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Zinc in PDB 2jhg: 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: 2jhg 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) 19.83 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.186, 43.798, 92.516, 77.12, 87.44, 108.89
R / Rfree (%) 11.4 / 14.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase (pdb code 2jhg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase, PDB code: 2jhg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2jhg

Go back to Zinc Binding Sites List in 2jhg
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:9.0
occ:1.00
NE2 A:HIS67 2.0 8.0 1.0
O2 A:IBO404 2.1 8.2 0.6
O2 A:IBO404 2.1 11.8 0.4
SG A:CYS174 2.3 9.2 1.0
SG A:CYS46 2.3 8.9 1.0
CE1 A:HIS67 3.0 8.5 1.0
CD2 A:HIS67 3.0 8.4 1.0
C A:IBO404 3.1 8.1 0.6
C A:IBO404 3.1 17.5 0.4
NA A:IBO404 3.2 8.1 0.6
CB A:CYS46 3.2 8.9 1.0
CB A:CYS174 3.4 8.8 1.0
C5N A:NAD403 3.5 8.6 1.0
NA A:IBO404 3.5 19.0 0.4
OG A:SER48 4.0 8.9 1.0
C4N A:NAD403 4.0 9.6 1.0
C6N A:NAD403 4.1 8.9 1.0
CB A:SER48 4.1 8.6 1.0
ND1 A:HIS67 4.1 8.6 1.0
CG A:HIS67 4.2 8.0 1.0
CA A:IBO404 4.4 11.4 0.6
CA A:IBO404 4.5 19.6 0.4
OE1 A:GLU68 4.6 10.8 1.0
NH2 A:ARG369 4.6 10.6 1.0
CA A:CYS46 4.7 8.9 1.0
CA A:CYS174 4.7 8.6 1.0
N A:SER48 4.9 8.4 1.0
CB2 A:IBO404 4.9 20.6 0.4
N A:GLY175 5.0 9.1 1.0

Zinc binding site 2 out of 4 in 2jhg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:11.3
occ:1.00
SG A:CYS111 2.3 10.4 1.0
SG A:CYS100 2.3 11.4 1.0
SG A:CYS103 2.4 10.8 1.0
SG A:CYS97 2.4 13.6 1.0
CB A:CYS111 3.3 9.7 1.0
CB A:CYS100 3.4 12.6 1.0
CB A:CYS103 3.4 11.2 1.0
CB A:CYS97 3.4 12.7 1.0
N A:CYS97 3.6 10.6 1.0
CA A:CYS111 3.8 9.7 1.0
N A:CYS100 3.9 13.6 1.0
CA A:CYS97 3.9 11.8 1.0
N A:GLY98 4.0 12.7 1.0
N A:LEU112 4.0 11.0 1.0
CA A:CYS100 4.2 13.2 1.0
N A:CYS103 4.2 10.8 1.0
C A:CYS111 4.3 9.9 1.0
C A:CYS97 4.4 12.6 1.0
CA A:CYS103 4.4 11.4 1.0
N A:LYS99 4.5 15.4 1.0
C A:GLN96 4.6 10.6 1.0
CG A:LYS113 4.7 12.2 0.6
N A:LYS113 4.8 10.7 1.0
C A:CYS100 4.8 13.1 1.0
O A:CYS100 4.9 13.0 1.0
CA A:GLN96 4.9 10.3 1.0
CA A:GLY98 4.9 14.2 1.0

Zinc binding site 3 out of 4 in 2jhg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:11.3
occ:1.00
O2 B:IBO404 2.0 14.5 0.2
NE2 B:HIS67 2.0 10.6 1.0
O2 B:IBO404 2.1 11.2 0.8
SG B:CYS174 2.3 11.4 1.0
SG B:CYS46 2.3 10.8 1.0
C B:IBO404 3.0 14.3 0.8
CE1 B:HIS67 3.0 10.4 1.0
CD2 B:HIS67 3.1 10.2 1.0
C B:IBO404 3.1 15.5 0.2
NA B:IBO404 3.3 13.1 0.8
CB B:CYS46 3.3 11.2 1.0
CB B:CYS174 3.4 10.0 1.0
NA B:IBO404 3.4 14.5 0.2
C5N B:NAD403 3.4 10.8 1.0
OG B:SER48 4.0 11.6 1.0
C6N B:NAD403 4.0 11.0 1.0
C4N B:NAD403 4.0 10.4 1.0
CB B:SER48 4.1 11.3 1.0
ND1 B:HIS67 4.2 11.1 1.0
CG B:HIS67 4.2 10.8 1.0
CA B:IBO404 4.4 15.5 0.8
CA B:IBO404 4.4 15.5 0.2
NH2 B:ARG369 4.5 12.9 1.0
OE2 B:GLU68 4.6 13.3 1.0
CA B:CYS174 4.7 9.7 1.0
CA B:CYS46 4.7 12.0 1.0
CB2 B:IBO404 4.8 16.3 0.2
N B:SER48 4.9 11.1 1.0
N B:GLY175 5.0 10.7 1.0

Zinc binding site 4 out of 4 in 2jhg

Go back to Zinc Binding Sites List in 2jhg
Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:13.3
occ:1.00
SG B:CYS111 2.3 12.7 1.0
SG B:CYS100 2.3 13.2 1.0
SG B:CYS103 2.3 12.4 1.0
SG B:CYS97 2.4 15.7 1.0
CB B:CYS111 3.3 11.0 1.0
CB B:CYS100 3.4 15.4 1.0
CB B:CYS103 3.4 12.6 1.0
CB B:CYS97 3.5 16.4 1.0
N B:CYS97 3.6 13.4 1.0
CA B:CYS111 3.7 11.6 1.0
N B:CYS100 3.9 15.2 1.0
CA B:CYS97 4.0 15.0 1.0
N B:LEU112 4.0 12.5 1.0
N B:GLY98 4.0 15.3 1.0
CA B:CYS100 4.2 15.4 1.0
N B:CYS103 4.2 11.8 1.0
C B:CYS111 4.3 11.7 1.0
CA B:CYS103 4.4 12.2 1.0
C B:CYS97 4.4 15.4 1.0
N B:LYS99 4.5 17.0 1.0
NZ B:LYS113 4.5 26.1 0.5
C B:GLN96 4.6 12.9 1.0
CG B:LYS113 4.7 16.2 0.5
C B:CYS100 4.8 15.5 1.0
N B:LYS113 4.8 13.1 1.0
O B:CYS100 4.9 14.7 1.0
CA B:GLN96 4.9 11.5 1.0
CG B:LYS113 4.9 17.3 0.5
CA B:GLY98 5.0 15.9 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: Wed Dec 16 03:32:04 2020

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