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Chlorine 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 (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4jra

Go back to Chlorine Binding Sites List in 4jra
Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1301

b:37.8
occ:1.00
 HH21 A:ARG1013 2.9 16.9 1.0
O A:PHE1100 3.3 23.4 1.0
HA2 A:GLY1102 3.6 14.0 1.0
NH2 A:ARG1013 3.7 14.1 1.0
HE A:ARG1013 3.7 15.3 1.0
O A:ASP1099 3.8 11.6 1.0
C A:PHE1100 4.1 19.6 1.0
HH22 A:ARG1013 4.2 16.9 1.0
CA A:GLY1102 4.3 11.7 1.0
HA A:PHE1100 4.3 17.6 1.0
N A:GLY1102 4.3 12.1 1.0
H A:GLY1102 4.4 14.5 1.0
NE A:ARG1013 4.4 12.8 1.0
HA3 A:GLY1102 4.5 14.0 1.0
HB2 A:LYS1098 4.5 20.7 1.0
CZ A:ARG1013 4.5 11.9 1.0
O A:HOH1407 4.5 11.5 1.0
OE1 A:GLU1283 4.6 15.8 1.0
HB3 A:ARG1013 4.7 19.5 1.0
C A:TRP1101 4.7 12.9 1.0
CA A:PHE1100 4.8 14.6 1.0
HB3 A:LYS1098 4.9 20.7 1.0
C A:ASP1099 4.9 11.3 1.0
N A:TRP1101 4.9 20.3 1.0
CD A:GLU1283 5.0 18.6 1.0
O A:HOH1447 5.0 14.0 1.0

Chlorine binding site 2 out of 6 in 4jra

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Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1302

b:46.0
occ:1.00
 HH22 A:ARG1034 2.6 50.8 1.0
HE1 A:PHE999 3.0 16.6 1.0
NH2 A:ARG1034 3.2 42.4 1.0
HH21 A:ARG1034 3.3 50.8 1.0
HD12 A:ILE1036 3.7 11.8 1.0
CE1 A:PHE999 3.8 13.8 1.0
HH A:TYR1010 3.9 17.0 1.0
HD1 A:PHE999 4.1 24.8 1.0
OH A:TYR1010 4.2 14.2 1.0
O A:LYS1000 4.2 15.0 1.0
HE2 A:TYR1010 4.2 14.2 1.0
HG23 A:ILE1036 4.3 22.1 1.0
CZ A:ARG1034 4.4 42.7 1.0
CD1 A:PHE999 4.4 20.6 1.0
HH12 A:ARG1034 4.4 53.7 1.0
CE2 A:TYR1010 4.5 11.9 1.0
CZ A:TYR1010 4.5 11.4 1.0
CD1 A:ILE1036 4.6 9.8 1.0
CZ A:PHE999 4.8 11.8 1.0
HZ A:PHE999 4.8 14.1 1.0
HD11 A:ILE1036 4.8 11.8 1.0
NH1 A:ARG1034 4.8 44.8 1.0
HD13 A:ILE1036 5.0 11.8 1.0
CL A:CL1305 5.0 32.0 1.0

Chlorine binding site 3 out of 6 in 4jra

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Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl1303

b:30.4
occ:1.00
 H A:GLU1210 2.2 31.3 1.0
HB2 A:GLU1210 2.7 25.1 1.0
HA2 A:GLY1129 2.9 34.9 1.0
N A:GLU1210 3.0 26.1 1.0
HB3 A:GLU1210 3.3 25.1 1.0
HA A:LEU1209 3.3 32.7 1.0
CB A:GLU1210 3.3 20.9 1.0
HD13 A:LEU1209 3.4 44.2 1.0
CA A:GLY1129 3.8 29.1 1.0
CA A:GLU1210 3.8 25.2 1.0
HG12 A:VAL1128 3.8 18.6 1.0
HA3 A:GLY1129 3.8 34.9 1.0
HB2 A:ASP1213 3.8 37.3 1.0
C A:LEU1209 4.0 27.0 1.0
HB3 A:LEU1209 4.0 33.3 1.0
CA A:LEU1209 4.0 27.2 1.0
HD12 A:LEU1209 4.1 44.2 1.0
CD1 A:LEU1209 4.2 36.8 1.0
N A:GLY1129 4.4 28.4 1.0
H A:ILE1130 4.4 24.3 1.0
O A:GLU1210 4.4 21.0 1.0
H A:GLY1129 4.4 34.1 1.0
CB A:LEU1209 4.4 27.7 1.0
HB3 A:ASP1213 4.5 37.3 1.0
OE1 A:GLU1210 4.5 19.9 1.0
HA A:GLU1210 4.5 30.3 1.0
CG1 A:VAL1128 4.6 15.5 1.0
CB A:ASP1213 4.6 31.1 1.0
C A:GLU1210 4.6 21.2 1.0
HG13 A:VAL1128 4.7 18.6 1.0
CG A:GLU1210 4.7 22.5 1.0
HG11 A:VAL1128 4.7 18.6 1.0
HD11 A:LEU1209 4.9 44.2 1.0
CG A:LEU1209 4.9 28.9 1.0
OD2 A:ASP1213 4.9 43.9 1.0
C A:GLY1129 4.9 24.0 1.0
HG2 A:GLU1210 4.9 27.0 1.0
O A:ALA1208 5.0 15.6 1.0
N A:ILE1130 5.0 20.3 1.0

Chlorine binding site 4 out of 6 in 4jra

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Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1304

b:24.1
occ:1.00
 H A:LYS1098 2.5 24.3 1.0
HA A:LEU1097 2.8 21.4 1.0
HG2 A:LYS1098 3.2 14.6 1.0
N A:LYS1098 3.3 20.2 1.0
HZ2 A:LYS1236 3.5 21.9 1.0
HA A:SER1225 3.6 11.3 1.0
HD3 A:LYS1236 3.6 19.9 1.0
CA A:LEU1097 3.7 17.9 1.0
HB2 A:LYS1098 3.8 20.7 1.0
HG A:LEU1097 3.8 15.9 1.0
C A:LEU1097 3.9 19.9 1.0
CG A:LYS1098 4.0 12.2 1.0
HD23 A:LEU1097 4.2 15.2 1.0
CB A:LYS1098 4.2 17.2 1.0
HB3 A:LEU1097 4.2 18.4 1.0
HG3 A:LYS1098 4.2 14.6 1.0
HZ3 A:LYS1098 4.2 14.8 1.0
HB2 A:SER1225 4.2 12.4 1.0
CA A:LYS1098 4.2 17.4 1.0
NZ A:LYS1236 4.3 18.2 1.0
CB A:LEU1097 4.3 15.3 1.0
HZ3 A:LYS1236 4.3 21.9 1.0
O A:LYS1098 4.3 18.6 1.0
CG A:LEU1097 4.4 13.2 1.0
CA A:SER1225 4.5 9.4 1.0
CD A:LYS1236 4.5 16.6 1.0
HG2 A:LYS1236 4.5 20.1 1.0
OG A:SER1225 4.6 25.6 1.0
O A:ILE1096 4.6 26.9 1.0
CB A:SER1225 4.6 10.3 1.0
N A:LEU1097 4.8 24.2 1.0
C A:LYS1098 4.8 18.0 1.0
CD2 A:LEU1097 4.8 12.7 1.0
O A:SER1225 4.8 37.6 1.0
HZ2 A:LYS1098 4.8 14.8 1.0
HG3 A:LYS1236 4.9 20.1 1.0
CG A:LYS1236 4.9 16.8 1.0
HZ1 A:LYS1236 4.9 21.9 1.0
NZ A:LYS1098 4.9 12.3 1.0
CE A:LYS1236 5.0 20.7 1.0
HG A:SER1225 5.0 30.7 1.0
O A:LYS1224 5.0 11.7 1.0

Chlorine binding site 5 out of 6 in 4jra

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Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl1305

b:32.0
occ:1.00
 HD2 A:TYR1010 2.6 15.4 1.0
H A:SER1002 2.8 20.7 1.0
HE2 A:TYR1010 2.9 14.2 1.0
HB2 A:TYR1001 3.1 15.3 1.0
NA A:NA1306 3.2 22.3 1.0
HA A:TYR1001 3.2 19.1 1.0
CD2 A:TYR1010 3.2 12.8 1.0
CE2 A:TYR1010 3.4 11.9 1.0
N A:SER1002 3.6 17.2 1.0
CB A:TYR1001 3.8 12.7 1.0
CA A:TYR1001 3.9 15.9 1.0
HB3 A:TYR1001 3.9 15.3 1.0
O A:HOH1414 3.9 26.6 1.0
HD12 A:ILE1005 3.9 15.4 1.0
HD13 A:ILE1005 4.1 15.4 1.0
HB3 A:SER1002 4.2 25.9 1.0
C A:TYR1001 4.3 16.0 1.0
HB2 A:SER1002 4.3 25.9 1.0
CD1 A:ILE1005 4.4 12.8 1.0
CG A:TYR1010 4.5 13.5 1.0
HB2 A:TYR1010 4.5 22.4 1.0
CB A:SER1002 4.6 21.6 1.0
CA A:SER1002 4.6 18.4 1.0
O A:SER1002 4.6 19.6 1.0
CZ A:TYR1010 4.6 11.4 1.0
HD11 A:ILE1005 4.7 15.4 1.0
OG A:SER1008 4.7 12.5 1.0
H A:ASP1009 4.8 21.9 1.0
HZ A:PHE999 4.8 14.1 1.0
O A:LYS1000 4.8 15.0 1.0
HG21 A:ILE1005 4.9 15.6 1.0
HH A:TYR1010 4.9 17.0 1.0
CL A:CL1302 5.0 46.0 1.0

Chlorine binding site 6 out of 6 in 4jra

Go back to Chlorine Binding Sites List in 4jra
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl1308

b:24.1
occ:1.00
 H A:GLN1003 2.5 31.9 1.0
HH A:TYR980 2.6 25.5 1.0
HG2 A:MET1004 2.8 15.8 1.0
OH A:TYR980 3.0 21.3 1.0
HB2 A:GLN1003 3.1 29.1 1.0
N A:GLN1003 3.3 26.6 1.0
HE2 A:TYR980 3.3 19.9 1.0
H A:MET1004 3.4 30.0 1.0
HA A:SER1002 3.4 22.0 1.0
HG A:SER1002 3.5 32.4 1.0
CZ A:TYR980 3.6 21.0 1.0
HE2 A:MET1004 3.6 15.6 1.0
CG A:MET1004 3.7 13.2 1.0
HG3 A:GLN1003 3.7 23.0 1.0
CE2 A:TYR980 3.7 16.6 1.0
HG3 A:MET1004 3.8 15.8 1.0
CB A:GLN1003 3.8 24.2 1.0
N A:MET1004 3.9 25.0 1.0
OG A:SER1002 4.0 27.0 1.0
CA A:GLN1003 4.0 21.0 1.0
O A:HOH1423 4.2 10.8 1.0
CA A:SER1002 4.2 18.4 1.0
C A:SER1002 4.2 23.4 1.0
CG A:GLN1003 4.3 19.1 1.0
C A:GLN1003 4.3 22.4 1.0
CE A:MET1004 4.3 13.0 1.0
O A:ILE1148 4.4 14.6 1.0
HE3 A:MET1004 4.5 15.6 1.0
HB2 A:MET1004 4.5 10.6 1.0
CB A:MET1004 4.6 8.8 1.0
HE21 A:GLN1003 4.6 15.3 1.0
CE1 A:TYR980 4.6 18.0 1.0
HB3 A:GLN1003 4.6 29.1 1.0
SD A:MET1004 4.7 22.1 1.0
CB A:SER1002 4.7 21.6 1.0
CD2 A:TYR980 4.8 13.9 1.0
HE1 A:TYR980 4.9 21.6 1.0
HG2 A:GLN1003 4.9 23.0 1.0
CA A:MET1004 4.9 17.6 1.0
HA A:GLN1003 4.9 25.2 1.0
O A:TYR1001 5.0 18.7 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: Sun Jul 21 17:39:08 2024

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