Sodium in PDB 4jra: Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C
Enzymatic activity of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C
All present enzymatic activity of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C:
3.4.24.69;
Protein crystallography data
The structure of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C, PDB code: 4jra
was solved by
R.M.Benoit,
D.Frey,
M.M.Wieser,
R.Jaussi,
G.F.X.Schertler,
G.Capitani,
R.A.Kammerer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.93 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.440,
105.260,
127.960,
90.00,
90.02,
90.00
|
R / Rfree (%)
|
23.5 /
26.9
|
Other elements in 4jra:
The structure of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C
(pdb code 4jra). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C, PDB code: 4jra:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 4jra
Go back to
Sodium Binding Sites List in 4jra
Sodium binding site 1 out
of 2 in the Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1306
b:22.3
occ:1.00
|
OG
|
A:SER1008
|
2.2
|
12.5
|
1.0
|
HB2
|
A:SER1008
|
2.4
|
15.8
|
1.0
|
O
|
A:SER1002
|
2.6
|
19.6
|
1.0
|
CB
|
A:SER1008
|
2.8
|
13.1
|
1.0
|
HG21
|
A:ILE1005
|
2.8
|
15.6
|
1.0
|
HD13
|
A:ILE1005
|
3.1
|
15.4
|
1.0
|
HD2
|
A:TYR1010
|
3.1
|
15.4
|
1.0
|
CL
|
A:CL1305
|
3.2
|
32.0
|
1.0
|
HG13
|
A:ILE1011
|
3.3
|
14.6
|
1.0
|
HB2
|
A:TYR1001
|
3.3
|
15.3
|
1.0
|
HA
|
A:SER1008
|
3.4
|
19.7
|
1.0
|
HB3
|
A:SER1008
|
3.5
|
15.8
|
1.0
|
H
|
A:SER1002
|
3.5
|
20.7
|
1.0
|
HB2
|
A:TYR1010
|
3.6
|
22.4
|
1.0
|
HD12
|
A:ILE1011
|
3.6
|
11.9
|
1.0
|
CA
|
A:SER1008
|
3.7
|
16.4
|
1.0
|
C
|
A:SER1002
|
3.7
|
23.4
|
1.0
|
HD11
|
A:ILE1011
|
3.7
|
11.9
|
1.0
|
HD1
|
A:TYR1001
|
3.7
|
13.3
|
1.0
|
CG2
|
A:ILE1005
|
3.7
|
13.0
|
1.0
|
H
|
A:TYR1010
|
3.8
|
25.4
|
1.0
|
N
|
A:SER1002
|
3.9
|
17.2
|
1.0
|
CD1
|
A:ILE1005
|
3.9
|
12.8
|
1.0
|
CD1
|
A:ILE1011
|
4.0
|
9.9
|
1.0
|
CD2
|
A:TYR1010
|
4.0
|
12.8
|
1.0
|
HD12
|
A:ILE1005
|
4.0
|
15.4
|
1.0
|
H
|
A:ILE1011
|
4.0
|
23.4
|
1.0
|
H
|
A:ASP1009
|
4.0
|
21.9
|
1.0
|
HG22
|
A:ILE1005
|
4.0
|
15.6
|
1.0
|
CG1
|
A:ILE1011
|
4.1
|
12.1
|
1.0
|
HG23
|
A:ILE1005
|
4.1
|
15.6
|
1.0
|
HB3
|
A:SER1002
|
4.1
|
25.9
|
1.0
|
O
|
A:HOH1414
|
4.1
|
26.6
|
1.0
|
CB
|
A:TYR1001
|
4.3
|
12.7
|
1.0
|
CA
|
A:SER1002
|
4.3
|
18.4
|
1.0
|
CB
|
A:TYR1010
|
4.4
|
18.7
|
1.0
|
N
|
A:ASP1009
|
4.5
|
18.3
|
1.0
|
CD1
|
A:TYR1001
|
4.5
|
11.1
|
1.0
|
HD11
|
A:ILE1005
|
4.5
|
15.4
|
1.0
|
HA
|
A:GLN1003
|
4.5
|
25.2
|
1.0
|
N
|
A:TYR1010
|
4.5
|
21.1
|
1.0
|
C
|
A:SER1008
|
4.5
|
23.6
|
1.0
|
N
|
A:ILE1011
|
4.5
|
19.5
|
1.0
|
C
|
A:TYR1001
|
4.6
|
16.0
|
1.0
|
CG
|
A:TYR1010
|
4.7
|
13.5
|
1.0
|
HG12
|
A:ILE1011
|
4.7
|
14.6
|
1.0
|
HB
|
A:ILE1005
|
4.7
|
15.3
|
1.0
|
CB
|
A:ILE1005
|
4.7
|
12.7
|
1.0
|
CB
|
A:SER1002
|
4.7
|
21.6
|
1.0
|
N
|
A:SER1008
|
4.7
|
11.6
|
1.0
|
HB3
|
A:TYR1001
|
4.8
|
15.3
|
1.0
|
N
|
A:GLN1003
|
4.8
|
26.6
|
1.0
|
HE2
|
A:TYR1010
|
4.8
|
14.2
|
1.0
|
CG1
|
A:ILE1005
|
4.8
|
12.9
|
1.0
|
HA
|
A:TYR1001
|
4.8
|
19.1
|
1.0
|
HB
|
A:ILE1011
|
4.8
|
15.5
|
1.0
|
CG
|
A:TYR1001
|
4.8
|
11.6
|
1.0
|
CA
|
A:TYR1010
|
4.9
|
21.8
|
1.0
|
CE2
|
A:TYR1010
|
4.9
|
11.9
|
1.0
|
CA
|
A:TYR1001
|
4.9
|
15.9
|
1.0
|
HD13
|
A:ILE1011
|
4.9
|
11.9
|
1.0
|
H
|
A:SER1008
|
4.9
|
13.9
|
1.0
|
CB
|
A:ILE1011
|
5.0
|
12.9
|
1.0
|
|
Sodium binding site 2 out
of 2 in 4jra
Go back to
Sodium Binding Sites List in 4jra
Sodium binding site 2 out
of 2 in the Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Botulinum Neurotoxin A Receptor-Binding Domain in Complex with the Luminal Domain of SV2C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1307
b:15.9
occ:1.00
|
HH
|
A:TYR1111
|
2.1
|
19.9
|
1.0
|
OD2
|
A:ASP1099
|
2.4
|
12.8
|
1.0
|
O
|
A:TYR1104
|
2.5
|
21.2
|
1.0
|
OH
|
A:TYR1111
|
2.9
|
16.6
|
1.0
|
HG3
|
A:GLN1106
|
3.0
|
35.7
|
1.0
|
HA
|
A:LEU1105
|
3.1
|
12.7
|
1.0
|
HZ2
|
A:LYS1109
|
3.2
|
45.8
|
1.0
|
HB3
|
A:ASP1099
|
3.2
|
11.8
|
1.0
|
HE1
|
A:TYR1111
|
3.3
|
15.2
|
1.0
|
CG
|
A:ASP1099
|
3.4
|
11.6
|
1.0
|
HB2
|
A:ASP1103
|
3.6
|
15.4
|
1.0
|
C
|
A:TYR1104
|
3.6
|
18.9
|
1.0
|
O
|
A:HOH1417
|
3.7
|
14.7
|
1.0
|
HE2
|
A:LYS1109
|
3.7
|
41.3
|
1.0
|
HD3
|
A:LYS1109
|
3.8
|
35.5
|
1.0
|
CB
|
A:ASP1099
|
3.8
|
9.8
|
1.0
|
CZ
|
A:TYR1111
|
3.8
|
14.8
|
1.0
|
HG3
|
A:PRO1286
|
3.8
|
15.4
|
1.0
|
H
|
A:GLN1106
|
3.9
|
19.1
|
1.0
|
CE1
|
A:TYR1111
|
3.9
|
12.7
|
1.0
|
CA
|
A:LEU1105
|
3.9
|
10.6
|
1.0
|
CG
|
A:GLN1106
|
3.9
|
29.7
|
1.0
|
NZ
|
A:LYS1109
|
3.9
|
38.2
|
1.0
|
HD12
|
A:LEU1105
|
4.1
|
11.7
|
1.0
|
HB2
|
A:GLN1106
|
4.1
|
27.4
|
1.0
|
N
|
A:LEU1105
|
4.1
|
17.0
|
1.0
|
N
|
A:GLN1106
|
4.2
|
15.9
|
1.0
|
HZ3
|
A:LYS1109
|
4.2
|
45.8
|
1.0
|
CE
|
A:LYS1109
|
4.2
|
34.4
|
1.0
|
OE1
|
A:GLN1106
|
4.2
|
34.6
|
1.0
|
H
|
A:ASP1099
|
4.3
|
19.2
|
1.0
|
C
|
A:LEU1105
|
4.3
|
13.4
|
1.0
|
HB2
|
A:ASP1099
|
4.4
|
11.8
|
1.0
|
OD1
|
A:ASP1099
|
4.4
|
13.1
|
1.0
|
CB
|
A:ASP1103
|
4.4
|
12.8
|
1.0
|
HG2
|
A:GLN1106
|
4.5
|
35.7
|
1.0
|
HB3
|
A:ASP1103
|
4.5
|
15.4
|
1.0
|
CD
|
A:LYS1109
|
4.5
|
29.6
|
1.0
|
CB
|
A:GLN1106
|
4.5
|
22.8
|
1.0
|
O
|
A:ASP1103
|
4.5
|
14.2
|
1.0
|
CD
|
A:GLN1106
|
4.6
|
32.8
|
1.0
|
C
|
A:ASP1103
|
4.6
|
11.6
|
1.0
|
HZ1
|
A:LYS1109
|
4.6
|
45.8
|
1.0
|
N
|
A:TYR1104
|
4.7
|
15.3
|
1.0
|
CA
|
A:TYR1104
|
4.7
|
16.8
|
1.0
|
CG
|
A:PRO1286
|
4.8
|
12.8
|
1.0
|
N
|
A:ASP1099
|
4.8
|
16.0
|
1.0
|
HD3
|
A:PRO1286
|
4.9
|
16.9
|
1.0
|
H
|
A:LEU1105
|
4.9
|
20.4
|
1.0
|
CA
|
A:ASP1099
|
5.0
|
10.8
|
1.0
|
|
Reference:
R.M.Benoit,
D.Frey,
M.Hilbert,
J.T.Kevenaar,
M.M.Wieser,
C.U.Stirnimann,
D.Mcmillan,
T.Ceska,
F.Lebon,
R.Jaussi,
M.O.Steinmetz,
G.F.Schertler,
C.C.Hoogenraad,
G.Capitani,
R.A.Kammerer.
Structural Basis For Recognition of Synaptic Vesicle Protein 2C By Botulinum Neurotoxin A. Nature V. 505 108 2014.
ISSN: ISSN 0028-0836
PubMed: 24240280
DOI: 10.1038/NATURE12732
Page generated: Mon Oct 7 16:21:24 2024
|