Zinc in PDB 1vj0: Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Enzymatic activity of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
All present enzymatic activity of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution:
1.1.1.1;
Protein crystallography data
The structure of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution, PDB code: 1vj0
was solved by
Joint Center For Structural Genomics (Jcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
80.53 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.880,
104.919,
161.617,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.5 /
19.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
(pdb code 1vj0). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution, PDB code: 1vj0:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 1 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn400
b:22.7
occ:1.00
|
SG
|
A:CYS106
|
2.3
|
28.2
|
1.0
|
SG
|
A:CYS103
|
2.4
|
25.4
|
1.0
|
SG
|
A:CYS100
|
2.4
|
27.4
|
1.0
|
SG
|
A:CYS115
|
2.4
|
28.8
|
1.0
|
CB
|
A:CYS115
|
3.2
|
30.1
|
1.0
|
CB
|
A:CYS103
|
3.4
|
26.5
|
1.0
|
CB
|
A:CYS106
|
3.5
|
27.4
|
1.0
|
CB
|
A:CYS100
|
3.6
|
29.6
|
1.0
|
N
|
A:CYS100
|
3.6
|
30.2
|
1.0
|
N
|
A:CYS103
|
3.8
|
26.8
|
1.0
|
CA
|
A:CYS115
|
3.9
|
28.3
|
1.0
|
N
|
A:GLY101
|
4.0
|
29.6
|
1.0
|
CA
|
A:CYS100
|
4.0
|
30.2
|
1.0
|
N
|
A:CYS106
|
4.2
|
26.0
|
1.0
|
CA
|
A:CYS103
|
4.2
|
26.1
|
1.0
|
C
|
A:CYS100
|
4.4
|
30.3
|
1.0
|
CA
|
A:CYS106
|
4.4
|
26.0
|
1.0
|
N
|
A:GLU102
|
4.4
|
30.0
|
1.0
|
CD
|
A:PRO116
|
4.5
|
29.8
|
1.0
|
ND2
|
A:ASN117
|
4.5
|
38.2
|
1.0
|
CB
|
A:THR99
|
4.6
|
31.0
|
1.0
|
C
|
A:THR99
|
4.7
|
30.5
|
1.0
|
C
|
A:CYS115
|
4.8
|
28.9
|
1.0
|
C
|
A:CYS103
|
4.9
|
25.4
|
1.0
|
CA
|
A:GLY101
|
4.9
|
29.9
|
1.0
|
N
|
A:PRO116
|
4.9
|
29.8
|
1.0
|
C
|
A:GLU102
|
5.0
|
28.1
|
1.0
|
CA
|
A:THR99
|
5.0
|
30.1
|
1.0
|
|
Zinc binding site 2 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 2 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:35.8
occ:0.34
|
OE2
|
A:GLU66
|
2.3
|
41.6
|
1.0
|
NE2
|
A:HIS65
|
2.3
|
30.8
|
1.0
|
SG
|
A:CYS166
|
2.3
|
41.1
|
0.7
|
SG
|
A:CYS43
|
2.5
|
45.3
|
1.0
|
CB
|
A:CYS166
|
2.8
|
37.8
|
0.3
|
CB
|
A:CYS166
|
2.8
|
37.8
|
0.7
|
CB
|
A:CYS43
|
2.9
|
38.6
|
1.0
|
SG
|
A:CYS166
|
3.0
|
39.1
|
0.3
|
CD2
|
A:HIS65
|
3.2
|
29.6
|
1.0
|
CD
|
A:GLU66
|
3.3
|
34.0
|
1.0
|
CE1
|
A:HIS65
|
3.3
|
29.5
|
1.0
|
CG
|
A:GLU66
|
3.7
|
35.7
|
1.0
|
O
|
A:HOH2182
|
4.1
|
59.8
|
1.0
|
OG
|
A:SER45
|
4.3
|
34.3
|
1.0
|
CA
|
A:CYS43
|
4.3
|
37.6
|
1.0
|
CA
|
A:CYS166
|
4.3
|
38.1
|
1.0
|
CG
|
A:HIS65
|
4.3
|
28.2
|
1.0
|
OE1
|
A:GLU66
|
4.3
|
39.2
|
1.0
|
ND1
|
A:HIS65
|
4.3
|
27.6
|
1.0
|
O
|
A:HOH2180
|
4.6
|
40.1
|
1.0
|
O
|
A:HOH2179
|
4.7
|
38.8
|
1.0
|
O
|
A:HOH2020
|
4.7
|
20.5
|
1.0
|
N
|
A:SER167
|
4.9
|
32.9
|
1.0
|
C
|
A:CYS166
|
5.0
|
36.8
|
1.0
|
|
Zinc binding site 3 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 3 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn400
b:22.5
occ:1.00
|
SG
|
B:CYS103
|
2.3
|
26.4
|
1.0
|
SG
|
B:CYS106
|
2.3
|
28.8
|
1.0
|
SG
|
B:CYS100
|
2.4
|
28.8
|
1.0
|
SG
|
B:CYS115
|
2.4
|
27.7
|
1.0
|
CB
|
B:CYS115
|
3.2
|
26.6
|
1.0
|
CB
|
B:CYS103
|
3.4
|
28.0
|
1.0
|
CB
|
B:CYS106
|
3.5
|
27.3
|
1.0
|
CB
|
B:CYS100
|
3.6
|
30.1
|
1.0
|
N
|
B:CYS100
|
3.7
|
29.9
|
1.0
|
N
|
B:CYS103
|
3.8
|
28.7
|
1.0
|
N
|
B:GLY101
|
3.9
|
30.8
|
1.0
|
CA
|
B:CYS115
|
4.0
|
27.8
|
1.0
|
CA
|
B:CYS100
|
4.0
|
30.3
|
1.0
|
CA
|
B:CYS103
|
4.2
|
27.7
|
1.0
|
N
|
B:CYS106
|
4.2
|
24.9
|
1.0
|
C
|
B:CYS100
|
4.3
|
30.8
|
1.0
|
N
|
B:GLU102
|
4.4
|
32.6
|
1.0
|
CA
|
B:CYS106
|
4.5
|
26.2
|
1.0
|
CD
|
B:PRO116
|
4.5
|
28.1
|
1.0
|
ND2
|
B:ASN117
|
4.5
|
33.2
|
1.0
|
CB
|
B:THR99
|
4.5
|
29.3
|
1.0
|
C
|
B:THR99
|
4.7
|
30.3
|
1.0
|
C
|
B:CYS103
|
4.8
|
25.8
|
1.0
|
CA
|
B:GLY101
|
4.8
|
31.9
|
1.0
|
C
|
B:CYS115
|
4.8
|
27.8
|
1.0
|
N
|
B:PRO116
|
5.0
|
28.0
|
1.0
|
C
|
B:GLU102
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 4 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:26.3
occ:0.28
|
OE2
|
B:GLU66
|
2.1
|
42.3
|
1.0
|
NE2
|
B:HIS65
|
2.3
|
29.6
|
1.0
|
SG
|
B:CYS166
|
2.3
|
39.0
|
0.7
|
SG
|
B:CYS43
|
2.4
|
43.0
|
1.0
|
CB
|
B:CYS43
|
2.8
|
35.2
|
1.0
|
CB
|
B:CYS166
|
2.9
|
37.6
|
0.3
|
CB
|
B:CYS166
|
3.0
|
38.1
|
0.7
|
CD2
|
B:HIS65
|
3.2
|
27.8
|
1.0
|
SG
|
B:CYS166
|
3.2
|
38.2
|
0.3
|
CD
|
B:GLU66
|
3.2
|
36.0
|
1.0
|
CE1
|
B:HIS65
|
3.2
|
29.9
|
1.0
|
CG
|
B:GLU66
|
3.8
|
36.1
|
1.0
|
OG
|
B:SER45
|
4.0
|
33.0
|
1.0
|
OE1
|
B:GLU66
|
4.1
|
36.0
|
1.0
|
CA
|
B:CYS43
|
4.2
|
35.6
|
1.0
|
O
|
B:HOH2214
|
4.3
|
46.6
|
1.0
|
ND1
|
B:HIS65
|
4.3
|
29.0
|
1.0
|
CG
|
B:HIS65
|
4.3
|
28.8
|
1.0
|
CA
|
B:CYS166
|
4.4
|
36.9
|
1.0
|
O
|
B:HOH2009
|
4.7
|
20.5
|
1.0
|
O
|
B:HOH2269
|
4.8
|
32.7
|
1.0
|
N
|
B:SER167
|
4.9
|
32.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 1vj0
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Zinc Binding Sites List in 1vj0
Zinc binding site 5 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn400
b:22.1
occ:1.00
|
SG
|
C:CYS103
|
2.3
|
26.6
|
1.0
|
SG
|
C:CYS115
|
2.3
|
27.1
|
1.0
|
SG
|
C:CYS106
|
2.4
|
26.3
|
1.0
|
SG
|
C:CYS100
|
2.4
|
27.4
|
1.0
|
CB
|
C:CYS115
|
3.3
|
26.6
|
1.0
|
CB
|
C:CYS103
|
3.4
|
26.0
|
1.0
|
CB
|
C:CYS106
|
3.5
|
26.8
|
1.0
|
CB
|
C:CYS100
|
3.6
|
30.2
|
1.0
|
N
|
C:CYS100
|
3.6
|
30.1
|
1.0
|
N
|
C:CYS103
|
3.9
|
27.2
|
1.0
|
CA
|
C:CYS115
|
4.0
|
26.4
|
1.0
|
CA
|
C:CYS100
|
4.0
|
29.6
|
1.0
|
N
|
C:GLY101
|
4.0
|
28.2
|
1.0
|
CA
|
C:CYS103
|
4.2
|
26.8
|
1.0
|
N
|
C:CYS106
|
4.3
|
25.7
|
1.0
|
C
|
C:CYS100
|
4.3
|
29.8
|
1.0
|
CA
|
C:CYS106
|
4.4
|
24.5
|
1.0
|
N
|
C:GLU102
|
4.5
|
29.7
|
1.0
|
CD
|
C:PRO116
|
4.5
|
27.6
|
1.0
|
ND2
|
C:ASN117
|
4.5
|
29.5
|
1.0
|
CB
|
C:THR99
|
4.5
|
30.5
|
1.0
|
C
|
C:THR99
|
4.7
|
30.2
|
1.0
|
C
|
C:CYS115
|
4.8
|
25.7
|
1.0
|
C
|
C:CYS103
|
4.9
|
25.1
|
1.0
|
N
|
C:PRO116
|
4.9
|
26.8
|
1.0
|
CA
|
C:GLY101
|
4.9
|
29.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 6 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:33.5
occ:0.41
|
NE2
|
C:HIS65
|
2.2
|
28.9
|
1.0
|
SG
|
C:CYS43
|
2.4
|
40.0
|
1.0
|
SG
|
C:CYS166
|
2.4
|
40.2
|
0.7
|
OE2
|
C:GLU66
|
2.5
|
42.6
|
1.0
|
CB
|
C:CYS43
|
2.9
|
35.0
|
1.0
|
CB
|
C:CYS166
|
2.9
|
37.6
|
0.3
|
CB
|
C:CYS166
|
3.0
|
38.0
|
0.7
|
CE1
|
C:HIS65
|
3.2
|
32.8
|
1.0
|
CD2
|
C:HIS65
|
3.2
|
31.1
|
1.0
|
SG
|
C:CYS166
|
3.2
|
39.5
|
0.3
|
CD
|
C:GLU66
|
3.5
|
32.0
|
1.0
|
OG
|
C:SER45
|
3.8
|
36.7
|
1.0
|
CG
|
C:GLU66
|
4.0
|
35.1
|
1.0
|
ND1
|
C:HIS65
|
4.3
|
29.7
|
1.0
|
CG
|
C:HIS65
|
4.3
|
28.7
|
1.0
|
CA
|
C:CYS43
|
4.4
|
34.0
|
1.0
|
CA
|
C:CYS166
|
4.4
|
37.3
|
1.0
|
OE1
|
C:GLU66
|
4.5
|
39.4
|
1.0
|
O
|
C:HOH2174
|
4.7
|
33.8
|
1.0
|
O
|
C:HOH2022
|
4.8
|
19.6
|
1.0
|
N
|
C:SER167
|
5.0
|
34.5
|
1.0
|
CB
|
C:SER45
|
5.0
|
33.3
|
1.0
|
|
Zinc binding site 7 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 7 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn400
b:23.5
occ:1.00
|
SG
|
D:CYS103
|
2.3
|
26.4
|
1.0
|
SG
|
D:CYS115
|
2.3
|
29.3
|
1.0
|
SG
|
D:CYS100
|
2.4
|
29.7
|
1.0
|
SG
|
D:CYS106
|
2.4
|
29.7
|
1.0
|
CB
|
D:CYS115
|
3.3
|
28.7
|
1.0
|
CB
|
D:CYS106
|
3.5
|
28.2
|
1.0
|
CB
|
D:CYS103
|
3.5
|
27.1
|
1.0
|
N
|
D:CYS100
|
3.5
|
30.8
|
1.0
|
CB
|
D:CYS100
|
3.6
|
29.8
|
1.0
|
N
|
D:CYS103
|
3.9
|
28.2
|
1.0
|
N
|
D:GLY101
|
4.0
|
29.9
|
1.0
|
CA
|
D:CYS115
|
4.0
|
28.3
|
1.0
|
CA
|
D:CYS100
|
4.0
|
30.1
|
1.0
|
CA
|
D:CYS103
|
4.2
|
27.3
|
1.0
|
N
|
D:CYS106
|
4.3
|
27.9
|
1.0
|
ND2
|
D:ASN117
|
4.3
|
36.0
|
1.0
|
C
|
D:CYS100
|
4.4
|
30.9
|
1.0
|
N
|
D:GLU102
|
4.4
|
29.9
|
1.0
|
CA
|
D:CYS106
|
4.4
|
28.5
|
1.0
|
CB
|
D:THR99
|
4.5
|
29.6
|
1.0
|
CD
|
D:PRO116
|
4.6
|
28.8
|
1.0
|
C
|
D:THR99
|
4.6
|
30.3
|
1.0
|
C
|
D:CYS115
|
4.8
|
28.3
|
1.0
|
C
|
D:CYS103
|
4.9
|
26.8
|
1.0
|
CA
|
D:GLY101
|
4.9
|
30.6
|
1.0
|
CA
|
D:THR99
|
5.0
|
29.7
|
1.0
|
N
|
D:PRO116
|
5.0
|
28.7
|
1.0
|
C
|
D:GLU102
|
5.0
|
28.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 1vj0
Go back to
Zinc Binding Sites List in 1vj0
Zinc binding site 8 out
of 8 in the Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Alcohol Dehydrogenase (TM0436) From Thermotoga Maritima at 2.00 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:34.9
occ:0.33
|
OE2
|
D:GLU66
|
2.2
|
40.9
|
1.0
|
NE2
|
D:HIS65
|
2.2
|
28.6
|
1.0
|
SG
|
D:CYS43
|
2.3
|
41.5
|
1.0
|
SG
|
D:CYS166
|
2.4
|
40.1
|
0.7
|
CB
|
D:CYS166
|
2.8
|
37.1
|
0.3
|
CB
|
D:CYS166
|
2.8
|
37.3
|
0.7
|
CD2
|
D:HIS65
|
3.0
|
31.8
|
1.0
|
SG
|
D:CYS166
|
3.1
|
38.8
|
0.3
|
CB
|
D:CYS43
|
3.2
|
37.1
|
1.0
|
CD
|
D:GLU66
|
3.3
|
34.9
|
1.0
|
CE1
|
D:HIS65
|
3.3
|
30.0
|
1.0
|
CG
|
D:GLU66
|
3.8
|
35.7
|
1.0
|
OG
|
D:SER45
|
4.0
|
37.2
|
1.0
|
CG
|
D:HIS65
|
4.2
|
30.3
|
1.0
|
OE1
|
D:GLU66
|
4.2
|
36.4
|
1.0
|
CA
|
D:CYS166
|
4.3
|
37.0
|
1.0
|
ND1
|
D:HIS65
|
4.3
|
28.7
|
1.0
|
CA
|
D:CYS43
|
4.4
|
36.5
|
1.0
|
O
|
D:HOH2032
|
4.7
|
21.7
|
1.0
|
N
|
D:SER167
|
4.8
|
32.9
|
1.0
|
O
|
D:HOH2266
|
4.9
|
25.9
|
0.5
|
C
|
D:CYS166
|
4.9
|
35.6
|
1.0
|
|
Reference:
Joint Center For Structural Genomics (Jcsg),
Joint Center For Structural Genomics (Jcsg).
N/A N/A.
Page generated: Wed Oct 16 19:50:04 2024
|