Sodium in PDB 8fww: Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel

The structure of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Sodium atom in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel (pdb code 8fww). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel, PDB code: 8fww:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:26.3 occ:1.00 O A:GLN621 3.0 59.9 1.0 O B:GLN621 3.3 49.9 1.0 O C:GLN621 3.5 57.6 1.0 O D:GLN621 3.6 46.6 1.0 C A:GLN621 4.2 59.9 1.0 C B:GLN621 4.5 49.9 1.0 C C:GLN621 4.7 57.6 1.0 C D:GLN621 4.8 46.6 1.0 CA A:GLN622 4.9 59.9 1.0 CB A:GLN621 5.0 59.9 1.0

Sodium binding site 2 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:26.3 occ:1.00 CG2 A:THR652 3.9 37.0 1.0 CB A:ALA656 4.0 39.0 1.0 O A:THR652 4.0 37.0 1.0 O B:THR652 4.1 30.9 1.0 CG2 B:THR652 4.1 30.9 1.0 CG2 C:THR652 4.2 35.8 1.0 O D:THR652 4.3 28.0 1.0 CB B:ALA656 4.3 34.7 1.0 CG2 D:THR652 4.3 28.0 1.0 CB C:ALA656 4.4 38.6 1.0 CB D:ALA656 4.4 32.1 1.0 O C:THR652 4.5 35.8 1.0 C A:THR652 4.5 37.0 1.0 C B:THR652 4.6 30.9 1.0 CA A:ALA653 4.8 38.9 1.0 C D:THR652 4.8 28.0 1.0 CB A:THR652 4.9 37.0 1.0 CA D:ALA653 4.9 29.2 1.0 CA B:ALA653 4.9 31.5 1.0 N A:ALA653 4.9 38.9 1.0 CB B:THR652 4.9 30.9 1.0 C C:THR652 5.0 35.8 1.0

Sodium binding site 3 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:26.3 occ:1.00 OG1 A:THR660 3.0 54.7 1.0 OG1 C:THR660 3.3 53.9 1.0 O A:ALA656 3.5 39.0 1.0 OG1 B:THR660 3.6 47.6 1.0 O B:ALA656 3.9 34.7 1.0 CB A:THR660 3.9 54.7 1.0 OG1 D:THR660 3.9 45.3 1.0 O C:ALA656 4.0 38.6 1.0 CG2 A:THR660 4.1 54.7 1.0 O D:ALA656 4.1 32.1 1.0 CB C:THR660 4.2 53.9 1.0 CG2 C:THR660 4.3 53.9 1.0 C A:ALA656 4.3 39.0 1.0 CB B:ALA656 4.5 34.7 1.0 CB A:ALA656 4.5 39.0 1.0 CB B:THR660 4.5 47.6 1.0 C B:ALA656 4.5 34.7 1.0 CG2 B:THR660 4.6 47.6 1.0 CB D:ALA656 4.7 32.1 1.0 CB C:ALA656 4.7 38.6 1.0 C C:ALA656 4.7 38.6 1.0 CB D:THR660 4.8 45.3 1.0 C D:ALA656 4.8 32.1 1.0 CG2 D:THR660 4.8 45.3 1.0 CA A:ALA656 5.0 39.0 1.0

Sodium binding site 4 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1013 b:26.3 occ:1.00 OD2 A:ASP528 3.0 73.8 1.0 OD2 D:ASP776 3.0 74.8 1.0 OD1 A:ASP528 3.2 73.8 1.0 CG D:ASP776 3.3 74.8 1.0 CE A:MET770 3.3 83.1 1.0 CG A:ASP528 3.4 73.8 1.0 NH1 A:ARG775 3.5 75.7 1.0 OD1 D:ASP776 3.8 74.8 1.0 CB D:ASP776 4.0 74.8 1.0 SD A:MET770 4.3 83.1 1.0 N A:GLY771 4.6 84.9 1.0 CZ A:ARG775 4.8 75.7 1.0 CB A:ASP528 4.9 73.8 1.0 CA A:GLY771 4.9 84.9 1.0

Sodium binding site 5 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:26.3 occ:1.00 OD1 B:ASP528 2.5 68.1 1.0 O B:GLU524 2.9 61.6 1.0 CD1 C:ILE780 3.7 58.8 1.0 O B:ILE527 3.8 66.7 1.0 CG B:ASP528 3.8 68.1 1.0 C B:GLU524 4.1 61.6 1.0 OD2 B:ASP528 4.4 68.1 1.0 CG B:GLU524 4.5 61.6 1.0 C B:ILE527 4.6 66.7 1.0 CA B:ASP528 4.8 68.1 1.0 CB B:ASP528 4.8 68.1 1.0 CG1 C:ILE780 4.8 58.8 1.0 CA B:LYS525 4.9 66.5 1.0 N B:LYS525 5.0 66.5 1.0

Sodium binding site 6 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1007 b:26.3 occ:1.00 OD2 B:ASP776 3.1 74.7 1.0 OD2 C:ASP528 3.1 72.9 1.0 OD1 C:ASP528 3.2 72.9 1.0 CE C:MET770 3.4 82.6 1.0 CG B:ASP776 3.4 74.7 1.0 NH1 C:ARG775 3.4 75.8 1.0 CG C:ASP528 3.5 72.9 1.0 OD1 B:ASP776 3.9 74.7 1.0 CB B:ASP776 3.9 74.7 1.0 SD C:MET770 4.4 82.6 1.0 CZ C:ARG775 4.7 75.8 1.0 N C:GLY771 4.8 83.5 1.0 CB C:ASP528 4.9 72.9 1.0

Sodium binding site 7 out of 7 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Noncompetitive Inhibitor Perampanel within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1005 b:26.3 occ:1.00 OD1 D:ASP528 2.5 67.6 1.0 O D:GLU524 2.7 61.6 1.0 O D:ILE527 3.6 65.8 1.0 CD1 A:ILE780 3.7 58.6 1.0 CG D:ASP528 3.8 67.6 1.0 C D:GLU524 3.9 61.6 1.0 CG D:GLU524 4.2 61.6 1.0 C D:ILE527 4.5 65.8 1.0 OD2 D:ASP528 4.5 67.6 1.0 CA D:ASP528 4.7 67.6 1.0 CA D:LYS525 4.8 64.9 1.0 CA D:GLU524 4.8 61.6 1.0 CB D:ASP528 4.8 67.6 1.0 N D:LYS525 4.8 64.9 1.0 CG1 A:ILE780 4.9 58.6 1.0 C D:LYS525 4.9 64.9 1.0 N D:ASP528 5.0 67.6 1.0

S.P.Gangwar, L.Y.Yen, M.V.Yelshanskaya, A.I.Sobolevsky. Positive and Negative Allosteric Modulation of GLUK2 Kainate Receptors By BPAM344 and Antiepileptic Perampanel. Cell Rep V. 42 12124 2023.
ISSN: ESSN 2211-1247
PubMed: 36857176
DOI: 10.1016/J.CELREP.2023.112124