Chlorine in PDB 8r36: Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution

The structure of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution, PDB code: 8r36 was solved by Y.Bay, S.M.Frantsen, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.485, 71.485, 232.902, 90, 90, 90
R / Rfree (%)	16.4 / 19.9

The binding sites of Chlorine atom in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution (pdb code 8r36). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution, PDB code: 8r36:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:53.8 occ:1.00 N A:TYR479 3.2 35.0 1.0 O A:TYR479 3.3 33.9 1.0 CD1 A:TYR479 3.6 35.6 1.0 CE1 A:TYR479 3.7 34.6 1.0 CA A:LEU478 3.8 37.8 1.0 O A:HOH1123 4.0 45.8 1.0 CG A:TYR479 4.0 34.6 1.0 C A:LEU478 4.0 33.8 1.0 CD2 A:LEU478 4.0 48.7 1.0 CB A:LEU478 4.0 39.4 1.0 C A:TYR479 4.1 33.2 1.0 CA A:TYR479 4.1 33.6 1.0 CZ A:TYR479 4.2 38.9 1.0 ND2 A:ASN457 4.3 38.2 1.0 CD2 A:TYR479 4.5 34.0 1.0 CE2 A:TYR479 4.6 35.2 1.0 CB A:TYR479 4.6 35.5 1.0 CG A:LEU478 4.7 41.5 1.0 OH A:TYR479 4.9 40.8 1.0

Chlorine binding site 2 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl904 b:42.6 occ:1.00 O A:HOH1081 2.4 33.4 1.0 O B:HOH1100 2.6 30.7 1.0 NZ A:LYS531 3.1 26.6 1.0 NZ B:LYS531 3.4 26.4 1.0 CG B:LYS531 3.7 31.1 1.0 CG A:LYS531 3.8 31.9 1.0 O B:PHE529 4.0 22.5 1.0 CE B:LYS531 4.0 27.6 1.0 NH1 B:ARG775 4.1 36.0 1.0 CE A:LYS531 4.2 28.9 1.0 O A:PHE529 4.2 22.3 1.0 N B:LYS531 4.4 20.4 1.0 N A:LYS531 4.4 23.1 1.0 CD B:LYS531 4.5 31.4 1.0 O B:HOH1013 4.5 42.0 1.0 CZ B:ARG775 4.6 35.9 1.0 CD A:LYS531 4.6 34.3 1.0 O A:HOH1107 4.6 45.9 1.0 C B:SER530 4.7 22.5 1.0 CD B:ARG775 4.7 33.9 1.0 CA B:LYS531 4.7 20.1 1.0 OG1 A:THR779 4.7 26.4 1.0 C A:SER530 4.7 22.2 1.0 CA A:LYS531 4.8 24.8 1.0 OG1 B:THR779 4.8 23.7 1.0 NE B:ARG775 4.8 33.1 1.0 CB B:LYS531 4.9 23.1 1.0 O B:SER530 4.9 23.7 1.0 CB A:LYS531 4.9 27.2 1.0

Chlorine binding site 3 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl905 b:55.8 occ:1.00 N A:LEU758 2.9 27.9 1.0 CA A:GLY757 3.4 35.2 1.0 C A:GLY757 3.7 32.9 1.0 CG A:LEU758 3.7 42.0 1.0 CB A:LEU758 3.8 32.6 1.0 CA A:LEU758 3.9 27.5 1.0 O A:LEU758 4.4 30.9 1.0 CD2 A:LEU758 4.6 31.8 1.0 CD1 A:LEU758 4.7 46.6 1.0 C A:LEU758 4.7 30.6 1.0 N A:GLY757 4.8 30.6 1.0 O A:GLY757 4.9 29.2 1.0

Chlorine binding site 4 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl906 b:63.7 occ:1.00 NZ A:LYS503 3.1 57.8 1.0 N A:TRP498 3.2 28.1 1.0 CE A:LYS503 3.7 62.5 1.0 CD A:LYS503 3.8 43.5 1.0 CA A:GLU497 3.8 38.9 1.0 CB A:TRP498 3.9 29.8 1.0 CD1 A:TRP498 4.0 31.1 1.0 C A:GLU497 4.0 29.3 1.0 CA A:TRP498 4.1 28.1 1.0 O A:TRP498 4.3 29.4 1.0 O A:GLY496 4.3 39.5 1.0 CG A:TRP498 4.4 28.6 1.0 CB A:GLU497 4.5 38.2 1.0 CD1 A:ILE506 4.6 26.4 1.0 C A:TRP498 4.7 30.1 1.0 CG2 A:ILE506 4.9 33.7 1.0 N A:GLU497 5.0 37.8 1.0

Chlorine binding site 5 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl907 b:80.7 occ:1.00 OG1 A:THR678 3.2 52.5 1.0 N A:THR678 3.5 40.7 1.0 O A:HOH1149 3.5 58.3 1.0 CA A:GLN677 4.0 39.7 1.0 NZ A:LYS679 4.1 80.5 1.0 CB A:THR678 4.2 50.6 1.0 C A:GLN677 4.2 41.2 1.0 CA A:THR678 4.3 46.2 1.0 CB A:GLN677 4.3 40.0 1.0 N A:LYS679 4.4 40.8 1.0 CG2 A:THR678 4.6 52.0 1.0 CG A:LYS679 4.7 54.6 1.0 C A:THR678 4.7 46.4 1.0

Chlorine binding site 6 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A 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 GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl908 b:79.1 occ:1.00 O A:HOH1136 2.8 56.4 1.0 NZ A:LYS488 4.0 52.2 1.0 CE A:LYS488 4.6 53.5 1.0 O A:ASP486 4.8 31.6 1.0

Chlorine binding site 7 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl906 b:74.7 occ:1.00 N B:GLY545 3.6 60.8 1.0 O B:HOH1041 3.7 45.4 1.0 CA B:LYS544 4.2 50.5 1.0 CG2 B:THR753 4.3 45.0 1.0 C B:LYS544 4.4 52.6 1.0 CA B:GLY545 4.5 60.6 1.0 CB B:LYS544 4.5 53.8 1.0 CG B:LYS544 4.5 51.8 1.0 O B:THR546 4.6 57.9 1.0 N B:THR546 4.6 60.5 1.0

Chlorine binding site 8 out of 8 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and BPAM538 at 1.90 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl907 b:49.3 occ:1.00 N B:TYR479 3.2 30.4 1.0 O B:TYR479 3.5 26.9 1.0 CA B:LEU478 3.7 29.1 1.0 CD1 B:TYR479 3.7 28.8 1.0 CE1 B:TYR479 3.8 27.7 1.0 CB B:LEU478 3.9 31.4 1.0 C B:LEU478 4.0 32.5 1.0 CD2 B:LEU478 4.0 40.3 1.0 CG B:TYR479 4.2 30.8 1.0 O B:HOH1127 4.2 45.2 1.0 CA B:TYR479 4.2 25.7 1.0 C B:TYR479 4.3 29.8 1.0 CZ B:TYR479 4.3 32.5 1.0 ND2 B:ASN457 4.3 29.3 1.0 CG B:LEU478 4.6 40.3 1.0 CD2 B:TYR479 4.6 30.4 1.0 CE2 B:TYR479 4.7 27.9 1.0 CB B:TYR479 4.8 24.8 1.0 O B:PHE477 4.9 30.1 1.0 N B:LEU478 5.0 30.8 1.0

Y.Bay, F.J.M.Cabello, C.C.Koens, S.M.Frantsen, D.S.Pickering, K.Frydenvang, P.Francotte, B.Pirotte, A.S.Kristensen, D.Bowie, J.S.Kastrup. Crystal Structure of the GLUK1 Ligand-Binding Domain with Kainate and the Full-Spanning Positive Allosteric Modulator BPAM538. J.Struct.Biol. 08113 2024.
ISSN: ESSN 1095-8657
PubMed: 39079583
DOI: 10.1016/J.JSB.2024.108113