Zinc in PDB 8ecu: F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
Enzymatic activity of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
All present enzymatic activity of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide:
1.1.1.1;
Protein crystallography data
The structure of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 8ecu
was solved by
C.Zheng,
I.I.Mathews,
S.G.Boxer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.27 /
1.30
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.03,
49.77,
92.57,
93.27,
102.8,
108.49
|
R / Rfree (%)
|
14.2 /
16.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
(pdb code 8ecu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 8ecu:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8ecu
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Zinc Binding Sites List in 8ecu
Zinc binding site 1 out
of 4 in the F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:16.6
occ:1.00
|
NE2
|
A:HIS67
|
2.0
|
14.4
|
1.0
|
O9
|
A:CXF404
|
2.1
|
16.6
|
1.0
|
SG
|
A:CYS174
|
2.3
|
15.4
|
1.0
|
SG
|
A:CYS46
|
2.3
|
14.9
|
1.0
|
C7
|
A:CXF404
|
2.9
|
17.5
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
14.3
|
1.0
|
CD2
|
A:HIS67
|
3.0
|
14.2
|
1.0
|
CB
|
A:CYS46
|
3.3
|
14.7
|
1.0
|
CB
|
A:CYS174
|
3.3
|
14.4
|
1.0
|
C5N
|
A:NAI403
|
3.4
|
13.6
|
1.0
|
OG
|
A:SER48
|
3.9
|
14.3
|
1.0
|
C4N
|
A:NAI403
|
4.0
|
13.1
|
1.0
|
CB
|
A:SER48
|
4.0
|
13.4
|
1.0
|
ND1
|
A:HIS67
|
4.1
|
13.9
|
1.0
|
N8
|
A:CXF404
|
4.2
|
19.6
|
1.0
|
C6N
|
A:NAI403
|
4.2
|
13.4
|
1.0
|
CG
|
A:HIS67
|
4.2
|
12.8
|
1.0
|
OE1
|
A:GLU68
|
4.5
|
19.1
|
1.0
|
CA
|
A:CYS174
|
4.7
|
14.5
|
1.0
|
CA
|
A:CYS46
|
4.7
|
15.2
|
1.0
|
NH2
|
A:ARG369
|
4.7
|
16.9
|
1.0
|
N
|
A:GLY175
|
4.9
|
14.0
|
1.0
|
N
|
A:SER48
|
4.9
|
13.5
|
1.0
|
C
|
A:CYS174
|
5.0
|
14.5
|
1.0
|
C1
|
A:CXF404
|
5.0
|
20.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8ecu
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Zinc Binding Sites List in 8ecu
Zinc binding site 2 out
of 4 in the F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:16.3
occ:1.00
|
SG
|
A:CYS100
|
2.3
|
16.6
|
1.0
|
SG
|
A:CYS97
|
2.3
|
17.8
|
1.0
|
SG
|
A:CYS111
|
2.3
|
14.9
|
1.0
|
SG
|
A:CYS103
|
2.4
|
16.0
|
1.0
|
CB
|
A:CYS111
|
3.3
|
14.9
|
1.0
|
CB
|
A:CYS103
|
3.4
|
16.9
|
1.0
|
CB
|
A:CYS97
|
3.4
|
18.2
|
1.0
|
CB
|
A:CYS100
|
3.4
|
16.9
|
1.0
|
N
|
A:CYS97
|
3.5
|
15.7
|
1.0
|
CA
|
A:CYS111
|
3.7
|
14.0
|
1.0
|
N
|
A:CYS100
|
3.9
|
19.4
|
1.0
|
CA
|
A:CYS97
|
3.9
|
17.6
|
1.0
|
N
|
A:GLY98
|
3.9
|
17.7
|
1.0
|
N
|
A:LEU112
|
4.0
|
15.8
|
1.0
|
N
|
A:CYS103
|
4.2
|
16.8
|
1.0
|
CA
|
A:CYS100
|
4.2
|
18.1
|
1.0
|
C
|
A:CYS111
|
4.3
|
14.7
|
1.0
|
C
|
A:CYS97
|
4.3
|
18.4
|
1.0
|
CA
|
A:CYS103
|
4.4
|
16.9
|
1.0
|
N
|
A:LYS99
|
4.4
|
20.4
|
1.0
|
C
|
A:GLN96
|
4.6
|
16.1
|
1.0
|
CG
|
A:LYS113
|
4.8
|
20.6
|
1.0
|
N
|
A:LYS113
|
4.8
|
15.6
|
1.0
|
C
|
A:CYS100
|
4.9
|
17.6
|
1.0
|
CA
|
A:GLY98
|
4.9
|
20.4
|
1.0
|
O
|
A:CYS100
|
4.9
|
17.5
|
1.0
|
CA
|
A:GLN96
|
5.0
|
15.1
|
1.0
|
C
|
A:LYS99
|
5.0
|
22.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8ecu
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Zinc Binding Sites List in 8ecu
Zinc binding site 3 out
of 4 in the F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:19.4
occ:1.00
|
NE2
|
B:HIS67
|
2.1
|
18.4
|
1.0
|
O9
|
B:CXF404
|
2.1
|
20.3
|
1.0
|
SG
|
B:CYS174
|
2.3
|
18.0
|
1.0
|
SG
|
B:CYS46
|
2.3
|
17.8
|
1.0
|
C7
|
B:CXF404
|
2.9
|
19.9
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
17.7
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
18.5
|
1.0
|
CB
|
B:CYS46
|
3.3
|
18.6
|
1.0
|
CB
|
B:CYS174
|
3.4
|
17.0
|
1.0
|
C5N
|
B:NAI403
|
3.5
|
16.7
|
1.0
|
OG
|
B:SER48
|
4.0
|
16.6
|
1.0
|
C4N
|
B:NAI403
|
4.0
|
16.1
|
1.0
|
CB
|
B:SER48
|
4.1
|
17.1
|
1.0
|
ND1
|
B:HIS67
|
4.1
|
17.6
|
1.0
|
CG
|
B:HIS67
|
4.2
|
17.9
|
1.0
|
N8
|
B:CXF404
|
4.2
|
21.2
|
1.0
|
C6N
|
B:NAI403
|
4.2
|
16.3
|
1.0
|
OE1
|
B:GLU68
|
4.4
|
23.4
|
1.0
|
NH2
|
B:ARG369
|
4.7
|
19.6
|
1.0
|
CA
|
B:CYS174
|
4.7
|
16.4
|
1.0
|
CA
|
B:CYS46
|
4.7
|
18.4
|
1.0
|
N
|
B:GLY175
|
4.9
|
16.6
|
1.0
|
N
|
B:SER48
|
4.9
|
16.0
|
1.0
|
C
|
B:CYS174
|
5.0
|
17.0
|
1.0
|
C1
|
B:CXF404
|
5.0
|
21.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8ecu
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Zinc Binding Sites List in 8ecu
Zinc binding site 4 out
of 4 in the F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ec/8ecu-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of F93S Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:18.9
occ:1.00
|
SG
|
B:CYS103
|
2.3
|
18.6
|
1.0
|
SG
|
B:CYS111
|
2.3
|
18.4
|
1.0
|
SG
|
B:CYS100
|
2.3
|
19.6
|
1.0
|
SG
|
B:CYS97
|
2.3
|
21.2
|
1.0
|
CB
|
B:CYS111
|
3.3
|
18.0
|
1.0
|
CB
|
B:CYS103
|
3.4
|
18.6
|
1.0
|
CB
|
B:CYS100
|
3.4
|
22.0
|
1.0
|
CB
|
B:CYS97
|
3.4
|
20.9
|
1.0
|
N
|
B:CYS97
|
3.5
|
19.4
|
1.0
|
CA
|
B:CYS111
|
3.8
|
17.0
|
1.0
|
N
|
B:CYS100
|
3.8
|
23.1
|
1.0
|
CA
|
B:CYS97
|
3.9
|
21.0
|
1.0
|
N
|
B:GLY98
|
3.9
|
22.3
|
1.0
|
N
|
B:LEU112
|
4.0
|
18.5
|
1.0
|
N
|
B:CYS103
|
4.2
|
17.8
|
1.0
|
CA
|
B:CYS100
|
4.2
|
23.4
|
1.0
|
C
|
B:CYS97
|
4.3
|
21.4
|
1.0
|
C
|
B:CYS111
|
4.3
|
17.4
|
1.0
|
CA
|
B:CYS103
|
4.4
|
18.4
|
1.0
|
N
|
B:LYS99
|
4.4
|
25.3
|
1.0
|
C
|
B:GLN96
|
4.6
|
17.9
|
1.0
|
CG
|
B:LYS113
|
4.8
|
23.9
|
1.0
|
N
|
B:LYS113
|
4.8
|
19.8
|
1.0
|
C
|
B:CYS100
|
4.8
|
22.2
|
1.0
|
CA
|
B:GLY98
|
4.9
|
23.7
|
1.0
|
O
|
B:CYS100
|
4.9
|
22.8
|
1.0
|
CA
|
B:GLN96
|
4.9
|
17.2
|
1.0
|
C
|
B:LYS99
|
5.0
|
25.9
|
1.0
|
|
Reference:
C.Zheng,
I.I.Mathews,
S.G.Boxer.
Structure of F93S Horse Liver Alcohol Dehydrogenase at 1.30 Angstroms Resolution To Be Published.
Page generated: Thu Dec 28 12:57:36 2023
|