Zinc in PDB 7k35: Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Enzymatic activity of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
All present enzymatic activity of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21:
1.1.1.1;
Protein crystallography data
The structure of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21, PDB code: 7k35
was solved by
B.V.Plapp,
S.Ramaswamy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.96 /
1.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.220,
180.220,
86.860,
90.00,
106.12,
90.00
|
R / Rfree (%)
|
17.6 /
21
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
(pdb code 7k35). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Eqadh-Nadh-4-Methylbenzyl Alcohol, P21, PDB code: 7k35:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 1 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:23.2
occ:1.00
|
NE2
|
A:HIS67
|
2.1
|
20.8
|
1.0
|
SG
|
A:CYS174
|
2.1
|
21.9
|
1.0
|
O1
|
A:VTG404
|
2.2
|
21.4
|
1.0
|
SG
|
A:CYS46
|
2.3
|
22.1
|
1.0
|
CE1
|
A:HIS67
|
3.0
|
21.0
|
1.0
|
CD2
|
A:HIS67
|
3.1
|
20.6
|
1.0
|
C7
|
A:VTG404
|
3.2
|
22.4
|
1.0
|
CB
|
A:CYS46
|
3.3
|
19.7
|
1.0
|
CB
|
A:CYS174
|
3.3
|
16.3
|
1.0
|
C5N
|
A:NAI403
|
3.5
|
17.8
|
1.0
|
C6N
|
A:NAI403
|
3.9
|
18.4
|
1.0
|
OG
|
A:SER48
|
4.0
|
22.4
|
1.0
|
C4N
|
A:NAI403
|
4.0
|
19.6
|
1.0
|
ND1
|
A:HIS67
|
4.1
|
16.6
|
1.0
|
CB
|
A:SER48
|
4.2
|
18.8
|
1.0
|
CG
|
A:HIS67
|
4.2
|
16.6
|
1.0
|
C1
|
A:VTG404
|
4.6
|
20.6
|
1.0
|
OE2
|
A:GLU68
|
4.6
|
26.2
|
1.0
|
NH2
|
A:ARG369
|
4.6
|
25.4
|
1.0
|
CA
|
A:CYS174
|
4.7
|
16.6
|
1.0
|
CA
|
A:CYS46
|
4.7
|
19.2
|
1.0
|
CE2
|
A:PHE93
|
4.8
|
19.3
|
1.0
|
N
|
A:SER48
|
4.9
|
20.0
|
1.0
|
N
|
A:GLY175
|
4.9
|
19.8
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 2 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:20.6
occ:1.00
|
SG
|
A:CYS111
|
2.3
|
20.3
|
1.0
|
SG
|
A:CYS97
|
2.3
|
22.0
|
1.0
|
SG
|
A:CYS103
|
2.3
|
21.1
|
1.0
|
SG
|
A:CYS100
|
2.3
|
20.8
|
1.0
|
CB
|
A:CYS111
|
3.3
|
20.0
|
1.0
|
CB
|
A:CYS103
|
3.4
|
19.5
|
1.0
|
CB
|
A:CYS97
|
3.4
|
24.4
|
1.0
|
CB
|
A:CYS100
|
3.4
|
24.8
|
1.0
|
N
|
A:CYS97
|
3.6
|
19.8
|
1.0
|
CA
|
A:CYS111
|
3.7
|
20.6
|
1.0
|
N
|
A:CYS100
|
3.8
|
24.2
|
1.0
|
CA
|
A:CYS97
|
3.9
|
20.1
|
1.0
|
N
|
A:GLY98
|
4.0
|
21.1
|
1.0
|
N
|
A:LEU112
|
4.0
|
18.6
|
1.0
|
CA
|
A:CYS100
|
4.2
|
24.7
|
1.0
|
N
|
A:CYS103
|
4.2
|
21.2
|
1.0
|
C
|
A:CYS111
|
4.2
|
18.4
|
1.0
|
CA
|
A:CYS103
|
4.3
|
21.6
|
1.0
|
C
|
A:CYS97
|
4.4
|
21.6
|
1.0
|
N
|
A:LYS99
|
4.5
|
23.0
|
1.0
|
C
|
A:GLN96
|
4.6
|
20.0
|
1.0
|
N
|
A:LYS113
|
4.8
|
21.4
|
1.0
|
C
|
A:CYS100
|
4.8
|
23.0
|
1.0
|
CG
|
A:LYS113
|
4.9
|
24.1
|
1.0
|
CA
|
A:GLN96
|
5.0
|
19.5
|
1.0
|
O
|
A:CYS100
|
5.0
|
23.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 3 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:23.1
occ:1.00
|
NE2
|
B:HIS67
|
2.1
|
20.1
|
1.0
|
SG
|
B:CYS174
|
2.1
|
22.3
|
1.0
|
O1
|
B:VTG404
|
2.2
|
22.9
|
1.0
|
SG
|
B:CYS46
|
2.4
|
20.2
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
20.0
|
1.0
|
CD2
|
B:HIS67
|
3.1
|
21.2
|
1.0
|
C7
|
B:VTG404
|
3.2
|
23.9
|
1.0
|
CB
|
B:CYS46
|
3.3
|
21.6
|
1.0
|
CB
|
B:CYS174
|
3.4
|
19.0
|
1.0
|
C5N
|
B:NAI403
|
3.4
|
19.6
|
1.0
|
C4N
|
B:NAI403
|
3.9
|
19.4
|
1.0
|
OG
|
B:SER48
|
4.0
|
21.1
|
1.0
|
C6N
|
B:NAI403
|
4.0
|
19.8
|
1.0
|
CB
|
B:SER48
|
4.1
|
22.1
|
1.0
|
ND1
|
B:HIS67
|
4.2
|
20.3
|
1.0
|
CG
|
B:HIS67
|
4.2
|
19.9
|
1.0
|
NH2
|
B:ARG369
|
4.6
|
23.9
|
1.0
|
C1
|
B:VTG404
|
4.6
|
22.8
|
1.0
|
OE2
|
B:GLU68
|
4.6
|
25.8
|
1.0
|
CA
|
B:CYS46
|
4.7
|
22.5
|
1.0
|
CA
|
B:CYS174
|
4.7
|
16.7
|
1.0
|
CE2
|
B:PHE93
|
4.9
|
21.0
|
1.0
|
N
|
B:SER48
|
5.0
|
19.0
|
1.0
|
N
|
B:GLY175
|
5.0
|
20.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 4 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:22.7
occ:0.96
|
SG
|
B:CYS100
|
2.3
|
22.7
|
1.0
|
SG
|
B:CYS97
|
2.3
|
24.4
|
1.0
|
SG
|
B:CYS111
|
2.4
|
22.5
|
1.0
|
SG
|
B:CYS103
|
2.4
|
24.0
|
1.0
|
CB
|
B:CYS111
|
3.3
|
22.4
|
1.0
|
CB
|
B:CYS103
|
3.4
|
22.9
|
1.0
|
CB
|
B:CYS97
|
3.4
|
23.0
|
1.0
|
CB
|
B:CYS100
|
3.5
|
24.6
|
1.0
|
N
|
B:CYS97
|
3.6
|
22.6
|
1.0
|
CA
|
B:CYS111
|
3.7
|
21.4
|
1.0
|
N
|
B:CYS100
|
3.9
|
27.4
|
1.0
|
CA
|
B:CYS97
|
3.9
|
23.9
|
1.0
|
N
|
B:LEU112
|
4.0
|
20.6
|
1.0
|
N
|
B:GLY98
|
4.0
|
23.5
|
1.0
|
CA
|
B:CYS100
|
4.2
|
25.9
|
1.0
|
N
|
B:CYS103
|
4.2
|
21.6
|
1.0
|
C
|
B:CYS111
|
4.3
|
22.8
|
1.0
|
CA
|
B:CYS103
|
4.4
|
22.8
|
1.0
|
C
|
B:CYS97
|
4.4
|
26.2
|
1.0
|
N
|
B:LYS99
|
4.5
|
25.6
|
1.0
|
C
|
B:GLN96
|
4.6
|
21.2
|
1.0
|
O
|
B:HOH761
|
4.8
|
35.0
|
1.0
|
C
|
B:CYS100
|
4.8
|
21.4
|
1.0
|
CA
|
B:GLN96
|
4.9
|
20.7
|
1.0
|
N
|
B:LYS113
|
4.9
|
21.8
|
1.0
|
O
|
B:CYS100
|
5.0
|
23.1
|
1.0
|
CA
|
B:GLY98
|
5.0
|
24.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 5 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:23.1
occ:1.00
|
NE2
|
C:HIS67
|
2.1
|
19.6
|
1.0
|
SG
|
C:CYS174
|
2.1
|
20.9
|
1.0
|
O1
|
C:VTG404
|
2.2
|
23.3
|
1.0
|
SG
|
C:CYS46
|
2.3
|
21.0
|
1.0
|
CE1
|
C:HIS67
|
3.0
|
21.6
|
1.0
|
CD2
|
C:HIS67
|
3.1
|
19.4
|
1.0
|
C7
|
C:VTG404
|
3.2
|
22.7
|
1.0
|
CB
|
C:CYS46
|
3.3
|
19.8
|
1.0
|
CB
|
C:CYS174
|
3.3
|
17.8
|
1.0
|
C5N
|
C:NAI403
|
3.5
|
15.3
|
1.0
|
C6N
|
C:NAI403
|
4.0
|
15.7
|
1.0
|
C4N
|
C:NAI403
|
4.0
|
17.5
|
1.0
|
OG
|
C:SER48
|
4.0
|
21.4
|
1.0
|
CB
|
C:SER48
|
4.2
|
18.8
|
1.0
|
ND1
|
C:HIS67
|
4.2
|
16.8
|
1.0
|
CG
|
C:HIS67
|
4.2
|
15.7
|
1.0
|
C1
|
C:VTG404
|
4.6
|
23.2
|
1.0
|
OE2
|
C:GLU68
|
4.6
|
22.1
|
1.0
|
NH2
|
C:ARG369
|
4.6
|
22.9
|
1.0
|
CA
|
C:CYS174
|
4.7
|
18.3
|
1.0
|
CA
|
C:CYS46
|
4.8
|
19.6
|
1.0
|
N
|
C:GLY175
|
4.9
|
19.1
|
1.0
|
CE2
|
C:PHE93
|
4.9
|
19.9
|
1.0
|
N
|
C:SER48
|
4.9
|
19.6
|
1.0
|
C
|
C:CYS174
|
5.0
|
17.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 6 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn402
b:23.0
occ:1.00
|
SG
|
C:CYS97
|
2.3
|
24.2
|
1.0
|
SG
|
C:CYS111
|
2.3
|
22.1
|
1.0
|
SG
|
C:CYS100
|
2.3
|
23.1
|
1.0
|
SG
|
C:CYS103
|
2.4
|
23.2
|
1.0
|
CB
|
C:CYS111
|
3.3
|
21.0
|
1.0
|
CB
|
C:CYS97
|
3.4
|
24.2
|
1.0
|
CB
|
C:CYS103
|
3.4
|
20.9
|
1.0
|
CB
|
C:CYS100
|
3.4
|
27.3
|
1.0
|
N
|
C:CYS97
|
3.6
|
22.0
|
1.0
|
CA
|
C:CYS111
|
3.7
|
22.3
|
1.0
|
N
|
C:CYS100
|
3.8
|
25.8
|
1.0
|
CA
|
C:CYS97
|
3.9
|
22.5
|
1.0
|
N
|
C:LEU112
|
4.0
|
21.7
|
1.0
|
N
|
C:GLY98
|
4.0
|
23.3
|
1.0
|
CA
|
C:CYS100
|
4.2
|
26.2
|
1.0
|
N
|
C:CYS103
|
4.2
|
21.8
|
1.0
|
C
|
C:CYS111
|
4.2
|
22.2
|
1.0
|
CA
|
C:CYS103
|
4.3
|
22.5
|
1.0
|
C
|
C:CYS97
|
4.3
|
25.1
|
1.0
|
N
|
C:LYS99
|
4.5
|
27.6
|
1.0
|
O
|
C:HOH782
|
4.6
|
41.6
|
1.0
|
C
|
C:GLN96
|
4.7
|
21.3
|
1.0
|
N
|
C:LYS113
|
4.9
|
21.3
|
1.0
|
C
|
C:CYS100
|
4.9
|
24.8
|
1.0
|
CG
|
C:LYS113
|
4.9
|
28.7
|
1.0
|
O
|
C:CYS100
|
5.0
|
25.8
|
1.0
|
CA
|
C:GLN96
|
5.0
|
23.3
|
1.0
|
C
|
C:LYS99
|
5.0
|
29.1
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 7 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:23.5
occ:1.00
|
NE2
|
D:HIS67
|
2.1
|
19.4
|
1.0
|
O1
|
D:VTG404
|
2.1
|
22.0
|
1.0
|
SG
|
D:CYS174
|
2.2
|
22.0
|
1.0
|
SG
|
D:CYS46
|
2.3
|
19.9
|
1.0
|
CD2
|
D:HIS67
|
3.0
|
21.1
|
1.0
|
CE1
|
D:HIS67
|
3.1
|
19.3
|
1.0
|
C7
|
D:VTG404
|
3.2
|
25.2
|
1.0
|
CB
|
D:CYS46
|
3.3
|
20.8
|
1.0
|
CB
|
D:CYS174
|
3.4
|
18.4
|
1.0
|
C5N
|
D:NAI403
|
3.4
|
20.2
|
1.0
|
C4N
|
D:NAI403
|
3.9
|
20.0
|
1.0
|
C6N
|
D:NAI403
|
4.0
|
19.1
|
1.0
|
OG
|
D:SER48
|
4.0
|
20.7
|
1.0
|
CB
|
D:SER48
|
4.2
|
21.7
|
1.0
|
ND1
|
D:HIS67
|
4.2
|
18.4
|
1.0
|
CG
|
D:HIS67
|
4.2
|
21.0
|
1.0
|
NH2
|
D:ARG369
|
4.5
|
23.9
|
1.0
|
C1
|
D:VTG404
|
4.6
|
21.4
|
1.0
|
CA
|
D:CYS174
|
4.7
|
17.7
|
1.0
|
CA
|
D:CYS46
|
4.7
|
21.0
|
1.0
|
CE2
|
D:PHE93
|
4.8
|
23.0
|
1.0
|
OE2
|
D:GLU68
|
4.8
|
25.9
|
1.0
|
N
|
D:SER48
|
5.0
|
20.2
|
1.0
|
N
|
D:GLY175
|
5.0
|
19.8
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7k35
Go back to
Zinc Binding Sites List in 7k35
Zinc binding site 8 out
of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:21.4
occ:1.00
|
SG
|
D:CYS103
|
2.3
|
23.9
|
1.0
|
SG
|
D:CYS111
|
2.3
|
20.6
|
1.0
|
SG
|
D:CYS100
|
2.3
|
21.0
|
1.0
|
SG
|
D:CYS97
|
2.4
|
22.6
|
1.0
|
CB
|
D:CYS111
|
3.3
|
20.2
|
1.0
|
CB
|
D:CYS103
|
3.4
|
23.6
|
1.0
|
CB
|
D:CYS100
|
3.4
|
22.7
|
1.0
|
CB
|
D:CYS97
|
3.5
|
23.7
|
1.0
|
N
|
D:CYS97
|
3.6
|
20.7
|
1.0
|
CA
|
D:CYS111
|
3.7
|
17.6
|
1.0
|
N
|
D:CYS100
|
3.9
|
23.7
|
1.0
|
CA
|
D:CYS97
|
3.9
|
20.8
|
1.0
|
N
|
D:GLY98
|
4.0
|
22.1
|
1.0
|
N
|
D:LEU112
|
4.0
|
18.2
|
1.0
|
CA
|
D:CYS100
|
4.2
|
23.2
|
1.0
|
N
|
D:CYS103
|
4.2
|
20.4
|
1.0
|
C
|
D:CYS111
|
4.3
|
17.8
|
1.0
|
CA
|
D:CYS103
|
4.4
|
23.7
|
1.0
|
C
|
D:CYS97
|
4.4
|
23.3
|
1.0
|
N
|
D:LYS99
|
4.5
|
22.2
|
1.0
|
C
|
D:GLN96
|
4.7
|
19.8
|
1.0
|
C
|
D:CYS100
|
4.8
|
21.5
|
1.0
|
N
|
D:LYS113
|
4.9
|
22.3
|
1.0
|
O
|
D:HOH739
|
4.9
|
36.1
|
1.0
|
O
|
D:CYS100
|
4.9
|
21.9
|
1.0
|
CA
|
D:GLN96
|
4.9
|
20.2
|
1.0
|
CA
|
D:GLY98
|
5.0
|
23.4
|
1.0
|
CG
|
D:LYS113
|
5.0
|
25.4
|
1.0
|
|
Reference:
B.V.Plapp,
S.Ramaswamy.
Alternative Binding Modes in Abortive Nadh and Alcohol Complexes of Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Tue Oct 29 21:13:50 2024
|