Zinc in PDB 8e7u: F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
Enzymatic activity of F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
All present enzymatic activity of F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide:
1.1.1.1;
Protein crystallography data
The structure of F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 8e7u
was solved by
C.Zheng,
S.G.Boxer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.02 /
1.19
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.245,
50.771,
92.686,
92.32,
102.96,
109.31
|
R / Rfree (%)
|
14.5 /
15.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
(pdb code 8e7u). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide, PDB code: 8e7u:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8e7u
Go back to
Zinc Binding Sites List in 8e7u
Zinc binding site 1 out
of 4 in the F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/e7/8e7u-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/e7/8e7u-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 F93A 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:10.5
occ:1.00
|
NE2
|
A:HIS67
|
2.0
|
9.6
|
1.0
|
O9
|
A:CXF404
|
2.1
|
10.2
|
1.0
|
SG
|
A:CYS174
|
2.3
|
9.5
|
1.0
|
SG
|
A:CYS46
|
2.3
|
9.7
|
1.0
|
C7
|
A:CXF404
|
2.9
|
10.9
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
10.0
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
10.3
|
1.0
|
CB
|
A:CYS46
|
3.3
|
10.3
|
1.0
|
CB
|
A:CYS174
|
3.3
|
9.2
|
1.0
|
C5N
|
A:NAI403
|
3.4
|
9.4
|
1.0
|
OG
|
A:SER48
|
4.0
|
9.9
|
1.0
|
C4N
|
A:NAI403
|
4.0
|
9.6
|
1.0
|
CB
|
A:SER48
|
4.1
|
9.4
|
1.0
|
ND1
|
A:HIS67
|
4.1
|
10.2
|
1.0
|
C6N
|
A:NAI403
|
4.1
|
10.1
|
1.0
|
N8
|
A:CXF404
|
4.2
|
12.0
|
1.0
|
CG
|
A:HIS67
|
4.2
|
9.3
|
1.0
|
OE2
|
A:GLU68
|
4.5
|
11.7
|
1.0
|
CA
|
A:CYS174
|
4.7
|
9.5
|
1.0
|
NH2
|
A:ARG369
|
4.7
|
11.4
|
1.0
|
CA
|
A:CYS46
|
4.7
|
9.7
|
1.0
|
N
|
A:GLY175
|
4.9
|
9.6
|
1.0
|
N
|
A:SER48
|
4.9
|
9.2
|
1.0
|
O
|
A:HOH801
|
5.0
|
10.9
|
1.0
|
C1
|
A:CXF404
|
5.0
|
12.5
|
1.0
|
C
|
A:CYS174
|
5.0
|
9.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8e7u
Go back to
Zinc Binding Sites List in 8e7u
Zinc binding site 2 out
of 4 in the F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/e7/8e7u-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/e7/8e7u-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 F93A 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:12.0
occ:1.00
|
SG
|
A:CYS97
|
2.3
|
12.6
|
1.0
|
SG
|
A:CYS103
|
2.3
|
11.2
|
1.0
|
SG
|
A:CYS111
|
2.3
|
10.8
|
1.0
|
SG
|
A:CYS100
|
2.3
|
11.5
|
1.0
|
CB
|
A:CYS111
|
3.3
|
10.3
|
1.0
|
CB
|
A:CYS97
|
3.4
|
13.0
|
1.0
|
CB
|
A:CYS100
|
3.4
|
12.5
|
1.0
|
CB
|
A:CYS103
|
3.4
|
11.8
|
1.0
|
N
|
A:CYS97
|
3.5
|
11.4
|
1.0
|
CA
|
A:CYS111
|
3.7
|
10.3
|
1.0
|
N
|
A:CYS100
|
3.8
|
14.6
|
1.0
|
CA
|
A:CYS97
|
3.9
|
13.7
|
1.0
|
N
|
A:GLY98
|
4.0
|
12.9
|
1.0
|
N
|
A:LEU112
|
4.0
|
10.9
|
1.0
|
CA
|
A:CYS100
|
4.2
|
13.2
|
1.0
|
N
|
A:CYS103
|
4.2
|
11.4
|
1.0
|
C
|
A:CYS111
|
4.3
|
11.6
|
1.0
|
C
|
A:CYS97
|
4.3
|
13.3
|
1.0
|
CA
|
A:CYS103
|
4.4
|
11.8
|
1.0
|
N
|
A:LYS99
|
4.4
|
14.0
|
1.0
|
C
|
A:GLN96
|
4.6
|
11.5
|
1.0
|
CG
|
A:LYS113
|
4.7
|
16.1
|
1.0
|
C
|
A:CYS100
|
4.8
|
12.6
|
1.0
|
N
|
A:LYS113
|
4.8
|
11.1
|
1.0
|
O
|
A:CYS100
|
4.9
|
13.2
|
1.0
|
CA
|
A:GLN96
|
4.9
|
10.2
|
1.0
|
CA
|
A:GLY98
|
5.0
|
14.6
|
1.0
|
C
|
A:LYS99
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8e7u
Go back to
Zinc Binding Sites List in 8e7u
Zinc binding site 3 out
of 4 in the F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/e7/8e7u-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/e7/8e7u-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 F93A 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:12.8
occ:1.00
|
NE2
|
B:HIS67
|
2.1
|
12.8
|
1.0
|
O9
|
B:CXF404
|
2.1
|
13.0
|
1.0
|
SG
|
B:CYS174
|
2.3
|
11.6
|
1.0
|
SG
|
B:CYS46
|
2.3
|
12.1
|
1.0
|
C7
|
B:CXF404
|
2.9
|
13.2
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
13.0
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
12.4
|
1.0
|
CB
|
B:CYS46
|
3.3
|
12.9
|
1.0
|
CB
|
B:CYS174
|
3.3
|
11.6
|
1.0
|
C5N
|
B:NAI403
|
3.4
|
11.7
|
1.0
|
OG
|
B:SER48
|
3.9
|
12.4
|
1.0
|
C4N
|
B:NAI403
|
4.0
|
11.4
|
1.0
|
CB
|
B:SER48
|
4.0
|
12.6
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
12.6
|
1.0
|
C6N
|
B:NAI403
|
4.2
|
11.7
|
1.0
|
N8
|
B:CXF404
|
4.2
|
14.2
|
1.0
|
CG
|
B:HIS67
|
4.2
|
12.2
|
1.0
|
OE2
|
B:GLU68
|
4.6
|
13.7
|
1.0
|
NH2
|
B:ARG369
|
4.7
|
12.7
|
1.0
|
CA
|
B:CYS174
|
4.7
|
11.9
|
1.0
|
CA
|
B:CYS46
|
4.7
|
11.2
|
1.0
|
N
|
B:SER48
|
4.9
|
11.4
|
1.0
|
N
|
B:GLY175
|
4.9
|
11.7
|
1.0
|
O
|
B:HOH737
|
5.0
|
13.0
|
1.0
|
C1
|
B:CXF404
|
5.0
|
15.1
|
1.0
|
C
|
B:CYS174
|
5.0
|
11.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8e7u
Go back to
Zinc Binding Sites List in 8e7u
Zinc binding site 4 out
of 4 in the F93A Horse Liver Alcohol Dehydrogenase in Complex with Nadh and N- Cyclohexylformamide
![](/pictures/ZN/pdb/e7/8e7u-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/e7/8e7u-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 F93A 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:14.8
occ:1.00
|
SG
|
B:CYS111
|
2.3
|
13.2
|
1.0
|
SG
|
B:CYS97
|
2.3
|
15.5
|
1.0
|
SG
|
B:CYS103
|
2.4
|
13.2
|
1.0
|
SG
|
B:CYS100
|
2.4
|
14.2
|
1.0
|
CB
|
B:CYS111
|
3.3
|
12.2
|
1.0
|
CB
|
B:CYS97
|
3.4
|
16.9
|
1.0
|
CB
|
B:CYS103
|
3.4
|
13.7
|
1.0
|
CB
|
B:CYS100
|
3.4
|
16.0
|
1.0
|
N
|
B:CYS97
|
3.5
|
13.6
|
1.0
|
CA
|
B:CYS111
|
3.8
|
12.1
|
1.0
|
N
|
B:CYS100
|
3.8
|
17.0
|
1.0
|
CA
|
B:CYS97
|
3.9
|
15.3
|
1.0
|
N
|
B:GLY98
|
3.9
|
14.6
|
1.0
|
N
|
B:LEU112
|
4.0
|
12.9
|
1.0
|
CA
|
B:CYS100
|
4.2
|
17.6
|
1.0
|
N
|
B:CYS103
|
4.2
|
13.1
|
1.0
|
C
|
B:CYS111
|
4.3
|
13.2
|
1.0
|
C
|
B:CYS97
|
4.3
|
15.6
|
1.0
|
CA
|
B:CYS103
|
4.4
|
13.4
|
1.0
|
N
|
B:LYS99
|
4.5
|
17.1
|
1.0
|
C
|
B:GLN96
|
4.6
|
14.4
|
1.0
|
CG
|
B:LYS113
|
4.8
|
18.9
|
1.0
|
N
|
B:LYS113
|
4.8
|
13.7
|
1.0
|
C
|
B:CYS100
|
4.8
|
15.9
|
1.0
|
O
|
B:CYS100
|
4.9
|
16.0
|
1.0
|
CA
|
B:GLN96
|
4.9
|
12.7
|
1.0
|
CA
|
B:GLY98
|
4.9
|
17.4
|
1.0
|
C
|
B:LYS99
|
5.0
|
18.7
|
1.0
|
|
Reference:
C.Zheng,
S.G.Boxer.
Structure of F93A Horse Liver Alcohol Dehydrogenase at 1.20 Angstroms Resolution To Be Published.
Page generated: Thu Dec 28 12:57:33 2023
|