Zinc in PDB 3bto: Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide:
1.1.1.1;
Protein crystallography data
The structure of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide, PDB code: 3bto
was solved by
S.Ramaswamy,
B.V.Plapp,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.66
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.930,
180.200,
86.800,
90.00,
106.00,
90.00
|
R / Rfree (%)
|
18.5 /
22.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
(pdb code 3bto). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide, PDB code: 3bto:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 1 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn375
b:10.7
occ:1.00
|
SG
|
A:CYS46
|
2.1
|
10.0
|
1.0
|
NE2
|
A:HIS67
|
2.1
|
3.8
|
1.0
|
O6
|
A:SSB378
|
2.2
|
6.0
|
1.0
|
SG
|
A:CYS174
|
2.3
|
9.0
|
1.0
|
CD2
|
A:HIS67
|
3.0
|
5.3
|
1.0
|
S1
|
A:SSB378
|
3.1
|
11.8
|
1.0
|
CE1
|
A:HIS67
|
3.2
|
7.8
|
1.0
|
CB
|
A:CYS46
|
3.2
|
8.4
|
1.0
|
CB
|
A:CYS174
|
3.3
|
6.4
|
1.0
|
C5N
|
A:NAD377
|
3.4
|
7.0
|
1.0
|
C6N
|
A:NAD377
|
4.0
|
5.3
|
1.0
|
OG
|
A:SER48
|
4.0
|
8.8
|
1.0
|
C4N
|
A:NAD377
|
4.0
|
4.7
|
1.0
|
C5
|
A:SSB378
|
4.1
|
12.1
|
1.0
|
CB
|
A:SER48
|
4.2
|
6.1
|
1.0
|
CG
|
A:HIS67
|
4.2
|
6.2
|
1.0
|
ND1
|
A:HIS67
|
4.2
|
5.6
|
1.0
|
NH2
|
A:ARG369
|
4.5
|
11.2
|
1.0
|
OE2
|
A:GLU68
|
4.6
|
12.7
|
1.0
|
CA
|
A:CYS46
|
4.6
|
7.8
|
1.0
|
C2
|
A:SSB378
|
4.6
|
13.2
|
1.0
|
CA
|
A:CYS174
|
4.7
|
6.8
|
1.0
|
N
|
A:SER48
|
4.9
|
7.3
|
1.0
|
N
|
A:GLY175
|
4.9
|
7.2
|
1.0
|
CE2
|
A:PHE93
|
4.9
|
9.2
|
1.0
|
|
Zinc binding site 2 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 2 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn376
b:9.6
occ:1.00
|
SG
|
A:CYS103
|
2.3
|
10.4
|
1.0
|
SG
|
A:CYS100
|
2.3
|
8.7
|
1.0
|
SG
|
A:CYS111
|
2.3
|
8.7
|
1.0
|
SG
|
A:CYS97
|
2.3
|
10.9
|
1.0
|
CB
|
A:CYS103
|
3.3
|
12.1
|
1.0
|
CB
|
A:CYS111
|
3.3
|
7.3
|
1.0
|
CB
|
A:CYS100
|
3.4
|
12.1
|
1.0
|
CB
|
A:CYS97
|
3.5
|
10.2
|
1.0
|
N
|
A:CYS97
|
3.6
|
9.4
|
1.0
|
CA
|
A:CYS111
|
3.7
|
9.0
|
1.0
|
N
|
A:CYS100
|
3.9
|
13.3
|
1.0
|
N
|
A:LEU112
|
3.9
|
8.5
|
1.0
|
CA
|
A:CYS97
|
3.9
|
9.1
|
1.0
|
N
|
A:GLY98
|
3.9
|
12.1
|
1.0
|
CA
|
A:CYS100
|
4.2
|
13.2
|
1.0
|
N
|
A:CYS103
|
4.2
|
11.4
|
1.0
|
C
|
A:CYS111
|
4.2
|
8.0
|
1.0
|
C
|
A:CYS97
|
4.3
|
12.8
|
1.0
|
CA
|
A:CYS103
|
4.3
|
11.3
|
1.0
|
N
|
A:LYS99
|
4.5
|
15.3
|
1.0
|
C
|
A:GLN96
|
4.7
|
10.4
|
1.0
|
N
|
A:LYS113
|
4.7
|
10.1
|
1.0
|
O
|
A:HOH595
|
4.8
|
23.7
|
1.0
|
CG
|
A:LYS113
|
4.8
|
13.3
|
1.0
|
O
|
A:CYS100
|
4.9
|
12.8
|
1.0
|
C
|
A:CYS100
|
4.9
|
13.7
|
1.0
|
CA
|
A:GLY98
|
4.9
|
13.2
|
1.0
|
CA
|
A:GLN96
|
5.0
|
8.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 3 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn375
b:10.0
occ:1.00
|
SG
|
B:CYS46
|
2.1
|
11.2
|
1.0
|
NE2
|
B:HIS67
|
2.1
|
4.0
|
1.0
|
O6
|
B:SSB378
|
2.2
|
6.3
|
1.0
|
SG
|
B:CYS174
|
2.3
|
8.4
|
1.0
|
CD2
|
B:HIS67
|
3.0
|
3.6
|
1.0
|
S1
|
B:SSB378
|
3.1
|
9.4
|
1.0
|
CE1
|
B:HIS67
|
3.1
|
7.8
|
1.0
|
CB
|
B:CYS46
|
3.2
|
8.6
|
1.0
|
CB
|
B:CYS174
|
3.4
|
7.4
|
1.0
|
C5N
|
B:NAD377
|
3.4
|
6.1
|
1.0
|
OG
|
B:SER48
|
4.0
|
6.8
|
1.0
|
C4N
|
B:NAD377
|
4.0
|
5.7
|
1.0
|
C6N
|
B:NAD377
|
4.0
|
6.2
|
1.0
|
CB
|
B:SER48
|
4.1
|
5.1
|
1.0
|
C5
|
B:SSB378
|
4.2
|
11.6
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
4.6
|
1.0
|
CG
|
B:HIS67
|
4.2
|
5.2
|
1.0
|
NH2
|
B:ARG369
|
4.5
|
8.1
|
1.0
|
OE2
|
B:GLU68
|
4.6
|
10.6
|
1.0
|
C2
|
B:SSB378
|
4.6
|
10.4
|
1.0
|
CA
|
B:CYS46
|
4.7
|
8.1
|
1.0
|
CA
|
B:CYS174
|
4.7
|
7.7
|
1.0
|
N
|
B:SER48
|
4.9
|
6.2
|
1.0
|
N
|
B:GLY175
|
4.9
|
6.0
|
1.0
|
CE2
|
B:PHE93
|
4.9
|
7.6
|
1.0
|
C
|
B:CYS174
|
5.0
|
7.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 4 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn376
b:11.3
occ:1.00
|
SG
|
B:CYS111
|
2.3
|
10.2
|
1.0
|
SG
|
B:CYS103
|
2.3
|
11.2
|
1.0
|
SG
|
B:CYS100
|
2.3
|
10.9
|
1.0
|
SG
|
B:CYS97
|
2.4
|
13.5
|
1.0
|
CB
|
B:CYS111
|
3.3
|
9.3
|
1.0
|
CB
|
B:CYS103
|
3.4
|
10.8
|
1.0
|
CB
|
B:CYS100
|
3.4
|
14.2
|
1.0
|
CB
|
B:CYS97
|
3.5
|
12.4
|
1.0
|
N
|
B:CYS97
|
3.6
|
10.5
|
1.0
|
CA
|
B:CYS111
|
3.7
|
10.0
|
1.0
|
N
|
B:CYS100
|
3.9
|
17.4
|
1.0
|
CA
|
B:CYS97
|
3.9
|
11.2
|
1.0
|
N
|
B:LEU112
|
4.0
|
9.7
|
1.0
|
N
|
B:GLY98
|
4.0
|
14.0
|
1.0
|
N
|
B:CYS103
|
4.2
|
11.6
|
1.0
|
CA
|
B:CYS100
|
4.2
|
15.3
|
1.0
|
C
|
B:CYS111
|
4.3
|
8.9
|
1.0
|
C
|
B:CYS97
|
4.3
|
15.3
|
1.0
|
CA
|
B:CYS103
|
4.3
|
11.4
|
1.0
|
N
|
B:LYS99
|
4.5
|
16.3
|
1.0
|
C
|
B:GLN96
|
4.6
|
11.5
|
1.0
|
O
|
B:HOH607
|
4.8
|
32.4
|
1.0
|
N
|
B:LYS113
|
4.8
|
9.7
|
1.0
|
C
|
B:CYS100
|
4.9
|
15.8
|
1.0
|
CG
|
B:LYS113
|
4.9
|
16.4
|
1.0
|
O
|
B:CYS100
|
4.9
|
14.6
|
1.0
|
CA
|
B:GLN96
|
4.9
|
9.5
|
1.0
|
CA
|
B:GLY98
|
5.0
|
14.2
|
1.0
|
|
Zinc binding site 5 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 5 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn375
b:12.3
occ:1.00
|
NE2
|
C:HIS67
|
2.1
|
9.4
|
1.0
|
SG
|
C:CYS46
|
2.2
|
10.4
|
1.0
|
O6
|
C:SSB378
|
2.2
|
12.4
|
1.0
|
SG
|
C:CYS174
|
2.3
|
12.7
|
1.0
|
CD2
|
C:HIS67
|
3.0
|
7.6
|
1.0
|
S1
|
C:SSB378
|
3.1
|
14.1
|
1.0
|
CE1
|
C:HIS67
|
3.1
|
9.2
|
1.0
|
CB
|
C:CYS46
|
3.2
|
10.1
|
1.0
|
CB
|
C:CYS174
|
3.4
|
10.1
|
1.0
|
C5N
|
C:NAD377
|
3.4
|
10.4
|
1.0
|
OG
|
C:SER48
|
4.0
|
10.1
|
1.0
|
C4N
|
C:NAD377
|
4.1
|
7.9
|
1.0
|
C6N
|
C:NAD377
|
4.1
|
8.6
|
1.0
|
C5
|
C:SSB378
|
4.1
|
14.4
|
1.0
|
CG
|
C:HIS67
|
4.2
|
10.3
|
1.0
|
ND1
|
C:HIS67
|
4.3
|
7.5
|
1.0
|
CB
|
C:SER48
|
4.3
|
9.7
|
1.0
|
NH2
|
C:ARG369
|
4.5
|
12.2
|
1.0
|
C2
|
C:SSB378
|
4.6
|
15.3
|
1.0
|
OE2
|
C:GLU68
|
4.7
|
13.1
|
1.0
|
CA
|
C:CYS46
|
4.7
|
10.0
|
1.0
|
CA
|
C:CYS174
|
4.7
|
9.5
|
1.0
|
N
|
C:SER48
|
4.9
|
6.7
|
1.0
|
CE2
|
C:PHE93
|
4.9
|
10.4
|
1.0
|
N
|
C:GLY175
|
5.0
|
8.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 6 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn376
b:10.2
occ:1.00
|
SG
|
C:CYS103
|
2.1
|
12.0
|
1.0
|
SG
|
C:CYS100
|
2.3
|
10.7
|
1.0
|
SG
|
C:CYS111
|
2.3
|
8.3
|
1.0
|
SG
|
C:CYS97
|
2.4
|
10.7
|
1.0
|
CB
|
C:CYS103
|
3.3
|
11.8
|
1.0
|
CB
|
C:CYS100
|
3.3
|
11.2
|
1.0
|
CB
|
C:CYS111
|
3.4
|
9.5
|
1.0
|
CB
|
C:CYS97
|
3.6
|
8.7
|
1.0
|
N
|
C:CYS97
|
3.6
|
8.3
|
1.0
|
CA
|
C:CYS111
|
3.7
|
8.2
|
1.0
|
N
|
C:CYS100
|
3.9
|
13.0
|
1.0
|
CA
|
C:CYS97
|
3.9
|
7.0
|
1.0
|
N
|
C:LEU112
|
4.0
|
8.0
|
1.0
|
N
|
C:GLY98
|
4.0
|
12.9
|
1.0
|
CA
|
C:CYS100
|
4.2
|
11.4
|
1.0
|
N
|
C:CYS103
|
4.2
|
9.1
|
1.0
|
C
|
C:CYS111
|
4.2
|
7.5
|
1.0
|
CA
|
C:CYS103
|
4.3
|
9.8
|
1.0
|
C
|
C:CYS97
|
4.3
|
12.1
|
1.0
|
N
|
C:LYS99
|
4.5
|
13.4
|
1.0
|
C
|
C:GLN96
|
4.6
|
7.2
|
1.0
|
N
|
C:LYS113
|
4.9
|
10.3
|
1.0
|
O
|
C:CYS100
|
4.9
|
10.2
|
1.0
|
CA
|
C:GLN96
|
4.9
|
7.9
|
1.0
|
CG
|
C:LYS113
|
4.9
|
14.7
|
1.0
|
C
|
C:CYS100
|
4.9
|
10.7
|
1.0
|
CA
|
C:GLY98
|
5.0
|
12.8
|
1.0
|
|
Zinc binding site 7 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 7 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn375
b:12.2
occ:1.00
|
NE2
|
D:HIS67
|
2.1
|
10.4
|
1.0
|
O6
|
D:SSB378
|
2.2
|
14.4
|
1.0
|
SG
|
D:CYS174
|
2.2
|
10.5
|
1.0
|
SG
|
D:CYS46
|
2.3
|
10.8
|
1.0
|
CD2
|
D:HIS67
|
3.0
|
8.8
|
1.0
|
CE1
|
D:HIS67
|
3.1
|
11.4
|
1.0
|
S1
|
D:SSB378
|
3.1
|
14.6
|
1.0
|
CB
|
D:CYS46
|
3.3
|
10.7
|
1.0
|
CB
|
D:CYS174
|
3.4
|
9.2
|
1.0
|
C5N
|
D:NAD377
|
3.4
|
6.6
|
1.0
|
C6N
|
D:NAD377
|
4.1
|
5.5
|
1.0
|
C4N
|
D:NAD377
|
4.1
|
7.5
|
1.0
|
OG
|
D:SER48
|
4.1
|
10.3
|
1.0
|
C5
|
D:SSB378
|
4.1
|
16.5
|
1.0
|
CG
|
D:HIS67
|
4.2
|
10.4
|
1.0
|
CB
|
D:SER48
|
4.2
|
9.5
|
1.0
|
ND1
|
D:HIS67
|
4.2
|
9.5
|
1.0
|
NH2
|
D:ARG369
|
4.5
|
10.6
|
1.0
|
OE2
|
D:GLU68
|
4.6
|
11.7
|
1.0
|
C2
|
D:SSB378
|
4.6
|
14.4
|
1.0
|
CA
|
D:CYS46
|
4.7
|
10.9
|
1.0
|
CA
|
D:CYS174
|
4.7
|
8.1
|
1.0
|
N
|
D:SER48
|
4.9
|
5.2
|
1.0
|
N
|
D:GLY175
|
5.0
|
7.1
|
1.0
|
CE2
|
D:PHE93
|
5.0
|
9.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 3bto
Go back to
Zinc Binding Sites List in 3bto
Zinc binding site 8 out
of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3S)3-Butylthiolane 1-Oxide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn376
b:11.8
occ:1.00
|
SG
|
D:CYS103
|
2.3
|
13.4
|
1.0
|
SG
|
D:CYS111
|
2.3
|
10.4
|
1.0
|
SG
|
D:CYS100
|
2.3
|
14.0
|
1.0
|
SG
|
D:CYS97
|
2.4
|
11.4
|
1.0
|
CB
|
D:CYS100
|
3.4
|
13.4
|
1.0
|
CB
|
D:CYS111
|
3.4
|
9.5
|
1.0
|
CB
|
D:CYS103
|
3.4
|
11.9
|
1.0
|
CB
|
D:CYS97
|
3.5
|
7.7
|
1.0
|
N
|
D:CYS97
|
3.5
|
8.3
|
1.0
|
CA
|
D:CYS111
|
3.7
|
10.0
|
1.0
|
N
|
D:CYS100
|
3.8
|
14.8
|
1.0
|
CA
|
D:CYS97
|
3.9
|
9.1
|
1.0
|
N
|
D:GLY98
|
4.0
|
14.1
|
1.0
|
N
|
D:LEU112
|
4.0
|
10.4
|
1.0
|
N
|
D:CYS103
|
4.2
|
11.6
|
1.0
|
CA
|
D:CYS100
|
4.2
|
14.4
|
1.0
|
C
|
D:CYS97
|
4.3
|
14.2
|
1.0
|
C
|
D:CYS111
|
4.3
|
11.2
|
1.0
|
CA
|
D:CYS103
|
4.4
|
10.9
|
1.0
|
N
|
D:LYS99
|
4.5
|
16.8
|
1.0
|
C
|
D:GLN96
|
4.6
|
8.7
|
1.0
|
O
|
D:HOH603
|
4.8
|
27.2
|
1.0
|
N
|
D:LYS113
|
4.9
|
11.4
|
1.0
|
CA
|
D:GLN96
|
4.9
|
8.3
|
1.0
|
C
|
D:CYS100
|
4.9
|
12.5
|
1.0
|
CA
|
D:GLY98
|
4.9
|
15.3
|
1.0
|
O
|
D:CYS100
|
4.9
|
12.8
|
1.0
|
CG
|
D:LYS113
|
4.9
|
17.6
|
1.0
|
|
Reference:
H.Cho,
S.Ramaswamy,
B.V.Plapp.
Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides. Biochemistry V. 36 382 1997.
ISSN: ISSN 0006-2960
PubMed: 9003191
DOI: 10.1021/BI9624604
Page generated: Thu Oct 24 11:37:19 2024
|