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Zinc in PDB 2ohx: Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution

Enzymatic activity of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution

All present enzymatic activity of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution:
1.1.1.1;

Protein crystallography data

The structure of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution, PDB code: 2ohx was solved by S.Al-Karadaghi, E.S.Cedergren-Zeppezauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.760, 44.540, 94.610, 104.80, 102.30, 70.60
R / Rfree (%) 17.3 / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution (pdb code 2ohx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution, PDB code: 2ohx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ohx

Go back to Zinc Binding Sites List in 2ohx
Zinc binding site 1 out of 4 in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.0
occ:1.00
 NE2 A:HIS67 2.1 16.6 1.0
SG A:CYS46 2.2 15.9 1.0
O A:DMS404 2.3 17.1 1.0
SG A:CYS174 2.3 16.3 1.0
CE1 A:HIS67 3.0 14.8 1.0
CB A:CYS46 3.1 14.1 1.0
S A:DMS404 3.2 20.7 1.0
CD2 A:HIS67 3.2 16.0 1.0
C5N A:NAD403 3.4 14.6 1.0
CB A:CYS174 3.5 15.8 1.0
C6N A:NAD403 4.0 14.2 1.0
OG A:SER48 4.0 15.4 1.0
CB A:SER48 4.1 16.2 1.0
C4N A:NAD403 4.2 15.2 1.0
ND1 A:HIS67 4.2 14.8 1.0
C1 A:DMS404 4.2 17.5 1.0
CG A:HIS67 4.3 14.5 1.0
NH2 A:ARG369 4.4 16.0 1.0
C2 A:DMS404 4.6 19.6 1.0
CA A:CYS46 4.6 17.9 1.0
OE1 A:GLU68 4.7 18.6 1.0
CA A:CYS174 4.9 16.5 1.0
N A:SER48 4.9 15.8 1.0
CE2 A:PHE93 5.0 18.4 1.0

Zinc binding site 2 out of 4 in 2ohx

Go back to Zinc Binding Sites List in 2ohx
Zinc binding site 2 out of 4 in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:23.9
occ:1.00
 SG A:CYS103 2.3 22.9 1.0
SG A:CYS100 2.3 22.4 1.0
SG A:CYS111 2.3 20.0 1.0
SG A:CYS97 2.4 25.8 1.0
CB A:CYS111 3.3 17.5 1.0
CB A:CYS103 3.4 22.2 1.0
CB A:CYS100 3.4 25.9 1.0
CB A:CYS97 3.5 26.1 1.0
N A:CYS97 3.5 22.7 1.0
CA A:CYS111 3.8 19.0 1.0
N A:CYS100 3.8 28.9 1.0
CA A:CYS97 3.9 24.9 1.0
N A:LEU112 3.9 21.4 1.0
N A:GLY98 4.0 27.5 1.0
N A:CYS103 4.2 21.2 1.0
CA A:CYS100 4.2 26.3 1.0
C A:CYS111 4.3 19.2 1.0
C A:CYS97 4.3 26.9 1.0
CA A:CYS103 4.3 22.5 1.0
C A:GLN96 4.6 22.8 1.0
N A:LYS99 4.6 29.9 1.0
C A:CYS100 4.8 26.0 1.0
O A:CYS100 4.8 27.0 1.0
CG A:LYS113 4.8 28.5 1.0
N A:LYS113 4.9 22.0 1.0
CA A:GLN96 5.0 21.0 1.0
C A:LYS99 5.0 30.2 1.0
CA A:GLY98 5.0 28.6 1.0

Zinc binding site 3 out of 4 in 2ohx

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Zinc binding site 3 out of 4 in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:23.6
occ:1.00
 NE2 B:HIS67 2.0 23.7 1.0
O B:DMS404 2.1 22.4 1.0
SG B:CYS46 2.2 22.2 1.0
SG B:CYS174 2.3 22.7 1.0
CE1 B:HIS67 2.9 22.2 1.0
CD2 B:HIS67 3.1 24.0 1.0
CB B:CYS46 3.2 23.1 1.0
S B:DMS404 3.2 25.3 1.0
CB B:CYS174 3.4 20.9 1.0
C5N B:NAD403 3.5 20.6 1.0
ND1 B:HIS67 4.1 22.8 1.0
OG B:SER48 4.1 20.7 1.0
C6N B:NAD403 4.1 20.8 1.0
CB B:SER48 4.2 19.2 1.0
CG B:HIS67 4.2 22.2 1.0
C1 B:DMS404 4.2 22.1 1.0
C4N B:NAD403 4.2 20.0 1.0
NH2 B:ARG369 4.5 24.0 1.0
CA B:CYS46 4.7 23.3 1.0
OE2 B:GLU68 4.7 23.8 1.0
C2 B:DMS404 4.8 25.6 1.0
CA B:CYS174 4.8 20.1 1.0
N B:SER48 4.9 20.1 1.0
CE2 B:PHE93 4.9 20.5 1.0
N B:GLY175 5.0 19.8 1.0

Zinc binding site 4 out of 4 in 2ohx

Go back to Zinc Binding Sites List in 2ohx
Zinc binding site 4 out of 4 in the Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:26.7
occ:1.00
 SG B:CYS103 2.3 22.9 1.0
SG B:CYS100 2.3 26.8 1.0
SG B:CYS111 2.4 25.1 1.0
SG B:CYS97 2.4 27.8 1.0
CB B:CYS111 3.3 19.5 1.0
CB B:CYS103 3.3 25.1 1.0
N B:CYS97 3.4 27.1 1.0
CB B:CYS97 3.4 29.2 1.0
CB B:CYS100 3.5 29.1 1.0
N B:CYS100 3.8 33.8 1.0
CA B:CYS111 3.8 19.6 1.0
CA B:CYS97 3.9 28.6 1.0
N B:GLY98 3.9 30.2 1.0
N B:LEU112 4.1 24.3 1.0
N B:CYS103 4.2 23.1 1.0
CA B:CYS100 4.2 30.7 1.0
C B:CYS97 4.3 30.4 1.0
CA B:CYS103 4.3 24.2 1.0
C B:CYS111 4.4 21.8 1.0
N B:LYS99 4.5 34.5 1.0
C B:GLN96 4.5 26.4 1.0
CA B:GLN96 4.8 24.2 1.0
O B:CYS100 4.8 28.9 1.0
C B:CYS100 4.9 29.1 1.0
C B:LYS99 4.9 35.0 1.0
N B:LYS113 4.9 26.7 1.0
CG B:LYS113 4.9 27.6 1.0
CA B:GLY98 4.9 31.2 1.0
O B:HOH576 4.9 65.9 1.0

Reference:

S.Al-Karadaghi, E.S.Cedergren-Zeppezauer, S.Hovmoller. Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 A Resolution. Acta Crystallogr.,Sect.D V. 50 793 1994.
ISSN: ISSN 0907-4449
PubMed: 15299346
DOI: 10.1107/S0907444994005263
Page generated: Wed Dec 16 03:46:08 2020

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