Chlorine in PDB 8qez: Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution

The structure of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution, PDB code: 8qez was solved by J.Dorosz, S.Laulumaa, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.316, 163.416, 47.466, 90, 90, 90
R / Rfree (%)	16.8 / 19.5

The structure of Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution also contains other interesting chemical elements:

Zinc	(Zn)	7 atoms
Arsenic	(As)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution (pdb code 8qez). 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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution, PDB code: 8qez:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:35.5 occ:1.00 CL1 A:UF5310 0.0 35.5 1.0 C1 A:UF5310 1.7 19.3 1.0 HG B:SER108 2.1 24.7 0.6 C2 A:UF5310 2.8 20.4 1.0 S1 A:UF5310 2.9 20.6 1.0 OG B:SER108 3.0 20.6 0.6 HA B:SER108 3.0 19.4 0.6 HA B:SER108 3.0 19.4 0.4 HB3 B:SER108 3.0 22.5 0.4 H1 A:UF5310 3.1 24.5 1.0 HA3 B:GLY219 3.3 19.9 1.0 H1 B:UF5307 3.3 21.3 1.0 O B:LYS218 3.3 16.9 1.0 HG3 B:PRO105 3.3 17.4 1.0 HB2 B:PRO105 3.4 16.4 1.0 H3 B:UF5307 3.5 22.9 1.0 O B:HOH448 3.5 30.8 1.0 C2 B:UF5307 3.6 17.8 1.0 CB B:SER108 3.6 18.7 0.4 CB B:SER108 3.7 18.7 0.6 HB2 B:SER108 3.7 22.5 0.4 CL1 B:UF5307 3.7 30.6 1.0 HB3 B:SER108 3.7 22.5 0.6 C1 B:UF5307 3.7 17.9 1.0 CA B:SER108 3.7 16.2 0.4 CA B:SER108 3.7 16.1 0.6 CG B:PRO105 3.8 14.5 1.0 HG2 B:PRO105 3.9 17.4 1.0 O B:HOH452 3.9 19.1 1.0 CB B:PRO105 3.9 13.7 1.0 HB3 B:PRO105 3.9 16.4 1.0 C B:LYS218 4.0 14.7 1.0 C3 A:UF5310 4.0 18.6 1.0 CA B:GLY219 4.0 16.6 1.0 C4 A:UF5310 4.1 19.6 1.0 HA2 B:GLY219 4.1 19.9 1.0 H4 B:UF5307 4.1 22.9 1.0 C7 B:UF5307 4.2 19.1 1.0 O B:MET107 4.2 18.5 1.0 N B:SER108 4.3 14.1 1.0 N B:GLY219 4.3 15.5 1.0 HG A:SER108 4.4 27.0 0.7 HG3 A:PRO105 4.5 19.8 1.0 C B:MET107 4.5 15.5 1.0 C3 B:UF5307 4.5 18.1 1.0 HB2 B:SER108 4.6 22.5 0.6 H B:LEU109 4.6 21.5 1.0 HA B:LYS218 4.7 19.5 1.0 H B:SER108 4.8 17.0 0.4 H B:SER108 4.8 17.0 0.6 HG2 A:PRO105 4.9 19.8 1.0 CA B:LYS218 4.9 16.2 1.0 OG B:SER108 4.9 19.1 0.4 S1 B:UF5307 5.0 20.7 1.0 C B:SER108 5.0 18.7 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:31.6 occ:0.72 HG1 A:THR93 2.1 22.8 1.0 HH22 A:ARG149 2.5 57.7 1.0 O A:HOH509 2.7 30.4 1.0 HG23 A:VAL95 2.7 28.4 0.5 HG22 A:VAL95 2.9 28.4 0.5 HG21 A:VAL95 2.9 28.4 0.5 HG21 A:THR93 3.0 22.8 1.0 OG1 A:THR93 3.0 19.0 1.0 CG2 A:VAL95 3.0 23.7 0.5 HH12 A:ARG149 3.0 61.2 1.0 HG3 A:ARG96 3.2 19.2 1.0 NH2 A:ARG149 3.4 48.1 1.0 HB A:VAL95 3.4 29.2 0.5 HB A:THR93 3.6 25.3 1.0 CB A:THR93 3.7 21.0 1.0 HG3 A:GLU145 3.7 43.0 1.0 CG2 A:THR93 3.7 19.0 1.0 NH1 A:ARG149 3.8 51.0 1.0 HE A:ARG96 3.8 20.9 1.0 HA A:SER142 3.9 28.7 1.0 HB2 A:GLU145 3.9 39.6 1.0 NE A:ARG96 3.9 17.4 1.0 HD2 A:ARG96 3.9 20.2 1.0 HH21 A:ARG149 4.0 57.7 1.0 HG23 A:THR93 4.0 22.8 1.0 CZ A:ARG149 4.0 55.8 1.0 CG A:ARG96 4.1 16.0 1.0 O A:HOH503 4.1 37.6 1.0 H A:ARG96 4.2 20.6 1.0 CD A:ARG96 4.2 16.8 1.0 HB3 A:GLU145 4.2 39.6 1.0 HB3 A:SER142 4.3 29.4 1.0 O A:HOH406 4.4 30.4 1.0 CB A:VAL95 4.4 24.3 0.5 CB A:GLU145 4.4 33.0 1.0 CG A:GLU145 4.4 35.8 1.0 HG22 A:THR93 4.5 22.8 1.0 CZ A:ARG96 4.5 17.2 1.0 HH11 A:ARG149 4.5 61.2 1.0 CB A:VAL95 4.5 24.5 0.5 H A:VAL95 4.6 24.6 0.5 H A:VAL95 4.6 24.6 0.5 O A:HOH581 4.6 31.4 1.0 HG2 A:ARG96 4.6 19.2 1.0 HH2 A:TRP71 4.7 31.1 1.0 HB2 A:SER142 4.7 29.4 1.0 CA A:SER142 4.7 24.0 1.0 N A:ARG96 4.7 17.1 1.0 HG11 A:VAL95 4.7 31.8 0.5 HG12 A:VAL95 4.8 31.8 0.5 HH21 A:ARG96 4.8 21.0 1.0 HZ3 A:TRP71 4.8 28.3 1.0 CB A:SER142 4.8 24.5 1.0 HB A:VAL95 4.9 29.4 0.5 NH2 A:ARG96 4.9 17.5 1.0 HG2 A:GLU145 4.9 43.0 1.0 CG1 A:VAL95 4.9 26.5 0.5 HB2 A:ARG96 4.9 18.4 1.0 HG21 A:VAL95 5.0 32.4 0.5

Chlorine binding site 3 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl307 b:30.6 occ:1.00 CL1 B:UF5307 0.0 30.6 1.0 C1 B:UF5307 1.7 17.9 1.0 HG A:SER108 2.1 27.0 0.7 C2 B:UF5307 2.8 17.8 1.0 S1 B:UF5307 2.9 20.7 1.0 OG A:SER108 3.0 22.5 0.7 HA A:SER108 3.1 21.5 1.0 H1 B:UF5307 3.1 21.3 1.0 HB3 A:SER108 3.1 23.0 0.3 H1 A:UF5310 3.3 24.5 1.0 HA3 A:GLY219 3.4 17.8 1.0 O A:LYS218 3.4 16.7 1.0 HG3 A:PRO105 3.4 19.8 1.0 O B:HOH448 3.5 30.8 1.0 H4 A:UF5310 3.5 25.0 1.0 HB2 A:PRO105 3.5 18.9 1.0 HB2 A:SER108 3.5 23.0 0.3 HB3 A:SER108 3.6 22.9 0.7 C2 A:UF5310 3.6 20.4 1.0 CB A:SER108 3.6 19.1 0.3 CB A:SER108 3.6 19.1 0.7 CL1 A:UF5310 3.7 35.5 1.0 C1 A:UF5310 3.7 19.3 1.0 CA A:SER108 3.7 17.9 0.3 CA A:SER108 3.7 17.8 0.7 O A:HOH451 3.8 21.2 1.0 CG A:PRO105 3.9 16.5 1.0 CB A:PRO105 4.0 15.8 1.0 HB3 A:PRO105 4.0 18.9 1.0 C3 B:UF5307 4.0 18.1 1.0 HG2 A:PRO105 4.0 19.8 1.0 C A:LYS218 4.0 18.9 1.0 C4 B:UF5307 4.1 19.9 1.0 CA A:GLY219 4.1 14.8 1.0 HA2 A:GLY219 4.1 17.8 1.0 O A:MET107 4.3 18.2 1.0 H3 A:UF5310 4.3 25.0 1.0 C7 A:UF5310 4.3 20.9 1.0 HG B:SER108 4.3 24.7 0.6 N A:SER108 4.3 15.7 1.0 N A:GLY219 4.4 16.2 1.0 HG3 B:PRO105 4.5 17.4 1.0 C A:MET107 4.5 17.1 1.0 C3 A:UF5310 4.5 18.6 1.0 HB2 A:SER108 4.5 22.9 0.7 H A:LEU109 4.6 19.9 1.0 HA A:LYS218 4.8 21.4 1.0 HG2 B:PRO105 4.8 17.4 1.0 H A:SER108 4.8 18.8 1.0 OG B:SER108 4.9 20.6 0.6 S1 A:UF5310 5.0 20.6 1.0 OG A:SER108 5.0 18.8 0.3 CA A:LYS218 5.0 17.8 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl308 b:39.0 occ:0.69 HG1 B:THR93 2.1 26.1 1.0 O B:HOH511 2.7 30.2 1.0 HG21 B:THR93 2.8 23.9 1.0 OG1 B:THR93 2.9 21.8 1.0 HG22 B:VAL95 3.1 37.4 1.0 HG23 B:VAL95 3.2 37.4 1.0 HG3 B:ARG96 3.2 23.5 1.0 HG21 B:VAL95 3.3 37.4 1.0 CG2 B:VAL95 3.4 31.1 1.0 CG2 B:THR93 3.4 19.9 1.0 CB B:THR93 3.5 22.1 1.0 HB B:THR93 3.5 26.5 1.0 HE B:ARG96 3.5 23.2 1.0 NE B:ARG96 3.6 19.3 1.0 HA B:SER142 3.6 23.9 1.0 HD2 B:ARG96 3.7 20.1 1.0 HG3 B:GLU145 3.7 50.2 1.0 HG23 B:THR93 3.7 23.9 1.0 O B:HOH484 3.9 32.0 1.0 HB3 B:SER142 3.9 23.5 1.0 CD B:ARG96 3.9 16.8 1.0 CG B:ARG96 4.0 19.6 1.0 HB2 B:GLU145 4.0 32.3 1.0 CZ B:ARG96 4.1 16.7 1.0 HG22 B:THR93 4.3 23.9 1.0 H B:ARG96 4.3 24.0 1.0 HB2 B:SER142 4.4 23.5 1.0 HB3 B:GLU145 4.4 32.3 1.0 CB B:SER142 4.4 19.6 1.0 CA B:SER142 4.4 19.9 1.0 HH21 B:ARG96 4.4 24.1 1.0 O A:HOH437 4.5 24.7 1.0 NH2 B:ARG96 4.5 20.0 1.0 CG B:GLU145 4.5 41.8 1.0 HG2 B:ARG96 4.5 23.5 1.0 CB B:GLU145 4.5 26.9 1.0 NH1 B:ARG96 4.6 15.7 1.0 HH11 B:ARG96 4.7 18.9 1.0 H B:VAL95 4.8 26.4 1.0 HB2 B:ARG96 4.9 20.4 1.0 CB B:VAL95 4.9 25.6 1.0 N B:ARG96 4.9 20.0 1.0 HD3 B:ARG96 4.9 20.1 1.0 HG2 B:GLU145 4.9 50.2 1.0 O B:HOH569 4.9 35.5 1.0 HZ3 B:TRP71 5.0 34.8 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl309 b:28.3 occ:1.00 CL1 C:UF5309 0.0 28.3 1.0 C1 C:UF5309 1.7 18.6 1.0 C2 C:UF5309 2.8 15.6 1.0 S1 C:UF5309 2.9 18.5 1.0 H1 C:UF5309 3.1 18.7 1.0 O C:HOH436 3.3 23.5 0.5 C3 C:UF5309 4.0 15.5 1.0 C4 C:UF5309 4.1 16.1 1.0 HG3 C:PRO105 4.5 15.9 1.0 HG C:SER108 4.7 22.4 0.6 HG2 C:PRO105 4.8 15.9 1.0 OG C:SER108 5.0 18.7 0.6

Chlorine binding site 6 out of 6 in the Crystal Structure of the Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution


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 Ampa Receptor GLUA2-L504Y-N775S Ligand Binding Domain in Complex with L-Glutamate and Positive Allosteric Modulator BPAM395 at 1.55A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl310 b:31.3 occ:0.63 HG1 C:THR93 2.1 20.4 1.0 O C:HOH649 2.4 28.6 1.0 HG21 C:THR93 2.7 18.2 1.0 O C:HOH489 2.7 25.9 1.0 OG1 C:THR93 2.8 16.9 1.0 HG23 C:VAL95 3.0 25.8 1.0 HG22 C:VAL95 3.1 25.8 1.0 HG3 C:ARG96 3.2 16.7 1.0 CG2 C:VAL95 3.3 21.5 1.0 HG21 C:VAL95 3.3 25.8 1.0 HB C:THR93 3.4 18.4 1.0 CG2 C:THR93 3.4 15.1 1.0 CB C:THR93 3.4 15.3 1.0 HE C:ARG96 3.5 19.5 1.0 NE C:ARG96 3.6 16.2 1.0 HG2 C:GLU145 3.6 27.6 0.5 HD2 C:ARG96 3.6 18.2 1.0 HG3 C:GLU145 3.8 31.6 0.5 HA C:SER142 3.8 21.7 1.0 HG23 C:THR93 3.8 18.2 1.0 CD C:ARG96 3.9 15.2 1.0 HB3 C:SER142 3.9 22.9 1.0 CG C:ARG96 4.0 13.9 1.0 CZ C:ARG96 4.1 14.9 1.0 HG22 C:THR93 4.2 18.2 1.0 HB3 C:GLU145 4.2 28.6 0.5 H C:ARG96 4.2 18.8 1.0 HB2 C:GLU145 4.2 28.6 0.5 HH21 C:ARG96 4.4 19.4 1.0 CG C:GLU145 4.5 23.0 0.5 NH2 C:ARG96 4.5 16.1 1.0 CB C:SER142 4.5 19.1 1.0 HG2 C:ARG96 4.5 16.7 1.0 HB2 C:SER142 4.6 22.9 1.0 O C:HOH562 4.6 25.2 1.0 CA C:SER142 4.6 18.1 1.0 CG C:GLU145 4.6 26.3 0.5 HB3 C:GLU145 4.6 28.6 0.5 HB2 C:GLU145 4.6 28.6 0.5 NH1 C:ARG96 4.7 14.3 1.0 H C:VAL95 4.7 20.2 1.0 CB C:GLU145 4.7 23.8 0.5 CB C:GLU145 4.7 23.8 0.5 HH11 C:ARG96 4.7 17.2 1.0 HB2 C:ARG96 4.8 16.9 1.0 N C:ARG96 4.8 15.7 1.0 CB C:VAL95 4.8 20.1 1.0 HG2 C:GLU145 4.9 31.6 0.5 O C:HOH601 4.9 27.1 1.0 HD3 C:ARG96 4.9 18.2 1.0 CA C:THR93 4.9 14.4 1.0 HZ3 C:TRP71 4.9 28.3 1.0 CB C:ARG96 5.0 14.1 1.0 O C:GLY62 5.0 23.3 1.0 HG3 C:GLU145 5.0 27.6 0.5

P.Francotte, Y.Bay, E.Goffin, T.Colson, C.Lesenfants, J.Dorosz, S.Laulumaa, P.Fraikin, P.De Tullio, C.Beaufour, I.Botez, D.S.Pickering, K.Frydenvang, L.Danober, A.S.Kristensen, J.S.Kastrup, B.Pirotte. Exploring Thienothiadiazine Dioxides As Isosteric Analogues of Benzo- and Pyridothiadiazine Dioxides in the Search of New Ampa and Kainate Receptor Positive Allosteric Modulators. Eur.J.Med.Chem. V. 264 16036 2023.
ISSN: ISSN 0223-5234
PubMed: 38101041
DOI: 10.1016/J.EJMECH.2023.116036