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Cadmium in PDB 1hf3: 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: 1hf3 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) 15.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.900, 179.000, 50.500, 90.00, 107.50, 90.00
R / Rfree (%) 16.4 / 21.4

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 1hf3). 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: 1hf3:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1hf3

Go back to Cadmium Binding Sites List in 1hf3
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:28.0
occ:1.00
NE2 A:HIS67 2.3 22.2 1.0
SG A:CYS46 2.3 18.8 1.0
SG A:CYS174 2.4 23.1 1.0
O A:HOH2025 2.4 20.3 0.5
O A:HOH2024 2.8 24.6 0.5
CB A:CYS46 3.2 23.6 1.0
C5N A:NAD402 3.2 22.1 1.0
OE1 A:GLU68 3.2 26.7 0.2
CD2 A:HIS67 3.2 23.4 1.0
CB A:CYS174 3.3 25.4 1.0
CE1 A:HIS67 3.3 25.0 1.0
C6N A:NAD402 3.8 23.7 1.0
C4N A:NAD402 4.1 25.7 1.0
NH2 A:ARG369 4.1 26.2 1.0
OG A:SER48 4.3 21.7 1.0
CB A:SER48 4.3 22.7 1.0
CD A:GLU68 4.4 27.4 0.2
ND1 A:HIS67 4.4 22.4 1.0
CG A:HIS67 4.4 23.2 1.0
C1 A:MRD403 4.4 20.0 1.0
N A:GLY175 4.6 25.6 1.0
OE2 A:GLU68 4.6 29.8 0.8
CA A:CYS174 4.6 25.3 1.0
CA A:CYS46 4.7 22.9 1.0
C A:CYS174 4.8 27.1 1.0
N A:SER48 5.0 18.9 1.0

Cadmium binding site 2 out of 4 in 1hf3

Go back to Cadmium Binding Sites List in 1hf3
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:29.3
occ:1.00
SG A:CYS103 2.3 23.3 1.0
SG A:CYS100 2.5 25.3 1.0
SG A:CYS111 2.5 23.1 1.0
SG A:CYS97 2.7 26.4 1.0
CB A:CYS111 3.3 22.2 1.0
CB A:CYS97 3.3 32.6 1.0
CB A:CYS103 3.4 29.9 1.0
CB A:CYS100 3.5 30.2 1.0
N A:CYS100 3.5 35.8 1.0
N A:CYS97 3.5 30.8 1.0
CA A:CYS111 3.7 24.1 1.0
CA A:CYS97 3.9 33.0 1.0
N A:GLY98 3.9 35.2 1.0
N A:LEU112 3.9 24.4 1.0
CA A:CYS100 4.0 33.1 1.0
C A:CYS111 4.2 24.7 1.0
N A:CYS103 4.2 29.6 1.0
C A:CYS97 4.3 36.3 1.0
CA A:CYS103 4.4 31.6 1.0
C A:GLN96 4.5 30.7 1.0
N A:LYS99 4.5 39.7 1.0
C A:LYS99 4.6 40.0 1.0
N A:LYS113 4.8 30.0 1.0
C A:CYS100 4.8 31.2 1.0
CA A:GLN96 4.8 29.1 1.0
O A:CYS100 5.0 31.4 1.0
CA A:GLY98 5.0 38.5 1.0

Cadmium binding site 3 out of 4 in 1hf3

Go back to Cadmium Binding Sites List in 1hf3
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:24.5
occ:1.00
NE2 B:HIS67 2.3 16.9 1.0
SG B:CYS174 2.3 17.4 1.0
SG B:CYS46 2.4 17.4 1.0
O B:HOH2019 2.6 18.5 0.5
O B:HOH2020 2.9 19.2 0.5
CE1 B:HIS67 3.2 17.3 1.0
CB B:CYS46 3.2 21.9 1.0
CB B:CYS174 3.3 19.1 1.0
CD2 B:HIS67 3.3 16.9 1.0
C5N B:NAD402 3.4 16.8 1.0
C6N B:NAD402 3.8 20.6 1.0
OE2 B:GLU68 4.0 27.2 1.0
C4N B:NAD402 4.1 17.7 1.0
NH2 B:ARG369 4.2 18.8 1.0
OG B:SER48 4.3 21.6 1.0
C1 B:MRD403 4.4 40.9 1.0
ND1 B:HIS67 4.4 16.2 1.0
CB B:SER48 4.4 18.3 1.0
CG B:HIS67 4.5 16.0 1.0
N B:GLY175 4.5 19.2 1.0
CA B:CYS174 4.6 19.4 1.0
CA B:CYS46 4.7 19.6 1.0
C B:CYS174 4.8 17.9 1.0
CD B:GLU68 4.9 24.9 1.0
CA B:GLY175 5.0 20.8 1.0

Cadmium binding site 4 out of 4 in 1hf3

Go back to Cadmium Binding Sites List in 1hf3
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:25.2
occ:1.00
SG B:CYS111 2.4 19.0 1.0
SG B:CYS103 2.5 22.1 1.0
SG B:CYS100 2.5 23.0 1.0
SG B:CYS97 2.5 19.9 1.0
CB B:CYS97 3.4 25.7 1.0
CB B:CYS100 3.5 31.0 1.0
CB B:CYS111 3.5 19.9 1.0
N B:CYS100 3.5 36.0 1.0
N B:CYS97 3.5 25.6 1.0
CB B:CYS103 3.5 26.1 1.0
CA B:CYS111 3.8 20.7 1.0
CA B:CYS97 3.9 27.0 1.0
N B:LEU112 3.9 22.3 1.0
N B:GLY98 4.0 29.9 1.0
CA B:CYS100 4.1 32.4 1.0
N B:CYS103 4.2 23.6 1.0
C B:CYS111 4.2 22.2 1.0
C B:CYS97 4.3 32.6 1.0
CA B:CYS103 4.4 26.7 1.0
C B:LYS99 4.6 41.2 1.0
N B:LYS99 4.6 39.2 1.0
C B:GLN96 4.6 24.1 1.0
CG B:LYS113 4.7 27.5 0.5
C B:CYS100 4.8 30.7 1.0
CA B:LEU112 4.9 23.5 1.0
N B:LYS113 5.0 23.9 1.0
CA B:GLN96 5.0 22.9 1.0
CA B:GLY98 5.0 34.8 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: Wed Oct 28 09:53:27 2020
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