Zinc in PDB 7dvl: Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3, PDB code: 7dvl
was solved by
Y.Wu,
O.Leka,
R.Kammerer,
X.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.71 /
2.01
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.25,
97.42,
141.25,
90,
90,
90
|
R / Rfree (%)
|
20.5 /
23.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3
(pdb code 7dvl). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3, PDB code: 7dvl:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 7dvl
Go back to
Zinc Binding Sites List in 7dvl
Zinc binding site 1 out
of 2 in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:25.2
occ:1.00
|
NE2
|
A:HIS225
|
2.0
|
26.6
|
1.0
|
OE1
|
A:GLU264
|
2.1
|
41.9
|
1.0
|
NE2
|
A:HIS229
|
2.1
|
25.9
|
1.0
|
OE2
|
A:GLU264
|
2.1
|
45.0
|
1.0
|
O
|
A:HOH805
|
2.1
|
16.1
|
1.0
|
CD
|
A:GLU264
|
2.4
|
44.0
|
1.0
|
CD2
|
A:HIS225
|
2.9
|
27.0
|
1.0
|
CD2
|
A:HIS229
|
3.0
|
25.4
|
1.0
|
HD2
|
A:HIS225
|
3.0
|
32.5
|
1.0
|
HD2
|
A:HIS229
|
3.1
|
30.5
|
1.0
|
CE1
|
A:HIS225
|
3.1
|
27.8
|
1.0
|
CE1
|
A:HIS229
|
3.1
|
25.3
|
1.0
|
HE1
|
A:HIS229
|
3.4
|
30.4
|
1.0
|
HE1
|
A:HIS225
|
3.4
|
33.4
|
1.0
|
CG
|
A:GLU264
|
3.9
|
37.3
|
1.0
|
HG21
|
A:THR267
|
4.1
|
25.9
|
1.0
|
HA
|
A:GLU264
|
4.1
|
24.6
|
1.0
|
CG
|
A:HIS225
|
4.1
|
24.7
|
1.0
|
ND1
|
A:HIS225
|
4.2
|
27.2
|
1.0
|
CG
|
A:HIS229
|
4.2
|
23.0
|
1.0
|
ND1
|
A:HIS229
|
4.2
|
24.6
|
1.0
|
HG22
|
A:THR267
|
4.2
|
25.9
|
1.0
|
HG3
|
A:GLU264
|
4.3
|
44.8
|
1.0
|
OE1
|
A:GLN226
|
4.3
|
29.8
|
1.0
|
HG2
|
A:GLU264
|
4.3
|
44.8
|
1.0
|
HB
|
A:THR267
|
4.3
|
25.1
|
1.0
|
CG2
|
A:THR267
|
4.6
|
21.6
|
1.0
|
HB2
|
A:GLU264
|
4.6
|
29.7
|
1.0
|
CB
|
A:GLU264
|
4.7
|
24.7
|
1.0
|
HE22
|
A:GLN226
|
4.8
|
34.4
|
1.0
|
O
|
A:HOH722
|
4.8
|
25.7
|
1.0
|
CA
|
A:GLU264
|
4.8
|
20.6
|
1.0
|
CB
|
A:THR267
|
4.9
|
20.9
|
1.0
|
HD1
|
A:HIS225
|
5.0
|
32.6
|
1.0
|
HD1
|
A:HIS229
|
5.0
|
29.6
|
1.0
|
|
Zinc binding site 2 out
of 2 in 7dvl
Go back to
Zinc Binding Sites List in 7dvl
Zinc binding site 2 out
of 2 in the Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:34.5
occ:1.00
|
OE1
|
B:GLU264
|
2.0
|
41.4
|
1.0
|
NE2
|
B:HIS225
|
2.0
|
34.8
|
1.0
|
OE2
|
B:GLU264
|
2.1
|
41.2
|
1.0
|
NE2
|
B:HIS229
|
2.1
|
36.2
|
1.0
|
O
|
B:HOH817
|
2.2
|
13.3
|
1.0
|
CD
|
B:GLU264
|
2.3
|
45.9
|
1.0
|
CD2
|
B:HIS225
|
3.0
|
32.5
|
1.0
|
CE1
|
B:HIS225
|
3.0
|
32.4
|
1.0
|
CD2
|
B:HIS229
|
3.1
|
32.1
|
1.0
|
CE1
|
B:HIS229
|
3.1
|
33.2
|
1.0
|
HD2
|
B:HIS225
|
3.1
|
39.0
|
1.0
|
HD2
|
B:HIS229
|
3.2
|
38.5
|
1.0
|
HE1
|
B:HIS225
|
3.3
|
38.9
|
1.0
|
HE1
|
B:HIS229
|
3.3
|
39.9
|
1.0
|
CG
|
B:GLU264
|
3.9
|
41.4
|
1.0
|
HE22
|
B:GLN226
|
3.9
|
36.6
|
1.0
|
HA
|
B:GLU264
|
4.1
|
27.7
|
1.0
|
ND1
|
B:HIS225
|
4.1
|
30.6
|
1.0
|
CG
|
B:HIS225
|
4.1
|
28.8
|
1.0
|
HG21
|
B:THR267
|
4.2
|
28.6
|
1.0
|
ND1
|
B:HIS229
|
4.2
|
31.3
|
1.0
|
CG
|
B:HIS229
|
4.2
|
28.9
|
1.0
|
HB
|
B:THR267
|
4.3
|
28.7
|
1.0
|
HG2
|
B:GLU264
|
4.3
|
49.7
|
1.0
|
HG3
|
B:GLU264
|
4.3
|
49.7
|
1.0
|
HG22
|
B:THR267
|
4.3
|
28.6
|
1.0
|
NE2
|
B:GLN226
|
4.5
|
30.4
|
1.0
|
HB2
|
B:GLU264
|
4.5
|
34.6
|
1.0
|
CG2
|
B:THR267
|
4.6
|
23.8
|
1.0
|
CB
|
B:GLU264
|
4.6
|
28.8
|
1.0
|
O
|
B:HOH786
|
4.7
|
30.1
|
1.0
|
CA
|
B:GLU264
|
4.8
|
23.0
|
1.0
|
HE21
|
B:GLN226
|
4.9
|
36.6
|
1.0
|
CB
|
B:THR267
|
4.9
|
23.9
|
1.0
|
HD1
|
B:HIS225
|
4.9
|
36.8
|
1.0
|
HD1
|
B:HIS229
|
5.0
|
37.5
|
1.0
|
|
Reference:
O.Leka,
Y.Wu,
X.Li,
R.Kammerer.
Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3. J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Mon Jul 12 17:02:04 2021
|