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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:

Chlorine (Cl) 6 atoms

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

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