Zinc in PDB 2jhg: Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Enzymatic activity of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
All present enzymatic activity of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase:
1.1.1.1;
Protein crystallography data
The structure of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase, PDB code: 2jhg
was solved by
R.Meijers,
H.W.Adolph,
Z.Dauter,
K.S.Wilson,
V.S.Lamzin,
E.S.Cedergren-Zeppezauer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.83 /
1.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.186,
43.798,
92.516,
77.12,
87.44,
108.89
|
R / Rfree (%)
|
11.4 /
14.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
(pdb code 2jhg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase, PDB code: 2jhg:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2jhg
Go back to
Zinc Binding Sites List in 2jhg
Zinc binding site 1 out
of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:9.0
occ:1.00
|
NE2
|
A:HIS67
|
2.0
|
8.0
|
1.0
|
O2
|
A:IBO404
|
2.1
|
8.2
|
0.6
|
O2
|
A:IBO404
|
2.1
|
11.8
|
0.4
|
SG
|
A:CYS174
|
2.3
|
9.2
|
1.0
|
SG
|
A:CYS46
|
2.3
|
8.9
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
8.5
|
1.0
|
CD2
|
A:HIS67
|
3.0
|
8.4
|
1.0
|
C
|
A:IBO404
|
3.1
|
8.1
|
0.6
|
C
|
A:IBO404
|
3.1
|
17.5
|
0.4
|
NA
|
A:IBO404
|
3.2
|
8.1
|
0.6
|
CB
|
A:CYS46
|
3.2
|
8.9
|
1.0
|
CB
|
A:CYS174
|
3.4
|
8.8
|
1.0
|
C5N
|
A:NAD403
|
3.5
|
8.6
|
1.0
|
NA
|
A:IBO404
|
3.5
|
19.0
|
0.4
|
OG
|
A:SER48
|
4.0
|
8.9
|
1.0
|
C4N
|
A:NAD403
|
4.0
|
9.6
|
1.0
|
C6N
|
A:NAD403
|
4.1
|
8.9
|
1.0
|
CB
|
A:SER48
|
4.1
|
8.6
|
1.0
|
ND1
|
A:HIS67
|
4.1
|
8.6
|
1.0
|
CG
|
A:HIS67
|
4.2
|
8.0
|
1.0
|
CA
|
A:IBO404
|
4.4
|
11.4
|
0.6
|
CA
|
A:IBO404
|
4.5
|
19.6
|
0.4
|
OE1
|
A:GLU68
|
4.6
|
10.8
|
1.0
|
NH2
|
A:ARG369
|
4.6
|
10.6
|
1.0
|
CA
|
A:CYS46
|
4.7
|
8.9
|
1.0
|
CA
|
A:CYS174
|
4.7
|
8.6
|
1.0
|
N
|
A:SER48
|
4.9
|
8.4
|
1.0
|
CB2
|
A:IBO404
|
4.9
|
20.6
|
0.4
|
N
|
A:GLY175
|
5.0
|
9.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2jhg
Go back to
Zinc Binding Sites List in 2jhg
Zinc binding site 2 out
of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:11.3
occ:1.00
|
SG
|
A:CYS111
|
2.3
|
10.4
|
1.0
|
SG
|
A:CYS100
|
2.3
|
11.4
|
1.0
|
SG
|
A:CYS103
|
2.4
|
10.8
|
1.0
|
SG
|
A:CYS97
|
2.4
|
13.6
|
1.0
|
CB
|
A:CYS111
|
3.3
|
9.7
|
1.0
|
CB
|
A:CYS100
|
3.4
|
12.6
|
1.0
|
CB
|
A:CYS103
|
3.4
|
11.2
|
1.0
|
CB
|
A:CYS97
|
3.4
|
12.7
|
1.0
|
N
|
A:CYS97
|
3.6
|
10.6
|
1.0
|
CA
|
A:CYS111
|
3.8
|
9.7
|
1.0
|
N
|
A:CYS100
|
3.9
|
13.6
|
1.0
|
CA
|
A:CYS97
|
3.9
|
11.8
|
1.0
|
N
|
A:GLY98
|
4.0
|
12.7
|
1.0
|
N
|
A:LEU112
|
4.0
|
11.0
|
1.0
|
CA
|
A:CYS100
|
4.2
|
13.2
|
1.0
|
N
|
A:CYS103
|
4.2
|
10.8
|
1.0
|
C
|
A:CYS111
|
4.3
|
9.9
|
1.0
|
C
|
A:CYS97
|
4.4
|
12.6
|
1.0
|
CA
|
A:CYS103
|
4.4
|
11.4
|
1.0
|
N
|
A:LYS99
|
4.5
|
15.4
|
1.0
|
C
|
A:GLN96
|
4.6
|
10.6
|
1.0
|
CG
|
A:LYS113
|
4.7
|
12.2
|
0.6
|
N
|
A:LYS113
|
4.8
|
10.7
|
1.0
|
C
|
A:CYS100
|
4.8
|
13.1
|
1.0
|
O
|
A:CYS100
|
4.9
|
13.0
|
1.0
|
CA
|
A:GLN96
|
4.9
|
10.3
|
1.0
|
CA
|
A:GLY98
|
4.9
|
14.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2jhg
Go back to
Zinc Binding Sites List in 2jhg
Zinc binding site 3 out
of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:11.3
occ:1.00
|
O2
|
B:IBO404
|
2.0
|
14.5
|
0.2
|
NE2
|
B:HIS67
|
2.0
|
10.6
|
1.0
|
O2
|
B:IBO404
|
2.1
|
11.2
|
0.8
|
SG
|
B:CYS174
|
2.3
|
11.4
|
1.0
|
SG
|
B:CYS46
|
2.3
|
10.8
|
1.0
|
C
|
B:IBO404
|
3.0
|
14.3
|
0.8
|
CE1
|
B:HIS67
|
3.0
|
10.4
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
10.2
|
1.0
|
C
|
B:IBO404
|
3.1
|
15.5
|
0.2
|
NA
|
B:IBO404
|
3.3
|
13.1
|
0.8
|
CB
|
B:CYS46
|
3.3
|
11.2
|
1.0
|
CB
|
B:CYS174
|
3.4
|
10.0
|
1.0
|
NA
|
B:IBO404
|
3.4
|
14.5
|
0.2
|
C5N
|
B:NAD403
|
3.4
|
10.8
|
1.0
|
OG
|
B:SER48
|
4.0
|
11.6
|
1.0
|
C6N
|
B:NAD403
|
4.0
|
11.0
|
1.0
|
C4N
|
B:NAD403
|
4.0
|
10.4
|
1.0
|
CB
|
B:SER48
|
4.1
|
11.3
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
11.1
|
1.0
|
CG
|
B:HIS67
|
4.2
|
10.8
|
1.0
|
CA
|
B:IBO404
|
4.4
|
15.5
|
0.8
|
CA
|
B:IBO404
|
4.4
|
15.5
|
0.2
|
NH2
|
B:ARG369
|
4.5
|
12.9
|
1.0
|
OE2
|
B:GLU68
|
4.6
|
13.3
|
1.0
|
CA
|
B:CYS174
|
4.7
|
9.7
|
1.0
|
CA
|
B:CYS46
|
4.7
|
12.0
|
1.0
|
CB2
|
B:IBO404
|
4.8
|
16.3
|
0.2
|
N
|
B:SER48
|
4.9
|
11.1
|
1.0
|
N
|
B:GLY175
|
5.0
|
10.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2jhg
Go back to
Zinc Binding Sites List in 2jhg
Zinc binding site 4 out
of 4 in the Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:13.3
occ:1.00
|
SG
|
B:CYS111
|
2.3
|
12.7
|
1.0
|
SG
|
B:CYS100
|
2.3
|
13.2
|
1.0
|
SG
|
B:CYS103
|
2.3
|
12.4
|
1.0
|
SG
|
B:CYS97
|
2.4
|
15.7
|
1.0
|
CB
|
B:CYS111
|
3.3
|
11.0
|
1.0
|
CB
|
B:CYS100
|
3.4
|
15.4
|
1.0
|
CB
|
B:CYS103
|
3.4
|
12.6
|
1.0
|
CB
|
B:CYS97
|
3.5
|
16.4
|
1.0
|
N
|
B:CYS97
|
3.6
|
13.4
|
1.0
|
CA
|
B:CYS111
|
3.7
|
11.6
|
1.0
|
N
|
B:CYS100
|
3.9
|
15.2
|
1.0
|
CA
|
B:CYS97
|
4.0
|
15.0
|
1.0
|
N
|
B:LEU112
|
4.0
|
12.5
|
1.0
|
N
|
B:GLY98
|
4.0
|
15.3
|
1.0
|
CA
|
B:CYS100
|
4.2
|
15.4
|
1.0
|
N
|
B:CYS103
|
4.2
|
11.8
|
1.0
|
C
|
B:CYS111
|
4.3
|
11.7
|
1.0
|
CA
|
B:CYS103
|
4.4
|
12.2
|
1.0
|
C
|
B:CYS97
|
4.4
|
15.4
|
1.0
|
N
|
B:LYS99
|
4.5
|
17.0
|
1.0
|
NZ
|
B:LYS113
|
4.5
|
26.1
|
0.5
|
C
|
B:GLN96
|
4.6
|
12.9
|
1.0
|
CG
|
B:LYS113
|
4.7
|
16.2
|
0.5
|
C
|
B:CYS100
|
4.8
|
15.5
|
1.0
|
N
|
B:LYS113
|
4.8
|
13.1
|
1.0
|
O
|
B:CYS100
|
4.9
|
14.7
|
1.0
|
CA
|
B:GLN96
|
4.9
|
11.5
|
1.0
|
CG
|
B:LYS113
|
4.9
|
17.3
|
0.5
|
CA
|
B:GLY98
|
5.0
|
15.9
|
1.0
|
|
Reference:
R.Meijers,
H.W.Adolph,
Z.Dauter,
K.S.Wilson,
V.S.Lamzin,
E.S.Cedergren-Zeppezauer.
Structural Evidence For A Ligand Coordination Switch in Liver Alcohol Dehydrogenase Biochemistry V. 46 5446 2007.
ISSN: ISSN 0006-2960
PubMed: 17429946
DOI: 10.1021/BI6023594
Page generated: Thu Oct 17 01:13:47 2024
|