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

Enzymatic activity of 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;

Protein crystallography data

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

Cadmium Binding Sites:

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 2jhf

Go back to Cadmium Binding Sites List in 2jhf
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 2jhf

Go back to Cadmium Binding Sites List in 2jhf
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 2jhf

Go back to Cadmium Binding Sites List in 2jhf
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 2jhf

Go back to Cadmium Binding Sites List in 2jhf
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

Reference:

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
Page generated: Fri Aug 28 12:59:44 2020
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