Zinc in PDB 1het: Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
Enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
All present enzymatic activity of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh:
1.1.1.1;
Protein crystallography data
The structure of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh, PDB code: 1het
was solved by
R.Meijers,
R.J.Morris,
H.W.Adolph,
A.Merli,
V.S.Lamzin,
E.S.Cedergen-Zeppezauer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.15
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.100,
44.400,
94.000,
104.60,
101.50,
70.50
|
R / Rfree (%)
|
11.8 /
13.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
(pdb code 1het). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh, PDB code: 1het:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1het
Go back to
Zinc Binding Sites List in 1het
Zinc binding site 1 out
of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn400
b:8.9
occ:1.00
|
NE2
|
A:HIS67
|
2.1
|
8.9
|
1.0
|
O
|
A:HOH2741
|
2.1
|
7.8
|
0.4
|
SG
|
A:CYS174
|
2.3
|
7.5
|
1.0
|
O
|
A:HOH2740
|
2.3
|
9.7
|
0.6
|
SG
|
A:CYS46
|
2.3
|
7.7
|
1.0
|
CE1
|
A:HIS67
|
3.1
|
7.8
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
9.5
|
1.0
|
CB
|
A:CYS46
|
3.3
|
8.9
|
1.0
|
CB
|
A:CYS174
|
3.3
|
7.5
|
1.0
|
C5N
|
A:NAD402
|
3.6
|
9.3
|
1.0
|
C6N
|
A:NAD402
|
3.8
|
10.8
|
1.0
|
C4N
|
A:NAD402
|
4.1
|
9.1
|
1.0
|
OG
|
A:SER48
|
4.2
|
9.0
|
1.0
|
ND1
|
A:HIS67
|
4.2
|
8.4
|
1.0
|
CB
|
A:SER48
|
4.2
|
8.2
|
1.0
|
CG
|
A:HIS67
|
4.3
|
8.2
|
1.0
|
C1
|
A:MRD403
|
4.3
|
18.4
|
0.5
|
C1
|
A:MRD403
|
4.3
|
18.2
|
0.5
|
NH2
|
A:ARG369
|
4.4
|
9.7
|
1.0
|
OE2
|
A:GLU68
|
4.6
|
9.9
|
1.0
|
CA
|
A:CYS174
|
4.7
|
7.2
|
1.0
|
CA
|
A:CYS46
|
4.8
|
8.6
|
1.0
|
N
|
A:SER48
|
4.9
|
7.8
|
1.0
|
N1N
|
A:NAD402
|
4.9
|
9.0
|
1.0
|
N
|
A:GLY175
|
4.9
|
7.4
|
1.0
|
CE2
|
A:PHE93
|
5.0
|
9.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1het
Go back to
Zinc Binding Sites List in 1het
Zinc binding site 2 out
of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:7.8
occ:1.00
|
SG
|
A:CYS97
|
2.4
|
11.1
|
1.0
|
SG
|
A:CYS100
|
2.4
|
10.4
|
1.0
|
SG
|
A:CYS111
|
2.4
|
8.9
|
1.0
|
SG
|
A:CYS103
|
2.4
|
9.6
|
1.0
|
CB
|
A:CYS111
|
3.4
|
9.3
|
1.0
|
CB
|
A:CYS97
|
3.5
|
12.1
|
1.0
|
CB
|
A:CYS100
|
3.5
|
12.4
|
1.0
|
CB
|
A:CYS103
|
3.5
|
11.4
|
1.0
|
N
|
A:CYS97
|
3.6
|
9.5
|
1.0
|
CA
|
A:CYS111
|
3.8
|
8.9
|
1.0
|
N
|
A:CYS100
|
3.9
|
13.8
|
1.0
|
CA
|
A:CYS97
|
3.9
|
11.1
|
1.0
|
N
|
A:GLY98
|
4.0
|
11.3
|
1.0
|
N
|
A:LEU112
|
4.0
|
9.8
|
1.0
|
CA
|
A:CYS100
|
4.2
|
13.1
|
1.0
|
N
|
A:CYS103
|
4.3
|
10.2
|
1.0
|
C
|
A:CYS97
|
4.3
|
11.4
|
1.0
|
C
|
A:CYS111
|
4.3
|
9.3
|
1.0
|
CA
|
A:CYS103
|
4.5
|
11.0
|
1.0
|
N
|
A:LYS99
|
4.5
|
14.7
|
1.0
|
C
|
A:GLN96
|
4.7
|
9.6
|
1.0
|
CG
|
A:LYS113
|
4.7
|
10.9
|
0.6
|
N
|
A:LYS113
|
4.9
|
9.9
|
1.0
|
C
|
A:CYS100
|
4.9
|
12.6
|
1.0
|
CA
|
A:GLY98
|
5.0
|
13.9
|
1.0
|
O
|
A:CYS100
|
5.0
|
12.9
|
1.0
|
CA
|
A:GLN96
|
5.0
|
9.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1het
Go back to
Zinc Binding Sites List in 1het
Zinc binding site 3 out
of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn400
b:12.0
occ:1.00
|
NE2
|
B:HIS67
|
2.1
|
12.5
|
1.0
|
O
|
B:HOH2672
|
2.1
|
10.5
|
0.4
|
SG
|
B:CYS174
|
2.3
|
10.4
|
1.0
|
SG
|
B:CYS46
|
2.3
|
10.7
|
1.0
|
O
|
B:HOH2673
|
2.3
|
12.6
|
0.6
|
CE1
|
B:HIS67
|
3.1
|
11.8
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
12.8
|
1.0
|
CB
|
B:CYS46
|
3.3
|
11.2
|
1.0
|
CB
|
B:CYS174
|
3.4
|
10.1
|
1.0
|
C5N
|
B:NAD402
|
3.6
|
11.1
|
1.0
|
C6N
|
B:NAD402
|
3.8
|
13.3
|
1.0
|
C4N
|
B:NAD402
|
4.1
|
11.2
|
1.0
|
OG
|
B:SER48
|
4.2
|
11.6
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
11.6
|
1.0
|
CB
|
B:SER48
|
4.2
|
10.5
|
1.0
|
CG
|
B:HIS67
|
4.3
|
11.7
|
1.0
|
NH2
|
B:ARG369
|
4.3
|
12.1
|
1.0
|
C1
|
B:MRD403
|
4.4
|
17.1
|
0.5
|
OE2
|
B:GLU68
|
4.7
|
13.9
|
1.0
|
CA
|
B:CYS174
|
4.7
|
10.2
|
1.0
|
CA
|
B:CYS46
|
4.8
|
11.1
|
1.0
|
C1
|
B:MRD403
|
4.8
|
26.2
|
0.5
|
N
|
B:SER48
|
4.9
|
10.7
|
1.0
|
N1N
|
B:NAD402
|
4.9
|
11.4
|
1.0
|
C
|
B:CYS174
|
5.0
|
9.8
|
1.0
|
CE2
|
B:PHE93
|
5.0
|
11.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1het
Go back to
Zinc Binding Sites List in 1het
Zinc binding site 4 out
of 4 in the Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Atomic X-Ray Structure of Liver Alcohol Dehydrogenase Containing A Hydroxide Adduct to Nadh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:12.5
occ:1.00
|
SG
|
B:CYS100
|
2.4
|
14.5
|
1.0
|
SG
|
B:CYS103
|
2.4
|
13.1
|
1.0
|
SG
|
B:CYS111
|
2.4
|
13.0
|
1.0
|
SG
|
B:CYS97
|
2.5
|
17.7
|
1.0
|
CB
|
B:CYS111
|
3.4
|
12.0
|
1.0
|
CB
|
B:CYS100
|
3.4
|
17.3
|
1.0
|
CB
|
B:CYS103
|
3.5
|
13.8
|
1.0
|
CB
|
B:CYS97
|
3.5
|
18.0
|
1.0
|
N
|
B:CYS97
|
3.6
|
14.9
|
1.0
|
CA
|
B:CYS111
|
3.8
|
11.9
|
1.0
|
N
|
B:CYS100
|
3.9
|
17.9
|
1.0
|
CA
|
B:CYS97
|
4.0
|
16.3
|
1.0
|
N
|
B:GLY98
|
4.0
|
17.1
|
1.0
|
N
|
B:LEU112
|
4.0
|
13.6
|
1.0
|
CA
|
B:CYS100
|
4.2
|
16.7
|
1.0
|
N
|
B:CYS103
|
4.3
|
12.5
|
1.0
|
C
|
B:CYS111
|
4.4
|
12.8
|
1.0
|
C
|
B:CYS97
|
4.4
|
17.2
|
1.0
|
CA
|
B:CYS103
|
4.4
|
12.9
|
1.0
|
N
|
B:LYS99
|
4.6
|
17.8
|
1.0
|
C
|
B:GLN96
|
4.6
|
14.3
|
1.0
|
CG
|
B:LYS113
|
4.7
|
19.0
|
0.5
|
NZ
|
B:LYS113
|
4.8
|
28.2
|
0.5
|
C
|
B:CYS100
|
4.9
|
15.4
|
1.0
|
N
|
B:LYS113
|
4.9
|
14.0
|
1.0
|
CA
|
B:GLN96
|
5.0
|
12.9
|
1.0
|
O
|
B:CYS100
|
5.0
|
15.5
|
1.0
|
|
Reference:
R.Meijers,
R.J.Morris,
H.W.Adolph,
A.Merli,
V.S.Lamzin,
E.S.Cedergen-Zeppezauer.
On the Enzymatic Activation of Nadh J.Biol.Chem. V. 276 9316 2001.
ISSN: ISSN 0021-9258
PubMed: 11134046
DOI: 10.1074/JBC.M010870200
Page generated: Sun Oct 13 02:13:12 2024
|