Chlorine in PDB 5cc2: Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka

The structure of Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka, PDB code: 5cc2 was solved by P.Naur, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.58 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.210, 70.210, 134.500, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.9

The binding sites of Chlorine atom in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka (pdb code 5cc2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka, PDB code: 5cc2:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:32.2 occ:1.00 CL1 A:CKA301 0.0 32.2 1.0 C6 A:CKA301 1.8 18.1 1.0 C7 A:CKA301 2.7 24.1 1.0 C5 A:CKA301 2.7 26.3 1.0 CE1 A:PHE15 3.3 32.1 1.0 CG2 A:VAL197 3.5 26.7 1.0 OH A:TYR222 3.5 42.9 1.0 CG A:ASP194 3.5 39.4 1.0 CB A:ALA85 3.6 27.7 1.0 CB A:ASP194 3.6 35.5 1.0 CD1 A:PHE15 3.7 36.5 1.0 CG A:GLU12 3.7 43.6 1.0 OD1 A:ASP194 3.8 45.5 1.0 CZ A:TYR222 3.9 44.9 1.0 OD2 A:ASP194 3.9 40.3 1.0 CE2 A:TYR222 4.0 35.4 1.0 C4 A:CKA301 4.0 21.8 1.0 C8 A:CKA301 4.0 33.2 1.0 CZ A:PHE15 4.1 37.6 1.0 CD A:GLU12 4.3 51.1 1.0 OE1 A:GLU12 4.5 51.2 1.0 C3 A:CKA301 4.5 30.6 1.0 OH A:TYR58 4.7 42.5 1.0 CE1 A:TYR222 4.7 39.3 1.0 CG A:PHE15 4.7 40.0 1.0 CB A:GLU12 4.9 39.0 1.0 CD2 A:TYR222 4.9 33.5 1.0 CB A:VAL197 4.9 36.2 1.0 OE2 A:GLU12 4.9 50.3 1.0

Chlorine binding site 2 out of 4 in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:70.9 occ:1.00 CL1 A:CKA302 0.0 70.9 1.0 C6 A:CKA302 1.8 46.6 1.0 C7 A:CKA302 2.7 53.4 1.0 C5 A:CKA302 2.7 49.2 1.0 SD A:MET160 3.4 61.6 1.0 CG2 A:VAL143 3.6 35.0 1.0 CE A:MET160 3.7 39.0 1.0 CG1 A:VAL192 3.9 32.0 1.0 C4 A:CKA302 4.0 50.5 1.0 C8 A:CKA302 4.0 55.1 1.0 CD1 A:LEU120 4.2 48.8 1.0 CG2 A:VAL107 4.4 40.5 1.0 CD2 A:LEU120 4.4 50.7 1.0 CG1 A:VAL139 4.5 41.0 1.0 C3 A:CKA302 4.5 49.1 1.0 CG A:LEU120 4.8 48.7 1.0 CE1 A:TYR157 4.8 64.3 1.0 CB A:VAL192 4.9 35.5 1.0 CG2 A:VAL192 5.0 31.0 1.0

Chlorine binding site 3 out of 4 in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:48.4 occ:0.50 CL1 A:CKA303 0.0 48.4 0.5 C6 A:CKA303 1.8 26.6 0.5 C7 A:CKA303 2.7 27.4 0.5 C5 A:CKA303 2.7 24.1 0.5 CB A:GLN182 3.5 39.2 1.0 C4 A:CKA303 4.0 25.7 0.5 C8 A:CKA303 4.0 24.4 0.5 CG A:GLN182 4.1 44.6 1.0 NE2 A:GLN182 4.1 63.2 1.0 CD2 A:TYR186 4.2 33.8 1.0 CE2 A:TYR186 4.5 42.1 1.0 C3 A:CKA303 4.6 24.8 0.5 CD A:GLN182 4.7 58.4 1.0 O A:GLN182 4.7 45.7 1.0 CA A:GLN182 4.7 40.8 1.0 C A:GLN182 4.8 37.3 1.0

Chlorine binding site 4 out of 4 in the Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Ligand-Binding Domain of the Ionotropic Glutamate Receptor-Like GLUD2 in Complex with 7-Cka within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:71.1 occ:1.00 N A:TYR48 3.5 48.0 1.0 O A:TYR48 3.8 50.4 1.0 CD2 A:TYR48 3.9 31.1 1.0 CE2 A:TYR48 3.9 38.8 1.0 CB A:ASN47 4.0 49.8 1.0 CA A:ASN47 4.0 44.9 1.0 OD1 A:ASN47 4.2 64.6 1.0 C A:ASN47 4.3 49.3 1.0 CG A:TYR48 4.3 35.7 1.0 CZ A:TYR48 4.3 41.1 1.0 CA A:TYR48 4.5 44.4 1.0 C A:TYR48 4.5 50.7 1.0 CG A:ASN47 4.6 56.6 1.0 CD1 A:TYR48 4.6 41.3 1.0 CE1 A:TYR48 4.6 39.5 1.0 CB A:TYR48 4.9 35.6 1.0 OH A:TYR48 5.0 44.1 1.0

A.S.Kristensen, K.B.Hansen, P.Naur, L.Olsen, N.L.Kurtkaya, S.M.Dravid, T.Kvist, F.Yi, J.Phlsgaard, R.P.Clausen, M.Gajhede, J.S.Kastrup, S.F.Traynelis. Pharmacology and Structural Analysis of Ligand Binding to the Orthosteric Site of Glutamate-Like GLUD2 Receptors. Mol.Pharmacol. V. 89 253 2016.
ISSN: ESSN 1521-0111
PubMed: 26661043
DOI: 10.1124/MOL.115.100909