, A.Merli, V.S.Lamzin, E.S.Cedergen-Zeppezauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.100, 44.400, 94.000, 104.60, 101.50, 70.50
R / Rfree (%)	11.8 / 13.5

The binding sites of Zinc atom in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh (pdb code 1het). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh, PDB code: 1het:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:8.9 occ:1.00 NE2 A:HIS67 2.1 8.9 1.0 O A:HOH2741 2.1 7.8 0.4 SG A:CYS174 2.3 7.5 1.0 O A:HOH2740 2.3 9.7 0.6 SG A:CYS46 2.3 7.7 1.0 CE1 A:HIS67 3.1 7.8 1.0 CD2 A:HIS67 3.1 9.5 1.0 CB A:CYS46 3.3 8.9 1.0 CB A:CYS174 3.3 7.5 1.0 C5N A:NAD402 3.6 9.3 1.0 C6N A:NAD402 3.8 10.8 1.0 C4N A:NAD402 4.1 9.1 1.0 OG A:SER48 4.2 9.0 1.0 ND1 A:HIS67 4.2 8.4 1.0 CB A:SER48 4.2 8.2 1.0 CG A:HIS67 4.3 8.2 1.0 C1 A:MRD403 4.3 18.4 0.5 C1 A:MRD403 4.3 18.2 0.5 NH2 A:ARG369 4.4 9.7 1.0 OE2 A:GLU68 4.6 9.9 1.0 CA A:CYS174 4.7 7.2 1.0 CA A:CYS46 4.8 8.6 1.0 N A:SER48 4.9 7.8 1.0 N1N A:NAD402 4.9 9.0 1.0 N A:GLY175 4.9 7.4 1.0 CE2 A:PHE93 5.0 9.1 1.0

Zinc binding site 2 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:7.8 occ:1.00 SG A:CYS97 2.4 11.1 1.0 SG A:CYS100 2.4 10.4 1.0 SG A:CYS111 2.4 8.9 1.0 SG A:CYS103 2.4 9.6 1.0 CB A:CYS111 3.4 9.3 1.0 CB A:CYS97 3.5 12.1 1.0 CB A:CYS100 3.5 12.4 1.0 CB A:CYS103 3.5 11.4 1.0 N A:CYS97 3.6 9.5 1.0 CA A:CYS111 3.8 8.9 1.0 N A:CYS100 3.9 13.8 1.0 CA A:CYS97 3.9 11.1 1.0 N A:GLY98 4.0 11.3 1.0 N A:LEU112 4.0 9.8 1.0 CA A:CYS100 4.2 13.1 1.0 N A:CYS103 4.3 10.2 1.0 C A:CYS97 4.3 11.4 1.0 C A:CYS111 4.3 9.3 1.0 CA A:CYS103 4.5 11.0 1.0 N A:LYS99 4.5 14.7 1.0 C A:GLN96 4.7 9.6 1.0 CG A:LYS113 4.7 10.9 0.6 N A:LYS113 4.9 9.9 1.0 C A:CYS100 4.9 12.6 1.0 CA A:GLY98 5.0 13.9 1.0 O A:CYS100 5.0 12.9 1.0 CA A:GLN96 5.0 9.3 1.0

Zinc binding site 3 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:12.0 occ:1.00 NE2 B:HIS67 2.1 12.5 1.0 O B:HOH2672 2.1 10.5 0.4 SG B:CYS174 2.3 10.4 1.0 SG B:CYS46 2.3 10.7 1.0 O B:HOH2673 2.3 12.6 0.6 CE1 B:HIS67 3.1 11.8 1.0 CD2 B:HIS67 3.1 12.8 1.0 CB B:CYS46 3.3 11.2 1.0 CB B:CYS174 3.4 10.1 1.0 C5N B:NAD402 3.6 11.1 1.0 C6N B:NAD402 3.8 13.3 1.0 C4N B:NAD402 4.1 11.2 1.0 OG B:SER48 4.2 11.6 1.0 ND1 B:HIS67 4.2 11.6 1.0 CB B:SER48 4.2 10.5 1.0 CG B:HIS67 4.3 11.7 1.0 NH2 B:ARG369 4.3 12.1 1.0 C1 B:MRD403 4.4 17.1 0.5 OE2 B:GLU68 4.7 13.9 1.0 CA B:CYS174 4.7 10.2 1.0 CA B:CYS46 4.8 11.1 1.0 C1 B:MRD403 4.8 26.2 0.5 N B:SER48 4.9 10.7 1.0 N1N B:NAD402 4.9 11.4 1.0 C B:CYS174 5.0 9.8 1.0 CE2 B:PHE93 5.0 11.9 1.0

Zinc binding site 4 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.5 occ:1.00 SG B:CYS100 2.4 14.5 1.0 SG B:CYS103 2.4 13.1 1.0 SG B:CYS111 2.4 13.0 1.0 SG B:CYS97 2.5 17.7 1.0 CB B:CYS111 3.4 12.0 1.0 CB B:CYS100 3.4 17.3 1.0 CB B:CYS103 3.5 13.8 1.0 CB B:CYS97 3.5 18.0 1.0 N B:CYS97 3.6 14.9 1.0 CA B:CYS111 3.8 11.9 1.0 N B:CYS100 3.9 17.9 1.0 CA B:CYS97 4.0 16.3 1.0 N B:GLY98 4.0 17.1 1.0 N B:LEU112 4.0 13.6 1.0 CA B:CYS100 4.2 16.7 1.0 N B:CYS103 4.3 12.5 1.0 C B:CYS111 4.4 12.8 1.0 C B:CYS97 4.4 17.2 1.0 CA B:CYS103 4.4 12.9 1.0 N B:LYS99 4.6 17.8 1.0 C B:GLN96 4.6 14.3 1.0 CG B:LYS113 4.7 19.0 0.5 NZ B:LYS113 4.8 28.2 0.5 C B:CYS100 4.9 15.4 1.0 N B:LYS113 4.9 14.0 1.0 CA B:GLN96 5.0 12.9 1.0 O B:CYS100 5.0 15.5 1.0

R.Meijers, R.J.Morris, H.W.Adolph, A.Merli, V.S.Lamzin, E.S.Cedergen-Zeppezauer. On the Enzymatic Activation of Nadh J.Biol.Chem. V. 276 9316 2001.
ISSN: ISSN 0021-9258
PubMed: 11134046
DOI: 10.1074/JBC.M010870200