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Zinc in PDB 1hdy: Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences

Enzymatic activity of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences

All present enzymatic activity of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences:
1.1.1.1;

Protein crystallography data

The structure of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences, PDB code: 1hdy was solved by T.D.Hurley, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.360, 44.890, 93.850, 92.65, 103.21, 68.77
R / Rfree (%) 18.5 / n/a

Other elements in 1hdy:

The structure of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences (pdb code 1hdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences, PDB code: 1hdy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1hdy

Go back to Zinc Binding Sites List in 1hdy
Zinc binding site 1 out of 4 in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:28.7
occ:1.00
SG A:CYS100 2.2 24.6 1.0
SG A:CYS97 2.3 24.4 1.0
SG A:CYS103 2.3 23.8 1.0
SG A:CYS111 2.3 29.0 1.0
CB A:CYS100 3.2 27.2 1.0
CB A:CYS111 3.3 27.5 1.0
CB A:CYS103 3.3 22.7 1.0
CB A:CYS97 3.4 24.4 1.0
N A:CYS97 3.7 21.3 1.0
N A:CYS100 3.9 28.0 1.0
CA A:CYS111 3.9 25.5 1.0
CA A:CYS97 4.0 23.1 1.0
CA A:CYS100 4.1 26.6 1.0
N A:LEU112 4.1 29.7 1.0
N A:GLY98 4.2 26.0 1.0
C A:CYS97 4.4 24.1 1.0
CA A:CYS103 4.4 27.5 1.0
C A:CYS111 4.4 27.5 1.0
N A:CYS103 4.4 25.7 1.0
C A:GLN96 4.7 18.1 1.0
N A:LYS99 4.8 27.4 1.0
C A:CYS100 4.8 26.5 1.0
N A:LYS113 4.9 25.0 1.0
CA A:GLN96 4.9 15.5 1.0
NZ A:LYS99 5.0 27.9 1.0

Zinc binding site 2 out of 4 in 1hdy

Go back to Zinc Binding Sites List in 1hdy
Zinc binding site 2 out of 4 in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:21.2
occ:1.00
SG A:CYS174 2.1 19.3 1.0
N1 A:PYZ378 2.1 36.8 1.0
NE2 A:HIS67 2.2 11.4 1.0
SG A:CYS46 2.3 21.4 1.0
C5 A:PYZ378 3.0 37.5 1.0
CD2 A:HIS67 3.0 12.1 1.0
N2 A:PYZ378 3.1 29.4 1.0
CB A:CYS46 3.1 18.9 1.0
CE1 A:HIS67 3.2 2.0 1.0
C5N A:NAD377 3.3 23.9 1.0
CB A:CYS174 3.4 22.2 1.0
OG1 A:THR48 3.7 20.6 1.0
C4N A:NAD377 4.0 17.6 1.0
C6N A:NAD377 4.1 21.5 1.0
C4 A:PYZ378 4.2 34.7 1.0
CG A:HIS67 4.2 17.1 1.0
C3 A:PYZ378 4.2 31.8 1.0
ND1 A:HIS67 4.3 10.2 1.0
CB A:THR48 4.3 25.6 1.0
CA A:CYS46 4.6 19.5 1.0
CA A:CYS174 4.7 21.8 1.0
CE2 A:PHE93 4.9 11.0 1.0
CD2 A:PHE93 4.9 9.3 1.0
C A:CYS174 5.0 23.1 1.0

Zinc binding site 3 out of 4 in 1hdy

Go back to Zinc Binding Sites List in 1hdy
Zinc binding site 3 out of 4 in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:28.9
occ:1.00
SG B:CYS111 2.2 26.2 1.0
SG B:CYS103 2.2 21.8 1.0
SG B:CYS100 2.3 36.0 1.0
SG B:CYS97 2.3 32.5 1.0
CB B:CYS97 3.1 27.9 1.0
CB B:CYS111 3.2 29.4 1.0
CB B:CYS100 3.2 31.8 1.0
CB B:CYS103 3.3 26.4 1.0
N B:CYS97 3.5 24.5 1.0
CA B:CYS97 3.7 24.7 1.0
N B:CYS100 3.8 32.9 1.0
C B:CYS97 4.0 21.4 1.0
CA B:CYS111 4.0 28.8 1.0
CA B:CYS100 4.1 31.9 1.0
N B:LEU112 4.3 24.1 1.0
N B:GLY98 4.3 22.5 1.0
N B:CYS103 4.3 30.3 1.0
CA B:CYS103 4.4 30.1 1.0
O B:CYS100 4.5 33.7 1.0
C B:GLN96 4.5 24.7 1.0
O B:CYS97 4.5 23.1 1.0
C B:CYS111 4.5 26.5 1.0
C B:CYS100 4.6 32.8 1.0
N B:LYS99 4.9 24.2 1.0
CA B:GLN96 5.0 23.2 1.0
CB B:LEU112 5.0 22.0 1.0

Zinc binding site 4 out of 4 in 1hdy

Go back to Zinc Binding Sites List in 1hdy
Zinc binding site 4 out of 4 in the Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structures of Three Human Alcohol Dehydrogenase Variants: Correlations with Their Functional Differences within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:34.1
occ:1.00
SG B:CYS174 2.0 31.5 1.0
N1 B:PYZ378 2.0 23.4 1.0
NE2 B:HIS67 2.2 22.9 1.0
SG B:CYS46 2.4 29.8 1.0
N2 B:PYZ378 2.9 17.2 1.0
C5 B:PYZ378 3.0 23.3 1.0
CD2 B:HIS67 3.0 22.6 1.0
CB B:CYS174 3.1 30.9 1.0
CE1 B:HIS67 3.2 19.2 1.0
C5N B:NAD377 3.3 29.6 1.0
CB B:CYS46 3.4 29.8 1.0
C4N B:NAD377 3.9 29.8 1.0
OG1 B:THR48 4.0 13.8 1.0
C3 B:PYZ378 4.0 23.5 1.0
C4 B:PYZ378 4.1 22.8 1.0
C6N B:NAD377 4.2 28.2 1.0
CG B:HIS67 4.2 25.5 1.0
CE2 B:PHE93 4.2 21.7 1.0
ND1 B:HIS67 4.3 24.9 1.0
CB B:THR48 4.4 17.4 1.0
CA B:CYS174 4.5 30.6 1.0
CD2 B:PHE93 4.5 24.6 1.0
CZ B:PHE93 4.7 26.9 1.0
OE1 B:GLU68 4.8 41.3 1.0
CA B:CYS46 4.9 27.9 1.0

Reference:

T.D.Hurley, W.F.Bosron, C.L.Stone, L.M.Amzel. Structures of Three Human Beta Alcohol Dehydrogenase Variants. Correlations with Their Functional Differences. J.Mol.Biol. V. 239 415 1994.
ISSN: ISSN 0022-2836
PubMed: 8201622
DOI: 10.1006/JMBI.1994.1382
Page generated: Wed Dec 16 02:51:11 2020

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