Zinc in PDB 8hfa: The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
Enzymatic activity of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
All present enzymatic activity of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae:
3.5.1.41;
Protein crystallography data
The structure of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae, PDB code: 8hfa
was solved by
L.Liu,
Y.Zhou,
Q.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.36 /
2.64
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.617,
125.899,
127.007,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
22.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
(pdb code 8hfa). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the
The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae, PDB code: 8hfa:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
Zinc binding site 1 out
of 5 in 8hfa
Go back to
Zinc Binding Sites List in 8hfa
Zinc binding site 1 out
of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/hf/8hfa-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 The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:57.2
occ:1.00
|
OD1
|
A:ASP56
|
2.3
|
24.1
|
1.0
|
NE2
|
A:HIS112
|
2.3
|
42.5
|
1.0
|
NE2
|
A:HIS108
|
2.3
|
29.6
|
1.0
|
O
|
A:HOH463
|
2.5
|
31.1
|
1.0
|
CG
|
A:ASP56
|
3.1
|
25.1
|
1.0
|
OD2
|
A:ASP56
|
3.2
|
31.2
|
1.0
|
CE1
|
A:HIS112
|
3.2
|
39.9
|
1.0
|
CD2
|
A:HIS108
|
3.3
|
31.1
|
1.0
|
CD2
|
A:HIS112
|
3.3
|
43.1
|
1.0
|
CE1
|
A:HIS108
|
3.3
|
31.1
|
1.0
|
OD2
|
A:ASP55
|
4.1
|
28.5
|
1.0
|
CB
|
A:ASP55
|
4.1
|
19.3
|
1.0
|
ND1
|
A:HIS112
|
4.4
|
45.8
|
1.0
|
N
|
A:TYR149
|
4.4
|
30.8
|
1.0
|
CA
|
A:PRO148
|
4.4
|
36.1
|
1.0
|
NE2
|
A:HIS201
|
4.4
|
17.5
|
1.0
|
CG
|
A:HIS112
|
4.4
|
46.7
|
1.0
|
ND1
|
A:HIS108
|
4.5
|
28.5
|
1.0
|
CG
|
A:HIS108
|
4.5
|
29.7
|
1.0
|
CD2
|
A:HIS201
|
4.5
|
20.9
|
1.0
|
CB
|
A:ASP56
|
4.5
|
21.3
|
1.0
|
CG
|
A:ASP55
|
4.6
|
28.0
|
1.0
|
CB
|
A:PRO148
|
4.7
|
33.8
|
1.0
|
N
|
A:ASP56
|
4.9
|
31.9
|
1.0
|
C
|
A:PRO148
|
5.0
|
38.8
|
1.0
|
|
Zinc binding site 2 out
of 5 in 8hfa
Go back to
Zinc Binding Sites List in 8hfa
Zinc binding site 2 out
of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/hf/8hfa-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 The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:49.1
occ:1.00
|
OD1
|
B:ASP56
|
2.2
|
27.2
|
1.0
|
NE2
|
B:HIS108
|
2.3
|
32.1
|
1.0
|
NE2
|
B:HIS112
|
2.3
|
26.3
|
1.0
|
O
|
B:HOH459
|
2.5
|
16.7
|
1.0
|
O
|
B:HOH454
|
2.7
|
33.1
|
1.0
|
CG
|
B:ASP56
|
3.0
|
28.9
|
1.0
|
OD2
|
B:ASP56
|
3.0
|
29.7
|
1.0
|
CE1
|
B:HIS112
|
3.2
|
24.1
|
1.0
|
CD2
|
B:HIS108
|
3.2
|
27.4
|
1.0
|
CE1
|
B:HIS108
|
3.4
|
24.9
|
1.0
|
CD2
|
B:HIS112
|
3.4
|
28.2
|
1.0
|
CB
|
B:ASP55
|
4.0
|
23.9
|
1.0
|
OD2
|
B:ASP55
|
4.0
|
24.3
|
1.0
|
ND1
|
B:HIS112
|
4.3
|
28.6
|
1.0
|
CG
|
B:HIS108
|
4.4
|
25.2
|
1.0
|
N
|
B:TYR149
|
4.4
|
27.9
|
1.0
|
CB
|
B:ASP56
|
4.4
|
21.0
|
1.0
|
ND1
|
B:HIS108
|
4.4
|
26.6
|
1.0
|
CG
|
B:ASP55
|
4.5
|
25.7
|
1.0
|
O
|
B:HOH450
|
4.5
|
34.5
|
1.0
|
CG
|
B:HIS112
|
4.5
|
31.1
|
1.0
|
CA
|
B:PRO148
|
4.5
|
26.2
|
1.0
|
O
|
B:HOH498
|
4.6
|
21.9
|
1.0
|
CD2
|
B:HIS201
|
4.6
|
20.8
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
22.8
|
1.0
|
N
|
B:ASP56
|
4.8
|
29.8
|
1.0
|
CB
|
B:PRO148
|
4.9
|
29.2
|
1.0
|
CA
|
B:ASP56
|
4.9
|
24.5
|
1.0
|
|
Zinc binding site 3 out
of 5 in 8hfa
Go back to
Zinc Binding Sites List in 8hfa
Zinc binding site 3 out
of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/hf/8hfa-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 The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:46.4
occ:1.00
|
OD1
|
C:ASP56
|
2.0
|
22.4
|
1.0
|
O
|
C:HOH427
|
2.2
|
23.5
|
1.0
|
NE2
|
C:HIS112
|
2.3
|
24.5
|
1.0
|
NE2
|
C:HIS108
|
2.4
|
21.2
|
1.0
|
O
|
C:HOH441
|
2.4
|
16.9
|
1.0
|
CG
|
C:ASP56
|
2.9
|
20.3
|
1.0
|
OD2
|
C:ASP56
|
3.1
|
25.6
|
1.0
|
CE1
|
C:HIS112
|
3.2
|
24.4
|
1.0
|
CD2
|
C:HIS108
|
3.3
|
19.6
|
1.0
|
CD2
|
C:HIS112
|
3.3
|
20.9
|
1.0
|
CE1
|
C:HIS108
|
3.5
|
17.6
|
1.0
|
OD2
|
C:ASP55
|
3.9
|
21.6
|
1.0
|
CB
|
C:ASP55
|
4.0
|
20.7
|
1.0
|
O
|
C:HOH542
|
4.3
|
31.5
|
1.0
|
CB
|
C:ASP56
|
4.4
|
15.7
|
1.0
|
ND1
|
C:HIS112
|
4.4
|
20.6
|
1.0
|
CG
|
C:ASP55
|
4.4
|
20.0
|
1.0
|
CG
|
C:HIS112
|
4.4
|
22.7
|
1.0
|
N
|
C:TYR149
|
4.5
|
20.8
|
1.0
|
CD2
|
C:HIS201
|
4.5
|
19.6
|
1.0
|
CG
|
C:HIS108
|
4.5
|
21.6
|
1.0
|
O
|
C:HOH509
|
4.5
|
20.9
|
1.0
|
NE2
|
C:HIS201
|
4.5
|
20.7
|
1.0
|
CA
|
C:PRO148
|
4.5
|
19.7
|
1.0
|
ND1
|
C:HIS108
|
4.6
|
19.7
|
1.0
|
N
|
C:ASP56
|
4.7
|
23.7
|
1.0
|
CA
|
C:ASP56
|
4.8
|
17.9
|
1.0
|
CB
|
C:PRO148
|
4.9
|
18.9
|
1.0
|
|
Zinc binding site 4 out
of 5 in 8hfa
Go back to
Zinc Binding Sites List in 8hfa
Zinc binding site 4 out
of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/hf/8hfa-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 The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:46.5
occ:1.00
|
NE2
|
D:HIS112
|
2.3
|
24.7
|
1.0
|
O
|
D:HOH465
|
2.4
|
23.9
|
1.0
|
OD1
|
D:ASP56
|
2.4
|
21.6
|
1.0
|
NE2
|
D:HIS108
|
2.4
|
19.8
|
1.0
|
CE1
|
D:HIS112
|
3.1
|
19.0
|
1.0
|
CG
|
D:ASP56
|
3.2
|
23.9
|
1.0
|
OD2
|
D:ASP56
|
3.4
|
21.4
|
1.0
|
CD2
|
D:HIS108
|
3.4
|
20.8
|
1.0
|
CD2
|
D:HIS112
|
3.4
|
21.9
|
1.0
|
CE1
|
D:HIS108
|
3.4
|
19.8
|
1.0
|
OD2
|
D:ASP55
|
4.1
|
22.7
|
1.0
|
CB
|
D:ASP55
|
4.1
|
19.9
|
1.0
|
O
|
D:HOH516
|
4.1
|
27.5
|
1.0
|
ND1
|
D:HIS112
|
4.3
|
23.1
|
1.0
|
N
|
D:TYR149
|
4.3
|
22.6
|
1.0
|
NE2
|
D:HIS201
|
4.4
|
18.8
|
1.0
|
CD2
|
D:HIS201
|
4.4
|
17.9
|
1.0
|
CG
|
D:HIS112
|
4.5
|
20.2
|
1.0
|
ND1
|
D:HIS108
|
4.5
|
17.1
|
1.0
|
CA
|
D:PRO148
|
4.5
|
18.3
|
1.0
|
CG
|
D:HIS108
|
4.5
|
18.0
|
1.0
|
CG
|
D:ASP55
|
4.5
|
20.6
|
1.0
|
CB
|
D:ASP56
|
4.7
|
21.3
|
1.0
|
O
|
D:HOH480
|
4.8
|
28.5
|
1.0
|
CB
|
D:PRO148
|
4.9
|
17.4
|
1.0
|
N
|
D:ASP56
|
5.0
|
16.4
|
1.0
|
C
|
D:PRO148
|
5.0
|
21.9
|
1.0
|
|
Zinc binding site 5 out
of 5 in 8hfa
Go back to
Zinc Binding Sites List in 8hfa
Zinc binding site 5 out
of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/hf/8hfa-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:55.8
occ:1.00
|
NE2
|
E:HIS112
|
2.3
|
22.1
|
1.0
|
OD1
|
E:ASP56
|
2.4
|
20.2
|
1.0
|
NE2
|
E:HIS108
|
2.4
|
19.8
|
1.0
|
O
|
E:HOH446
|
2.5
|
22.9
|
1.0
|
O
|
E:HOH507
|
2.8
|
31.6
|
1.0
|
CE1
|
E:HIS112
|
3.1
|
18.9
|
1.0
|
CG
|
E:ASP56
|
3.2
|
18.0
|
1.0
|
OD2
|
E:ASP56
|
3.3
|
20.4
|
1.0
|
CD2
|
E:HIS108
|
3.4
|
19.9
|
1.0
|
CE1
|
E:HIS108
|
3.4
|
18.5
|
1.0
|
CD2
|
E:HIS112
|
3.4
|
21.5
|
1.0
|
CB
|
E:ASP55
|
4.1
|
19.1
|
1.0
|
OD2
|
E:ASP55
|
4.2
|
23.4
|
1.0
|
N
|
E:TYR149
|
4.3
|
23.8
|
1.0
|
ND1
|
E:HIS112
|
4.3
|
17.1
|
1.0
|
O
|
E:HOH529
|
4.3
|
28.9
|
1.0
|
CA
|
E:PRO148
|
4.4
|
18.1
|
1.0
|
NE2
|
E:HIS201
|
4.4
|
22.9
|
1.0
|
CG
|
E:HIS112
|
4.5
|
18.1
|
1.0
|
ND1
|
E:HIS108
|
4.5
|
21.1
|
1.0
|
CG
|
E:HIS108
|
4.5
|
22.7
|
1.0
|
CD2
|
E:HIS201
|
4.5
|
23.1
|
1.0
|
CG
|
E:ASP55
|
4.7
|
22.9
|
1.0
|
CB
|
E:ASP56
|
4.7
|
14.6
|
1.0
|
CB
|
E:PRO148
|
4.9
|
18.9
|
1.0
|
C
|
E:PRO148
|
4.9
|
19.8
|
1.0
|
|
Reference:
L.Liu,
Y.Zhou,
Q.Yang.
The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae To Be Published.
Page generated: Fri Jul 28 07:03:53 2023
|