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Cadmium in PDB 1heu: Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh

Enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh

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

Protein crystallography data

The structure of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh, PDB code: 1heu 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 (°) 51.180, 44.570, 94.100, 104.30, 101.07, 70.67
R / Rfree (%) 11.8 / 14.9

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 1 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd400

b:10.4
occ:0.90
 NE2 A:HIS67 2.3 8.8 1.0
O A:HOH2178 2.3 8.7 0.2
SG A:CYS174 2.4 6.8 1.0
SG A:CYS46 2.4 6.9 1.0
O A:HOH2177 2.7 14.2 0.8
OE2 A:GLU68 3.0 7.5 0.2
CE1 A:HIS67 3.3 7.9 1.0
CD2 A:HIS67 3.3 8.6 1.0
CB A:CYS174 3.4 7.5 1.0
CB A:CYS46 3.4 7.6 1.0
C5N A:NAD402 3.5 7.8 1.0
C6N A:NAD402 3.8 7.8 1.0
CD A:GLU68 3.9 7.8 0.2
C4N A:NAD402 4.0 6.7 1.0
CG A:GLU68 4.0 8.0 0.2
OG A:SER48 4.3 7.6 1.0
CB A:SER48 4.3 6.8 1.0
NH2 A:ARG369 4.3 9.4 1.0
OE1 A:GLU68 4.4 9.5 0.8
ND1 A:HIS67 4.4 6.8 1.0
CG A:HIS67 4.5 7.1 1.0
CM A:MRD403 4.5 15.4 1.0
CA A:CYS174 4.7 6.5 1.0
N A:GLY175 4.8 6.5 1.0
CA A:CYS46 4.9 7.5 1.0
N1N A:NAD402 4.9 6.8 1.0
C A:CYS174 4.9 6.4 1.0

Cadmium binding site 2 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 2 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:8.9
occ:1.00
 SG A:CYS100 2.5 8.4 1.0
SG A:CYS111 2.6 7.2 1.0
SG A:CYS97 2.6 9.3 1.0
SG A:CYS103 2.6 7.8 1.0
CB A:CYS111 3.5 7.6 1.0
CB A:CYS100 3.5 11.4 1.0
CB A:CYS97 3.5 10.2 1.0
CB A:CYS103 3.6 9.0 1.0
N A:CYS97 3.6 8.0 1.0
CA A:CYS111 3.8 7.1 1.0
N A:CYS100 3.9 12.4 1.0
CA A:CYS97 4.0 9.3 1.0
N A:LEU112 4.0 8.2 1.0
N A:GLY98 4.0 9.8 1.0
CA A:CYS100 4.3 11.9 1.0
N A:CYS103 4.3 8.6 1.0
C A:CYS111 4.4 7.3 1.0
C A:CYS97 4.4 9.7 1.0
N A:LYS99 4.5 13.1 1.0
CA A:CYS103 4.5 9.2 1.0
C A:GLN96 4.7 8.1 1.0
CG A:LYS113 4.8 10.4 0.6
N A:LYS113 4.9 8.8 1.0
C A:CYS100 4.9 10.8 1.0

Cadmium binding site 3 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 3 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd400

b:10.8
occ:0.90
 NE2 B:HIS67 2.3 10.2 1.0
SG B:CYS174 2.4 8.8 1.0
O B:HOH2614 2.4 12.4 0.7
SG B:CYS46 2.5 8.8 1.0
O B:HOH2616 2.8 13.4 0.3
CE1 B:HIS67 3.2 9.2 1.0
CD2 B:HIS67 3.3 10.5 1.0
CB B:CYS174 3.4 8.6 1.0
CB B:CYS46 3.4 10.2 1.0
C5N B:NAD402 3.6 10.6 1.0
C6N B:NAD402 3.9 10.0 1.0
C4N B:NAD402 4.0 9.7 1.0
OG B:SER48 4.3 9.6 1.0
CB B:SER48 4.3 8.9 1.0
NH2 B:ARG369 4.3 10.2 1.0
ND1 B:HIS67 4.4 9.5 1.0
CG B:HIS67 4.4 9.6 1.0
O2 B:MRD403 4.4 16.8 0.7
OE2 B:GLU68 4.5 13.5 1.0
CA B:CYS174 4.8 8.3 1.0
N B:GLY175 4.9 8.2 1.0
CA B:CYS46 4.9 10.3 1.0
N1N B:NAD402 4.9 8.0 1.0

Cadmium binding site 4 out of 4 in 1heu

Go back to Cadmium Binding Sites List in 1heu
Cadmium binding site 4 out of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing Cadmium and A Hydroxide Adduct to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd401

b:11.4
occ:1.00
 SG B:CYS100 2.5 10.5 1.0
SG B:CYS111 2.6 9.6 1.0
SG B:CYS97 2.6 12.3 1.0
SG B:CYS103 2.6 9.6 1.0
CB B:CYS111 3.5 10.4 1.0
CB B:CYS100 3.5 13.3 1.0
CB B:CYS97 3.5 13.8 1.0
CB B:CYS103 3.6 10.7 1.0
N B:CYS97 3.6 10.7 1.0
CA B:CYS111 3.9 9.4 1.0
N B:CYS100 3.9 13.8 1.0
CA B:CYS97 4.0 12.5 1.0
N B:LEU112 4.0 10.4 1.0
N B:GLY98 4.1 12.8 1.0
CA B:CYS100 4.3 12.8 1.0
N B:CYS103 4.3 10.3 1.0
C B:CYS111 4.4 10.3 1.0
C B:CYS97 4.4 13.0 1.0
CA B:CYS103 4.5 10.6 1.0
N B:LYS99 4.6 14.1 1.0
C B:GLN96 4.7 10.4 1.0
CG B:LYS113 4.8 18.5 1.0
C B:CYS100 4.9 12.6 1.0
N B:LYS113 4.9 11.2 1.0
CA B:GLN96 5.0 9.4 1.0

Reference:

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
Page generated: Fri Jul 19 13:28:07 2024

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