Zinc in PDB 1d1s: Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Enzymatic activity of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
All present enzymatic activity of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase:
1.1.1.1;
Protein crystallography data
The structure of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase, PDB code: 1d1s
was solved by
P.T.Xie,
T.D.Hurley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.400,
90.900,
121.100,
90.00,
99.60,
90.00
|
R / Rfree (%)
|
21.7 /
26.8
|
Other elements in 1d1s:
The structure of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
19;
Binding sites:
The binding sites of Zinc atom in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
(pdb code 1d1s). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 19 binding sites of Zinc where determined in the
Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase, PDB code: 1d1s:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 1 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn375
b:42.2
occ:1.00
|
SG
|
A:CYS103
|
2.1
|
37.8
|
1.0
|
SG
|
A:CYS111
|
2.2
|
44.9
|
1.0
|
SG
|
A:CYS100
|
2.4
|
44.5
|
1.0
|
SG
|
A:CYS97
|
2.4
|
45.4
|
1.0
|
CB
|
A:CYS111
|
3.1
|
43.2
|
1.0
|
CB
|
A:CYS103
|
3.3
|
39.6
|
1.0
|
N
|
A:CYS97
|
3.5
|
38.7
|
1.0
|
CB
|
A:CYS97
|
3.5
|
41.5
|
1.0
|
CB
|
A:CYS100
|
3.5
|
43.0
|
1.0
|
CA
|
A:CYS111
|
3.6
|
42.0
|
1.0
|
N
|
A:ILE112
|
3.7
|
43.3
|
1.0
|
N
|
A:ARG98
|
3.9
|
42.1
|
1.0
|
CA
|
A:CYS97
|
3.9
|
40.1
|
1.0
|
C
|
A:CYS111
|
4.1
|
41.4
|
1.0
|
CG2
|
A:ILE112
|
4.3
|
43.0
|
1.0
|
N
|
A:GLU99
|
4.3
|
41.9
|
1.0
|
C
|
A:CYS97
|
4.3
|
40.2
|
1.0
|
N
|
A:CYS100
|
4.3
|
44.1
|
1.0
|
C
|
A:GLN96
|
4.3
|
37.8
|
1.0
|
CA
|
A:CYS103
|
4.4
|
38.7
|
1.0
|
CA
|
A:CYS100
|
4.5
|
43.6
|
1.0
|
N
|
A:CYS103
|
4.5
|
38.5
|
1.0
|
C
|
A:GLU99
|
4.5
|
45.3
|
1.0
|
CA
|
A:GLN96
|
4.6
|
34.9
|
1.0
|
O
|
A:GLU99
|
4.8
|
46.7
|
1.0
|
CA
|
A:ARG98
|
4.8
|
41.7
|
1.0
|
N
|
A:CYS111
|
4.8
|
41.0
|
1.0
|
CA
|
A:ILE112
|
4.8
|
44.5
|
1.0
|
CB
|
A:ILE112
|
4.9
|
43.6
|
1.0
|
N
|
A:ARG113
|
5.0
|
44.9
|
1.0
|
|
Zinc binding site 2 out
of 19 in 1d1s
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Zinc Binding Sites List in 1d1s
Zinc binding site 2 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn376
b:33.8
occ:1.00
|
SG
|
A:CYS174
|
2.0
|
28.2
|
1.0
|
NE2
|
A:HIS67
|
2.2
|
31.4
|
1.0
|
SG
|
A:CYS46
|
2.4
|
29.3
|
1.0
|
O
|
A:ACT501
|
2.6
|
45.3
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
31.3
|
1.0
|
CE1
|
A:HIS67
|
3.2
|
28.2
|
1.0
|
CB
|
A:CYS174
|
3.4
|
29.2
|
1.0
|
CB
|
A:CYS46
|
3.4
|
33.1
|
1.0
|
C
|
A:ACT501
|
3.5
|
45.0
|
1.0
|
CH3
|
A:ACT501
|
3.6
|
43.0
|
1.0
|
C5N
|
A:NAD1377
|
3.8
|
20.6
|
1.0
|
CG
|
A:HIS67
|
4.3
|
32.0
|
1.0
|
C6N
|
A:NAD1377
|
4.3
|
21.5
|
1.0
|
C4N
|
A:NAD1377
|
4.3
|
25.1
|
1.0
|
OG1
|
A:THR48
|
4.3
|
31.9
|
1.0
|
ND1
|
A:HIS67
|
4.3
|
29.8
|
1.0
|
CB
|
A:THR48
|
4.3
|
31.4
|
1.0
|
OXT
|
A:ACT501
|
4.6
|
46.6
|
1.0
|
CA
|
A:CYS174
|
4.6
|
27.7
|
1.0
|
N
|
A:GLY175
|
4.7
|
28.9
|
1.0
|
NH1
|
A:ARG369
|
4.8
|
31.4
|
1.0
|
CE1
|
A:PHE93
|
4.9
|
41.6
|
1.0
|
CA
|
A:CYS46
|
4.9
|
33.6
|
1.0
|
|
Zinc binding site 3 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 3 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:40.3
occ:1.00
|
N7A
|
A:NAD1377
|
2.0
|
22.2
|
1.0
|
OXT
|
A:ACT504
|
2.1
|
20.4
|
1.0
|
NE2
|
A:HIS271
|
2.1
|
41.6
|
1.0
|
O
|
A:HOH749
|
2.2
|
40.6
|
1.0
|
CD2
|
A:HIS271
|
3.0
|
38.6
|
1.0
|
C8A
|
A:NAD1377
|
3.0
|
21.2
|
1.0
|
C5A
|
A:NAD1377
|
3.1
|
24.4
|
1.0
|
C
|
A:ACT504
|
3.2
|
20.5
|
1.0
|
CE1
|
A:HIS271
|
3.3
|
41.6
|
1.0
|
N6A
|
A:NAD1377
|
3.4
|
30.0
|
1.0
|
C6A
|
A:NAD1377
|
3.7
|
26.3
|
1.0
|
O
|
A:ACT504
|
3.7
|
23.8
|
1.0
|
CG
|
A:HIS271
|
4.2
|
37.5
|
1.0
|
N9A
|
A:NAD1377
|
4.2
|
21.6
|
1.0
|
C4A
|
A:NAD1377
|
4.2
|
22.1
|
1.0
|
ND1
|
A:HIS271
|
4.3
|
38.2
|
1.0
|
CG2
|
A:ILE269
|
4.5
|
18.0
|
1.0
|
CH3
|
A:ACT504
|
4.5
|
21.8
|
1.0
|
CD1
|
A:LEU224
|
4.9
|
20.7
|
1.0
|
|
Zinc binding site 4 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 4 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:40.0
occ:0.50
|
NE2
|
A:HIS138
|
2.0
|
48.5
|
1.0
|
OXT
|
A:ACT502
|
2.1
|
47.7
|
0.5
|
O
|
A:ACT513
|
2.3
|
52.2
|
0.5
|
OXT
|
A:ACT513
|
2.4
|
53.1
|
0.5
|
O
|
A:ACT502
|
2.5
|
46.8
|
0.5
|
C
|
A:ACT513
|
2.6
|
53.7
|
0.5
|
C
|
A:ACT502
|
2.6
|
47.9
|
0.5
|
CE1
|
A:HIS138
|
2.6
|
49.4
|
1.0
|
CD2
|
A:HIS138
|
3.2
|
48.7
|
1.0
|
ND1
|
A:HIS138
|
3.8
|
49.8
|
1.0
|
CG
|
A:HIS138
|
4.1
|
47.8
|
1.0
|
CH3
|
A:ACT502
|
4.1
|
47.8
|
0.5
|
CH3
|
A:ACT513
|
4.1
|
55.0
|
0.5
|
CD
|
A:LYS60
|
4.5
|
59.7
|
1.0
|
|
Zinc binding site 5 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 5 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:48.2
occ:1.00
|
OXT
|
B:ACT507
|
1.7
|
30.9
|
1.0
|
N7A
|
B:NAD2377
|
2.0
|
24.6
|
1.0
|
O
|
B:HOH735
|
2.0
|
35.9
|
1.0
|
NE2
|
B:HIS271
|
2.1
|
39.4
|
1.0
|
C
|
B:ACT507
|
2.9
|
28.4
|
1.0
|
C8A
|
B:NAD2377
|
3.0
|
26.2
|
1.0
|
CD2
|
B:HIS271
|
3.0
|
36.5
|
1.0
|
N6A
|
B:NAD2377
|
3.1
|
30.9
|
1.0
|
CE1
|
B:HIS271
|
3.1
|
39.0
|
1.0
|
C5A
|
B:NAD2377
|
3.1
|
25.6
|
1.0
|
C6A
|
B:NAD2377
|
3.6
|
27.9
|
1.0
|
O
|
B:ACT507
|
3.6
|
31.5
|
1.0
|
CH3
|
B:ACT507
|
4.0
|
20.7
|
1.0
|
CG
|
B:HIS271
|
4.2
|
38.3
|
1.0
|
ND1
|
B:HIS271
|
4.2
|
38.3
|
1.0
|
N9A
|
B:NAD2377
|
4.2
|
25.2
|
1.0
|
C4A
|
B:NAD2377
|
4.3
|
26.7
|
1.0
|
CG2
|
B:ILE269
|
4.4
|
26.0
|
1.0
|
N1A
|
B:NAD2377
|
5.0
|
26.6
|
1.0
|
CD1
|
B:LEU224
|
5.0
|
40.3
|
1.0
|
|
Zinc binding site 6 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 6 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn408
b:37.8
occ:1.00
|
OE2
|
A:GLU360
|
1.8
|
24.8
|
1.0
|
OE2
|
A:GLU357
|
1.9
|
13.2
|
1.0
|
O
|
A:HOH793
|
2.1
|
22.4
|
1.0
|
OE1
|
A:GLU357
|
2.4
|
20.5
|
1.0
|
CD
|
A:GLU357
|
2.4
|
21.4
|
1.0
|
CD
|
A:GLU360
|
3.0
|
36.1
|
1.0
|
OE1
|
A:GLU360
|
3.8
|
39.7
|
1.0
|
CG
|
A:GLU357
|
3.9
|
24.2
|
1.0
|
O
|
A:HOH727
|
3.9
|
46.9
|
1.0
|
CG
|
A:GLU360
|
4.0
|
35.2
|
1.0
|
CD2
|
A:LEU361
|
4.0
|
19.6
|
1.0
|
CB
|
A:GLU360
|
4.4
|
36.0
|
1.0
|
CG
|
A:LEU361
|
4.6
|
26.4
|
1.0
|
CB
|
A:GLU357
|
4.9
|
31.8
|
1.0
|
|
Zinc binding site 7 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 7 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn375
b:24.3
occ:1.00
|
SG
|
B:CYS111
|
2.2
|
23.8
|
1.0
|
SG
|
B:CYS97
|
2.2
|
25.7
|
1.0
|
SG
|
B:CYS103
|
2.3
|
20.7
|
1.0
|
SG
|
B:CYS100
|
2.4
|
25.0
|
1.0
|
CB
|
B:CYS111
|
3.1
|
25.9
|
1.0
|
CB
|
B:CYS103
|
3.3
|
22.7
|
1.0
|
CB
|
B:CYS97
|
3.4
|
23.2
|
1.0
|
CB
|
B:CYS100
|
3.5
|
16.8
|
1.0
|
N
|
B:CYS97
|
3.5
|
16.1
|
1.0
|
CA
|
B:CYS111
|
3.6
|
24.5
|
1.0
|
N
|
B:CYS100
|
3.9
|
19.6
|
1.0
|
N
|
B:ARG98
|
3.9
|
19.9
|
1.0
|
CA
|
B:CYS97
|
4.0
|
17.2
|
1.0
|
N
|
B:ILE112
|
4.1
|
22.5
|
1.0
|
CA
|
B:CYS100
|
4.2
|
19.0
|
1.0
|
C
|
B:CYS111
|
4.3
|
23.7
|
1.0
|
C
|
B:CYS97
|
4.3
|
17.5
|
1.0
|
C
|
B:GLN96
|
4.5
|
15.1
|
1.0
|
CA
|
B:CYS103
|
4.5
|
24.2
|
1.0
|
CG1
|
B:ILE112
|
4.5
|
23.5
|
1.0
|
N
|
B:GLU99
|
4.5
|
20.8
|
1.0
|
N
|
B:CYS103
|
4.5
|
21.1
|
1.0
|
CA
|
B:GLN96
|
4.6
|
13.6
|
1.0
|
CA
|
B:ARG98
|
4.8
|
21.6
|
1.0
|
N
|
B:CYS111
|
4.9
|
22.0
|
1.0
|
C
|
B:CYS100
|
4.9
|
22.1
|
1.0
|
O
|
B:CYS100
|
5.0
|
23.6
|
1.0
|
|
Zinc binding site 8 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 8 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn376
b:24.6
occ:1.00
|
SG
|
B:CYS174
|
2.1
|
16.4
|
1.0
|
NE2
|
B:HIS67
|
2.2
|
10.4
|
1.0
|
SG
|
B:CYS46
|
2.3
|
24.6
|
1.0
|
OXT
|
B:ACT506
|
2.5
|
29.1
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
7.4
|
1.0
|
CB
|
B:CYS46
|
3.2
|
25.1
|
1.0
|
CD2
|
B:HIS67
|
3.3
|
12.2
|
1.0
|
C
|
B:ACT506
|
3.3
|
27.5
|
1.0
|
CB
|
B:CYS174
|
3.4
|
17.7
|
1.0
|
CH3
|
B:ACT506
|
3.5
|
17.7
|
1.0
|
C5N
|
B:NAD2377
|
3.6
|
16.1
|
1.0
|
OG1
|
B:THR48
|
4.0
|
26.7
|
1.0
|
C6N
|
B:NAD2377
|
4.1
|
15.2
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
8.1
|
1.0
|
CB
|
B:THR48
|
4.2
|
24.8
|
1.0
|
C4N
|
B:NAD2377
|
4.3
|
16.9
|
1.0
|
CG
|
B:HIS67
|
4.4
|
12.8
|
1.0
|
O
|
B:ACT506
|
4.5
|
32.6
|
1.0
|
OE2
|
B:GLU68
|
4.6
|
31.0
|
1.0
|
NH2
|
B:ARG369
|
4.6
|
31.9
|
1.0
|
CA
|
B:CYS46
|
4.7
|
21.4
|
1.0
|
N
|
B:GLY175
|
4.7
|
22.9
|
1.0
|
CA
|
B:CYS174
|
4.8
|
18.3
|
1.0
|
|
Zinc binding site 9 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 9 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn404
b:27.7
occ:1.00
|
O
|
B:HOH725
|
1.8
|
10.4
|
1.0
|
NE2
|
B:HIS138
|
2.1
|
18.8
|
1.0
|
CE1
|
B:HIS138
|
2.9
|
17.0
|
1.0
|
CD2
|
B:HIS138
|
3.3
|
18.6
|
1.0
|
ND1
|
B:HIS138
|
4.1
|
18.3
|
1.0
|
CG
|
B:HIS138
|
4.3
|
19.9
|
1.0
|
O
|
B:HOH649
|
4.3
|
29.4
|
1.0
|
O
|
B:PHE61
|
4.4
|
31.4
|
1.0
|
CD
|
B:LYS60
|
4.7
|
38.1
|
1.0
|
CB
|
B:LYS60
|
4.9
|
29.8
|
1.0
|
|
Zinc binding site 10 out
of 19 in 1d1s
Go back to
Zinc Binding Sites List in 1d1s
Zinc binding site 10 out
of 19 in the Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Wild-Type Human Sigma (Class IV) Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn405
b:48.4
occ:1.00
|
OE1
|
D:GLU99
|
2.0
|
27.5
|
1.0
|
OD1
|
B:ASP341
|
2.4
|
41.8
|
1.0
|
O
|
D:ACT509
|
2.5
|
16.5
|
1.0
|
OD2
|
B:ASP341
|
2.7
|
46.0
|
1.0
|
CD
|
D:GLU99
|
2.8
|
29.3
|
1.0
|
OXT
|
D:ACT509
|
2.8
|
13.7
|
1.0
|
CG
|
B:ASP341
|
2.8
|
42.8
|
1.0
|
OE2
|
D:GLU99
|
2.9
|
31.3
|
1.0
|
O
|
D:ACT508
|
2.9
|
23.4
|
1.0
|
OXT
|
D:ACT508
|
2.9
|
22.4
|
1.0
|
C
|
D:ACT509
|
3.0
|
14.1
|
1.0
|
C
|
D:ACT508
|
3.2
|
21.3
|
1.0
|
CB
|
B:ASP341
|
4.2
|
40.2
|
1.0
|
CG
|
D:GLU99
|
4.2
|
25.4
|
1.0
|
O
|
B:HOH842
|
4.3
|
29.3
|
1.0
|
CH3
|
D:ACT509
|
4.4
|
13.2
|
1.0
|
CB
|
B:ASP343
|
4.6
|
28.3
|
1.0
|
CG
|
B:GLN344
|
4.6
|
46.3
|
1.0
|
CH3
|
D:ACT508
|
4.7
|
18.3
|
1.0
|
CB
|
D:GLU99
|
4.8
|
29.1
|
1.0
|
|
Reference:
P.T.Xie,
T.D.Hurley.
Methionine-141 Directly Influences the Binding of 4-Methylpyrazole in Human Sigma Sigma Alcohol Dehydrogenase. Protein Sci. V. 8 2639 1999.
ISSN: ISSN 0961-8368
PubMed: 10631979
Page generated: Sat Oct 12 23:25:35 2024
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