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Chlorine in PDB 3be8: Crystal Structure of the Synaptic Protein Neuroligin 4

Protein crystallography data

The structure of Crystal Structure of the Synaptic Protein Neuroligin 4, PDB code: 3be8 was solved by I.P.Fabrichny, P.Leone, G.Sulzenbacher, D.Comoletti, M.T.Miller, P.Taylor, Y.Bourne, P.Marchot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.730, 154.050, 81.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.1

Other elements in 3be8:

The structure of Crystal Structure of the Synaptic Protein Neuroligin 4 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Synaptic Protein Neuroligin 4 (pdb code 3be8). 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 Synaptic Protein Neuroligin 4, PDB code: 3be8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3be8

Go back to Chlorine Binding Sites List in 3be8
Chlorine binding site 1 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl624

b:0.6
occ:1.00
 O A:HOH757 2.9 40.5 1.0
O A:HOH725 3.0 32.0 1.0
N A:SER95 3.2 33.5 1.0
CA A:PRO94 3.8 30.4 1.0
CB A:PRO94 3.8 29.6 1.0
CD A:PRO81 3.9 30.7 1.0
O A:ALA79 4.0 26.9 1.0
CA A:SER80 4.0 28.2 1.0
C A:PRO94 4.0 31.9 1.0
CB A:SER95 4.1 37.5 1.0
CA A:SER95 4.2 35.9 1.0
OG A:SER80 4.4 31.2 1.0
OG A:SER95 4.4 41.7 1.0
N A:SER80 4.5 27.1 1.0
C A:ALA79 4.5 26.4 1.0
O A:SER95 4.6 35.4 1.0
CB A:SER80 4.7 29.2 1.0
CG A:PRO81 4.7 31.9 1.0
N A:PRO81 4.7 29.6 1.0
CB A:PRO77 4.8 26.6 1.0
O A:HOH774 4.8 30.0 1.0
C A:SER80 4.8 28.4 1.0
C A:SER95 4.9 35.5 1.0

Chlorine binding site 2 out of 6 in 3be8

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Chlorine binding site 2 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl625

b:38.3
occ:1.00
 O A:HOH848 2.9 55.1 1.0
O A:HOH865 3.0 45.0 1.0
C A:ARG583 3.4 31.1 1.0
N A:LYS586 3.4 29.6 1.0
CA A:ARG583 3.5 31.6 1.0
CG A:LYS586 3.6 29.8 1.0
O A:ARG583 3.6 29.5 1.0
N A:THR585 3.6 32.1 1.0
CB A:THR585 3.8 31.6 1.0
N A:ALA584 3.9 33.2 1.0
CB A:ARG583 4.0 30.9 1.0
CB A:LYS586 4.0 29.6 1.0
CA A:THR585 4.0 31.2 1.0
C A:THR585 4.2 29.4 1.0
OG1 A:THR585 4.3 32.6 1.0
CA A:LYS586 4.4 29.4 1.0
C A:ALA584 4.5 33.0 1.0
NZ A:LYS586 4.6 33.6 1.0
CD A:LYS586 4.7 30.9 1.0
CG A:ARG583 4.7 33.3 1.0
N A:ARG583 4.8 32.0 1.0
CA A:ALA584 4.8 34.0 1.0
CZ A:ARG583 4.9 34.0 1.0
CG2 A:THR585 4.9 32.1 1.0

Chlorine binding site 3 out of 6 in 3be8

Go back to Chlorine Binding Sites List in 3be8
Chlorine binding site 3 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl627

b:0.3
occ:1.00
 OH A:TYR171 3.0 23.2 1.0
N A:GLY174 3.2 21.8 1.0
CE A:MET184 3.7 31.1 0.7
CE2 A:TYR171 3.8 19.5 1.0
CZ A:TYR171 3.8 20.6 1.0
CA A:HIS173 3.9 20.8 1.0
CH2 A:TRP127 3.9 50.1 1.0
CB A:HIS173 4.0 20.7 1.0
C A:HIS173 4.1 21.4 1.0
CA A:GLY174 4.1 23.0 1.0
CB A:SER253 4.5 23.3 1.0
CZ2 A:TRP127 4.5 50.9 1.0
O A:SER253 4.6 22.3 1.0
C A:GLY174 4.7 23.0 1.0
CE1 A:PHE128 4.7 46.1 1.0
O A:GLY174 4.7 24.3 1.0
CD1 A:ILE185 4.9 36.1 1.0
CZ3 A:TRP127 4.9 51.0 1.0

Chlorine binding site 4 out of 6 in 3be8

Go back to Chlorine Binding Sites List in 3be8
Chlorine binding site 4 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl622

b:0.4
occ:1.00
 OH B:TYR171 2.8 31.1 1.0
CE B:MET184 3.4 37.4 0.5
N B:GLY174 3.5 27.8 1.0
CZ B:TYR171 3.7 29.6 1.0
CE2 B:TYR171 3.7 29.6 1.0
CH2 B:TRP127 3.9 96.5 1.0
CA B:HIS173 3.9 26.4 1.0
CB B:HIS173 4.1 26.9 1.0
C B:HIS173 4.2 26.9 1.0
CA B:GLY174 4.4 28.4 1.0
CB B:SER253 4.5 25.3 1.0
CZ2 B:TRP127 4.6 1.0 1.0
O B:SER253 4.7 23.4 1.0
CE1 B:PHE128 4.8 84.4 1.0
O B:GLY174 4.8 31.0 1.0
CZ3 B:TRP127 4.8 95.0 1.0
C B:GLY174 4.9 29.6 1.0
CG2 B:VAL493 5.0 30.3 1.0
CE1 B:TYR171 5.0 26.0 1.0
CG1 B:ILE185 5.0 38.6 1.0

Chlorine binding site 5 out of 6 in 3be8

Go back to Chlorine Binding Sites List in 3be8
Chlorine binding site 5 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl625

b:0.4
occ:1.00
 O B:HOH712 3.1 40.8 1.0
N B:SER95 3.3 42.6 1.0
O B:HOH804 3.3 44.7 1.0
CA B:PRO94 3.8 39.0 1.0
CD B:PRO81 3.8 39.2 1.0
CA B:SER80 3.9 36.7 1.0
O B:ALA79 3.9 35.1 1.0
CB B:PRO94 3.9 38.7 1.0
CB B:SER95 4.0 46.3 1.0
C B:PRO94 4.1 41.1 1.0
CA B:SER95 4.2 44.8 1.0
OG B:SER80 4.2 39.1 1.0
O B:HOH755 4.4 47.0 1.0
N B:SER80 4.4 35.2 1.0
C B:ALA79 4.5 34.2 1.0
OG B:SER95 4.5 47.9 1.0
CB B:SER80 4.5 37.8 1.0
O B:SER95 4.6 44.2 1.0
N B:PRO81 4.6 38.1 1.0
C B:SER80 4.7 36.8 1.0
CG B:PRO81 4.7 40.9 1.0
O B:HOH769 4.8 30.9 1.0
CB B:PRO77 4.8 35.8 1.0
C B:SER95 4.9 45.3 1.0

Chlorine binding site 6 out of 6 in 3be8

Go back to Chlorine Binding Sites List in 3be8
Chlorine binding site 6 out of 6 in the Crystal Structure of the Synaptic Protein Neuroligin 4


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 Synaptic Protein Neuroligin 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl626

b:38.6
occ:1.00
 O B:HOH857 3.0 49.9 1.0
O B:HOH844 3.2 58.5 1.0
C B:ARG583 3.4 28.7 1.0
N B:LYS586 3.4 25.5 1.0
CA B:ARG583 3.5 28.8 1.0
N B:THR585 3.6 28.5 1.0
O B:ARG583 3.6 28.3 1.0
CB B:THR585 3.7 28.2 1.0
CG B:LYS586 3.7 24.9 1.0
N B:ALA584 3.8 29.6 1.0
CA B:THR585 4.0 28.0 1.0
CB B:LYS586 4.0 25.3 1.0
CB B:ARG583 4.1 28.4 1.0
C B:THR585 4.2 26.4 1.0
OG1 B:THR585 4.3 30.2 1.0
CA B:LYS586 4.4 24.6 1.0
C B:ALA584 4.6 29.2 1.0
CG B:ARG583 4.7 30.1 1.0
N B:ARG583 4.7 28.9 1.0
CA B:ALA584 4.8 30.5 1.0
CD B:LYS586 4.8 26.9 1.0
NZ B:LYS586 4.8 28.4 1.0
CG2 B:THR585 4.8 28.8 1.0
CZ B:ARG583 4.9 33.9 1.0
NH2 B:ARG583 4.9 36.1 1.0

Reference:

I.P.Fabrichny, P.Leone, G.Sulzenbacher, D.Comoletti, M.T.Miller, P.Taylor, Y.Bourne, P.Marchot. Structural Analysis of the Synaptic Protein Neuroligin and Its Beta-Neurexin Complex: Determinants For Folding and Cell Adhesion Neuron V. 56 979 2007.
ISSN: ISSN 0896-6273
PubMed: 18093521
DOI: 10.1016/J.NEURON.2007.11.013
Page generated: Fri Jul 11 03:25:35 2025

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