Zinc in PDB 7ude: Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
Enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K:
1.1.1.1;
Protein crystallography data
The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude
was solved by
B.V.Plapp,
L.Gakhar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.97 /
1.10
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.28,
51.18,
92.59,
91.9,
103.02,
109.89
|
R / Rfree (%)
|
13.3 /
16
|
Other elements in 7ude:
The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
(pdb code 7ude). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7ude
Go back to
Zinc Binding Sites List in 7ude
Zinc binding site 1 out
of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
![](/pictures/ZN/pdb/ud/7ude-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ud/7ude-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 Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:10.4
occ:1.00
|
O
|
A:ETF404
|
1.9
|
10.4
|
1.0
|
NE2
|
A:HIS67
|
2.0
|
10.2
|
1.0
|
SG
|
A:CYS174
|
2.3
|
10.1
|
1.0
|
SG
|
A:CYS46
|
2.3
|
9.8
|
1.0
|
C2
|
A:ETF404
|
2.9
|
11.9
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
9.2
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
9.9
|
1.0
|
CB
|
A:CYS46
|
3.3
|
9.8
|
1.0
|
C5N
|
A:NAJ403
|
3.3
|
9.2
|
1.0
|
CB
|
A:CYS174
|
3.4
|
9.5
|
1.0
|
OG
|
A:SER48
|
3.7
|
9.8
|
1.0
|
C4N
|
A:NAJ403
|
4.0
|
9.3
|
1.0
|
C6N
|
A:NAJ403
|
4.0
|
9.0
|
1.0
|
CB
|
A:SER48
|
4.0
|
8.9
|
1.0
|
ND1
|
A:HIS67
|
4.2
|
9.2
|
1.0
|
CG
|
A:HIS67
|
4.2
|
8.8
|
1.0
|
C1
|
A:ETF404
|
4.2
|
14.2
|
1.0
|
F3
|
A:ETF404
|
4.6
|
17.0
|
1.0
|
NH2
|
A:ARG369
|
4.6
|
10.6
|
1.0
|
CA
|
A:CYS174
|
4.7
|
8.9
|
1.0
|
CA
|
A:CYS46
|
4.8
|
10.0
|
1.0
|
F1
|
A:ETF404
|
4.8
|
17.1
|
1.0
|
OE2
|
A:GLU68
|
4.8
|
11.8
|
1.0
|
N
|
A:SER48
|
4.8
|
8.9
|
1.0
|
CE2
|
A:PHE93
|
4.9
|
10.4
|
1.0
|
N1N
|
A:NAJ403
|
5.0
|
8.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7ude
Go back to
Zinc Binding Sites List in 7ude
Zinc binding site 2 out
of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
![](/pictures/ZN/pdb/ud/7ude-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ud/7ude-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 Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:11.3
occ:1.00
|
SG
|
A:CYS111
|
2.3
|
11.0
|
1.0
|
SG
|
A:CYS97
|
2.3
|
13.3
|
1.0
|
SG
|
A:CYS100
|
2.3
|
11.9
|
1.0
|
SG
|
A:CYS103
|
2.4
|
11.1
|
1.0
|
CB
|
A:CYS111
|
3.3
|
10.6
|
1.0
|
CB
|
A:CYS97
|
3.4
|
13.0
|
1.0
|
CB
|
A:CYS100
|
3.4
|
13.5
|
1.0
|
CB
|
A:CYS103
|
3.4
|
11.4
|
1.0
|
N
|
A:CYS97
|
3.5
|
10.9
|
1.0
|
CA
|
A:CYS111
|
3.7
|
10.4
|
1.0
|
N
|
A:CYS100
|
3.9
|
14.5
|
1.0
|
CA
|
A:CYS97
|
3.9
|
11.9
|
1.0
|
N
|
A:GLY98
|
4.0
|
12.8
|
1.0
|
N
|
A:LEU112
|
4.0
|
10.6
|
1.0
|
N
|
A:CYS103
|
4.2
|
10.8
|
1.0
|
CA
|
A:CYS100
|
4.2
|
14.4
|
1.0
|
C
|
A:CYS97
|
4.3
|
12.8
|
1.0
|
C
|
A:CYS111
|
4.3
|
10.8
|
1.0
|
CA
|
A:CYS103
|
4.4
|
10.8
|
1.0
|
N
|
A:LYS99
|
4.5
|
14.9
|
1.0
|
C
|
A:GLN96
|
4.6
|
10.7
|
1.0
|
C
|
A:CYS100
|
4.9
|
13.2
|
1.0
|
N
|
A:LYS113
|
4.9
|
11.2
|
1.0
|
CG
|
A:LYS113
|
4.9
|
16.3
|
1.0
|
O
|
A:CYS100
|
4.9
|
12.4
|
1.0
|
CA
|
A:GLN96
|
4.9
|
10.4
|
1.0
|
O
|
A:HOH886
|
4.9
|
32.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7ude
Go back to
Zinc Binding Sites List in 7ude
Zinc binding site 3 out
of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
![](/pictures/ZN/pdb/ud/7ude-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ud/7ude-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 Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:13.2
occ:1.00
|
O
|
B:ETF404
|
2.0
|
13.4
|
1.0
|
NE2
|
B:HIS67
|
2.0
|
13.1
|
1.0
|
SG
|
B:CYS174
|
2.3
|
12.8
|
1.0
|
SG
|
B:CYS46
|
2.3
|
12.8
|
1.0
|
C2
|
B:ETF404
|
2.9
|
14.5
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
12.0
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
13.0
|
1.0
|
CB
|
B:CYS46
|
3.3
|
13.0
|
1.0
|
C5N
|
B:NAJ403
|
3.4
|
11.0
|
1.0
|
CB
|
B:CYS174
|
3.4
|
11.8
|
1.0
|
OG
|
B:SER48
|
3.8
|
12.1
|
1.0
|
C4N
|
B:NAJ403
|
3.9
|
11.8
|
1.0
|
C6N
|
B:NAJ403
|
4.0
|
10.5
|
1.0
|
CB
|
B:SER48
|
4.0
|
11.2
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
12.6
|
1.0
|
CG
|
B:HIS67
|
4.2
|
11.9
|
1.0
|
C1
|
B:ETF404
|
4.3
|
17.4
|
1.0
|
F3
|
B:ETF404
|
4.6
|
19.8
|
1.0
|
NH2
|
B:ARG369
|
4.6
|
13.8
|
1.0
|
CA
|
B:CYS174
|
4.7
|
11.4
|
1.0
|
CA
|
B:CYS46
|
4.8
|
12.8
|
1.0
|
F1
|
B:ETF404
|
4.8
|
21.4
|
1.0
|
N
|
B:SER48
|
4.9
|
11.5
|
1.0
|
OE2
|
B:GLU68
|
4.9
|
14.3
|
1.0
|
CE2
|
B:PHE93
|
4.9
|
12.2
|
1.0
|
N1N
|
B:NAJ403
|
5.0
|
10.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7ude
Go back to
Zinc Binding Sites List in 7ude
Zinc binding site 4 out
of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K
![](/pictures/ZN/pdb/ud/7ude-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ud/7ude-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 Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:14.1
occ:1.00
|
SG
|
B:CYS111
|
2.3
|
13.7
|
1.0
|
SG
|
B:CYS97
|
2.3
|
17.1
|
1.0
|
SG
|
B:CYS100
|
2.3
|
14.9
|
1.0
|
SG
|
B:CYS103
|
2.4
|
13.0
|
1.0
|
CB
|
B:CYS111
|
3.3
|
13.1
|
1.0
|
CB
|
B:CYS100
|
3.4
|
17.0
|
1.0
|
CB
|
B:CYS103
|
3.4
|
14.1
|
1.0
|
CB
|
B:CYS97
|
3.4
|
17.4
|
1.0
|
N
|
B:CYS97
|
3.5
|
14.5
|
1.0
|
CA
|
B:CYS111
|
3.7
|
12.1
|
1.0
|
N
|
B:CYS100
|
3.9
|
16.5
|
1.0
|
CA
|
B:CYS97
|
3.9
|
15.9
|
1.0
|
N
|
B:LEU112
|
4.0
|
13.7
|
1.0
|
N
|
B:GLY98
|
4.0
|
16.5
|
1.0
|
CA
|
B:CYS100
|
4.2
|
17.0
|
1.0
|
N
|
B:CYS103
|
4.2
|
12.8
|
1.0
|
C
|
B:CYS111
|
4.3
|
12.5
|
1.0
|
C
|
B:CYS97
|
4.3
|
17.3
|
1.0
|
CA
|
B:CYS103
|
4.4
|
12.8
|
1.0
|
N
|
B:LYS99
|
4.5
|
17.5
|
1.0
|
C
|
B:GLN96
|
4.6
|
13.2
|
1.0
|
C
|
B:CYS100
|
4.8
|
15.1
|
1.0
|
N
|
B:LYS113
|
4.9
|
13.6
|
1.0
|
CG
|
B:LYS113
|
4.9
|
18.7
|
1.0
|
O
|
B:CYS100
|
4.9
|
15.5
|
1.0
|
CA
|
B:GLN96
|
4.9
|
12.5
|
1.0
|
|
Reference:
B.V.Plapp,
L.Gakhar,
R.Subramanian.
Dependence of Crystallographic Atomic Displacement Factors on Temperature (25-150 K) For Complexes of Horse Liver Alcohol Dehydrogenases Acta Crystallogr.,Sect.D V. D78 1221 2022.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322008361
Page generated: Sat Apr 8 04:10:00 2023
|