Cadmium in PDB 2jhf: Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase

All present enzymatic activity of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase:
1.1.1.1;

The structure of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase, PDB code: 2jhf was solved by R.Meijers, H.W.Adolph, Z.Dauter, K.S.Wilson, V.S.Lamzin, E.S.Cedergren-Zeppezauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.870, 44.460, 94.180, 104.40, 101.40, 71.10
R / Rfree (%)	12.5 / 15.2

The binding sites of Cadmium atom in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase (pdb code 2jhf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase, PDB code: 2jhf:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:7.3 occ:0.95 NE2 A:HIS67 2.3 9.9 1.0 O A:HOH2648 2.4 8.8 0.5 SG A:CYS46 2.4 9.5 1.0 SG A:CYS174 2.4 9.7 1.0 O A:DMS404 2.5 10.3 0.5 CE1 A:HIS67 3.2 9.5 1.0 CD2 A:HIS67 3.3 9.8 1.0 CB A:CYS46 3.3 9.8 1.0 CB A:CYS174 3.4 10.0 1.0 C5N A:NAD403 3.5 9.7 1.0 S A:DMS404 3.6 9.8 0.5 C6N A:NAD403 3.8 10.2 1.0 C4N A:NAD403 4.1 10.3 1.0 C2 A:DMS404 4.1 9.5 0.5 OG A:SER48 4.2 9.1 1.0 CB A:SER48 4.3 8.5 1.0 OE1 A:GLU68 4.3 11.6 1.0 ND1 A:HIS67 4.4 9.1 1.0 NH2 A:ARG369 4.4 10.5 1.0 CG A:HIS67 4.5 8.8 1.0 CA A:CYS174 4.7 9.6 1.0 C2 A:DMS404 4.7 13.6 0.5 N A:GLY175 4.8 9.2 1.0 CA A:CYS46 4.9 9.2 1.0 N1N A:NAD403 4.9 8.9 1.0 C A:CYS174 4.9 9.1 1.0 N A:SER48 4.9 8.4 1.0

Cadmium binding site 2 out of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:9.7 occ:0.95 SG A:CYS97 2.5 11.7 1.0 SG A:CYS100 2.5 10.7 1.0 SG A:CYS111 2.6 9.8 1.0 SG A:CYS103 2.6 10.2 1.0 CB A:CYS111 3.5 10.1 1.0 CB A:CYS97 3.5 11.8 1.0 CB A:CYS100 3.6 12.6 1.0 CB A:CYS103 3.6 11.6 1.0 N A:CYS97 3.6 10.2 1.0 CA A:CYS111 3.9 9.6 1.0 N A:CYS100 3.9 13.0 1.0 CA A:CYS97 4.0 10.8 1.0 N A:GLY98 4.0 12.1 1.0 N A:LEU112 4.1 10.3 1.0 CA A:CYS100 4.3 12.3 1.0 N A:CYS103 4.3 10.4 1.0 C A:CYS97 4.4 12.0 1.0 C A:CYS111 4.4 9.8 1.0 CA A:CYS103 4.5 10.4 1.0 N A:LYS99 4.5 14.9 1.0 C A:GLN96 4.7 10.3 1.0 CG A:LYS113 4.8 13.2 1.0 N A:LYS113 4.9 9.8 1.0 C A:CYS100 4.9 12.6 1.0 CA A:GLY98 5.0 14.3 1.0 O A:CYS100 5.0 12.3 1.0

Cadmium binding site 3 out of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd401 b:8.3 occ:0.95 NE2 B:HIS67 2.4 12.1 1.0 SG B:CYS46 2.4 11.6 1.0 O B:HOH2593 2.4 9.6 0.5 SG B:CYS174 2.4 11.1 1.0 O B:DMS404 2.5 13.6 0.5 CE1 B:HIS67 3.3 10.9 1.0 C5N B:NAD403 3.3 11.8 1.0 CB B:CYS46 3.4 12.2 1.0 CD2 B:HIS67 3.4 12.2 1.0 CB B:CYS174 3.4 11.6 1.0 C6N B:NAD403 3.6 10.6 1.0 S B:DMS404 3.7 14.3 0.5 C4N B:NAD403 4.0 9.6 1.0 C1 B:DMS404 4.2 12.1 0.5 OG B:SER48 4.2 11.0 1.0 CB B:SER48 4.3 10.9 1.0 NH2 B:ARG369 4.3 11.7 1.0 OE2 B:GLU68 4.4 13.2 1.0 ND1 B:HIS67 4.5 11.0 1.0 CG B:HIS67 4.5 11.0 1.0 N1N B:NAD403 4.8 9.8 1.0 C2 B:DMS404 4.8 14.6 0.5 CA B:CYS174 4.8 10.0 1.0 N B:GLY175 4.8 10.0 1.0 CA B:CYS46 4.8 10.7 1.0 C B:CYS174 4.9 10.8 1.0 N B:SER48 5.0 10.5 1.0

Cadmium binding site 4 out of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd402 b:12.4 occ:0.95 SG B:CYS100 2.5 13.8 1.0 SG B:CYS103 2.5 12.3 1.0 SG B:CYS97 2.6 16.3 1.0 SG B:CYS111 2.6 12.7 1.0 CB B:CYS111 3.5 11.9 1.0 CB B:CYS100 3.5 15.2 1.0 CB B:CYS103 3.6 12.9 1.0 CB B:CYS97 3.6 17.7 1.0 N B:CYS97 3.6 13.8 1.0 CA B:CYS111 3.9 11.1 1.0 N B:CYS100 3.9 16.9 1.0 CA B:CYS97 4.0 15.4 1.0 N B:GLY98 4.0 15.7 1.0 N B:LEU112 4.1 12.2 1.0 CA B:CYS100 4.3 15.3 1.0 N B:CYS103 4.3 11.3 1.0 C B:CYS111 4.4 11.6 1.0 C B:CYS97 4.4 17.1 1.0 N B:LYS99 4.5 18.0 1.0 CA B:CYS103 4.5 11.9 1.0 C B:GLN96 4.7 12.8 1.0 CG B:LYS113 4.8 18.6 1.0 N B:LYS113 4.9 13.0 1.0 C B:CYS100 4.9 14.3 1.0 O B:CYS100 5.0 14.1 1.0

R.Meijers, H.W.Adolph, Z.Dauter, K.S.Wilson, V.S.Lamzin, E.S.Cedergren-Zeppezauer. Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase Biochemistry V. 46 5446 2007.
ISSN: ISSN 0006-2960
PubMed: 17429946
DOI: 10.1021/BI6023594