Chlorine in PDB 5mfw: Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution

The structure of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution, PDB code: 5mfw was solved by A.P.Larsen, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.644, 68.644, 234.854, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.9

The structure of Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution (pdb code 5mfw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 A Resolution, PDB code: 5mfw:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 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 Bpam-121 at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:19.3 occ:0.69 CL1 A:7M6901 0.0 19.3 0.7 C5 A:7M6901 1.7 14.1 0.7 CG2 B:THR535 2.5 14.7 0.3 C4 A:7M6901 2.7 10.0 0.7 C6 A:7M6901 2.7 18.2 0.7 CB B:THR535 3.3 17.5 0.3 CB B:THR535 3.4 17.6 0.7 CG2 B:THR535 3.4 14.8 0.7 CA B:THR535 3.4 14.2 0.3 CA B:THR535 3.4 14.1 0.7 O B:LYS762 3.5 12.8 1.0 CA B:GLY763 3.5 10.4 1.0 C6 B:7M6901 3.6 19.1 0.6 CB B:PRO532 3.6 7.4 1.0 CG B:PRO532 3.7 13.8 1.0 C B:LYS762 3.8 9.2 1.0 O B:MET534 3.8 12.1 1.0 N B:GLY763 3.8 9.4 1.0 O B:HOH1136 3.8 23.8 1.0 C7 B:7M6901 4.0 13.8 0.6 C1 A:7M6901 4.0 15.5 0.7 C7 A:7M6901 4.0 15.8 0.7 C5 B:7M6901 4.1 15.5 0.6 N B:THR535 4.1 12.9 1.0 C B:MET534 4.2 12.8 1.0 F1 B:7M6901 4.3 17.0 0.6 CL1 B:7M6901 4.5 22.0 0.6 C2 A:7M6901 4.6 16.3 0.7 OG1 B:THR535 4.6 22.8 0.3 CG2 A:THR535 4.7 16.5 0.4 C B:THR535 4.7 17.4 1.0 C2 B:7M6901 4.8 13.7 0.6 C4 B:7M6901 4.8 10.6 0.6 OG1 B:THR535 4.8 27.5 0.7 CA B:LYS762 4.8 11.8 1.0 N B:LEU536 4.9 13.9 1.0 C B:GLY763 4.9 10.5 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 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 Bpam-121 at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl902 b:30.0 occ:1.00 O A:HOH1084 2.4 20.1 1.0 O B:HOH1076 2.6 13.6 1.0 NZ A:LYS531 3.2 8.2 1.0 NZ B:LYS531 3.4 11.8 1.0 CG A:LYS531 3.7 12.3 1.0 NH1 B:ARG775 3.9 12.6 1.0 CG B:LYS531 3.9 7.5 1.0 O B:PHE529 4.0 5.6 1.0 NH1 A:ARG775 4.0 29.7 1.0 CE A:LYS531 4.1 11.7 1.0 O A:PHE529 4.2 8.7 1.0 CE B:LYS531 4.3 6.6 1.0 O A:HOH1125 4.3 16.8 1.0 N A:LYS531 4.3 9.1 1.0 CZ B:ARG775 4.3 17.0 1.0 OG1 A:THR779 4.4 8.2 1.0 CD A:LYS531 4.6 19.0 1.0 O B:HOH1034 4.6 24.9 1.0 N B:LYS531 4.7 7.7 1.0 C A:SER530 4.7 9.6 1.0 CD B:ARG775 4.7 15.6 1.0 NE B:ARG775 4.7 17.4 1.0 CA A:LYS531 4.7 8.8 1.0 CD B:LYS531 4.8 11.9 1.0 CD A:ARG775 4.8 22.5 1.0 CZ A:ARG775 4.8 33.0 1.0 CB A:LYS531 4.8 13.4 1.0 C B:SER530 4.8 5.7 1.0 OG1 B:THR779 4.9 7.2 1.0 O A:HOH1003 5.0 29.0 1.0 CA B:LYS531 5.0 10.1 1.0 NH2 B:ARG775 5.0 15.7 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the GLUK1 Ligand-Binding Domain in Complex with Kainate and Bpam-121 at 2.10 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 Bpam-121 at 2.10 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:22.0 occ:0.61 CL1 B:7M6901 0.0 22.0 0.6 C5 B:7M6901 1.7 15.5 0.6 CG2 A:THR535 2.2 16.5 0.4 C4 B:7M6901 2.7 10.6 0.6 C6 B:7M6901 2.7 19.1 0.6 CB A:THR535 3.1 21.5 0.4 CG2 A:THR535 3.3 21.7 0.6 CG A:PRO532 3.3 11.9 1.0 CA A:THR535 3.3 16.0 0.4 CB A:THR535 3.4 21.9 0.6 CA A:THR535 3.4 16.0 0.6 O A:LYS762 3.4 11.8 1.0 CB A:PRO532 3.5 8.1 1.0 O A:MET534 3.6 13.3 1.0 CA A:GLY763 3.7 10.3 1.0 C6 A:7M6901 3.9 18.2 0.7 C A:LYS762 3.9 11.8 1.0 N A:THR535 3.9 13.5 1.0 C1 B:7M6901 4.0 15.9 0.6 C A:MET534 4.0 17.5 1.0 C7 B:7M6901 4.0 13.8 0.6 C5 A:7M6901 4.1 14.1 0.7 N A:GLY763 4.1 8.5 1.0 C7 A:7M6901 4.3 15.8 0.7 OG1 A:THR535 4.4 24.7 0.4 CL1 A:7M6901 4.5 19.3 0.7 C4 A:7M6901 4.6 10.0 0.7 C2 B:7M6901 4.6 13.7 0.6 C A:THR535 4.7 18.3 1.0 C2 A:7M6901 4.8 16.3 0.7 OG1 A:THR535 4.8 29.8 0.6 CD A:PRO532 4.8 10.9 1.0 N A:LEU536 4.8 13.2 1.0 C1 A:7M6901 4.9 15.5 0.7 CA A:PRO532 4.9 12.7 1.0 F1 A:7M6901 5.0 24.4 0.7 C A:GLY763 5.0 8.2 1.0 CA A:LYS762 5.0 13.1 1.0

A.P.Larsen, S.Fievre, K.Frydenvang, P.Francotte, B.Pirotte, J.S.Kastrup, C.Mulle. Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors. Mol. Pharmacol. V. 91 576 2017.
ISSN: ESSN 1521-0111
PubMed: 28360094
DOI: 10.1124/MOL.116.107599