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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 1het

Go back to Zinc Binding Sites List in 1het
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 1het

Go back to Zinc Binding Sites List in 1het
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 1het

Go back to Zinc Binding Sites List in 1het
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 1het

Go back to Zinc Binding Sites List in 1het
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

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 Dec 16 02:51:13 2020

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