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:
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: Sun Oct 13 02:09:02 2024
|