Sodium in PDB 8fwu: Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx

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

Fluorine	(F)	4 atoms
Chlorine	(Cl)	2 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 Competitive Antagonist Dnqx (pdb code 8fwu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 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 Competitive Antagonist Dnqx, PDB code: 8fwu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:35.5 occ:1.00 O C:HOH1101 2.5 30.9 1.0 CG2 C:THR652 3.2 5.8 1.0 CG2 B:THR652 3.3 13.7 1.0 CG2 A:THR652 3.4 10.4 1.0 CG2 D:THR652 3.5 23.2 1.0 CB C:THR652 4.3 5.8 1.0 CB B:THR652 4.3 13.7 1.0 O B:THR652 4.4 13.7 1.0 O C:THR652 4.4 5.8 1.0 CB A:THR652 4.4 10.4 1.0 O A:THR652 4.6 10.4 1.0 CB D:THR652 4.6 23.2 1.0 C B:THR652 4.6 13.7 1.0 O D:THR652 4.6 23.2 1.0 C C:THR652 4.6 5.8 1.0 C A:THR652 4.8 10.4 1.0 C D:THR652 4.9 23.2 1.0

Sodium binding site 2 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:36.0 occ:1.00 O B:HOH1103 2.6 37.4 1.0 O B:HOH1102 4.4 33.0 1.0 O D:HOH1102 4.4 33.3 1.0 OE1 B:GLN621 4.5 22.6 1.0 OE1 A:GLN621 4.6 20.0 1.0 OE1 C:GLN621 4.7 11.7 1.0 O D:HOH1101 4.8 31.9 1.0 O B:HOH1101 4.8 31.5 1.0 OE1 D:GLN621 4.8 33.0 1.0

Sodium binding site 3 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:30.7 occ:1.00 O B:ALA656 3.7 17.3 1.0 O D:ALA656 3.8 28.1 1.0 CG2 C:THR660 3.9 16.1 1.0 O C:ALA656 4.1 7.0 1.0 CG2 A:THR660 4.1 24.3 1.0 CB C:THR660 4.2 16.1 1.0 CG2 B:THR660 4.2 31.0 1.0 O A:ALA656 4.3 14.3 1.0 CG2 D:THR660 4.3 42.9 1.0 CB C:ALA656 4.4 7.0 1.0 CB A:THR660 4.5 24.3 1.0 OG1 C:THR660 4.5 16.1 1.0 C B:ALA656 4.5 17.3 1.0 CB A:ALA656 4.5 14.3 1.0 CB B:ALA656 4.5 17.3 1.0 C C:ALA656 4.6 7.0 1.0 CB D:ALA656 4.6 28.1 1.0 C D:ALA656 4.7 28.1 1.0 OG1 A:THR660 4.7 24.3 1.0 C A:ALA656 4.8 14.3 1.0

Sodium binding site 4 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1012 b:107.8 occ:1.00 OD1 A:ASP528 2.5 31.5 1.0 O A:GLU524 2.5 31.6 1.0 OE2 A:GLU524 2.6 31.6 1.0 CD A:GLU524 3.3 31.6 1.0 O A:ILE527 3.3 32.3 1.0 C A:GLU524 3.7 31.6 1.0 CG A:GLU524 3.7 31.6 1.0 CG A:ASP528 3.7 31.5 1.0 CA A:ASP528 4.0 31.5 1.0 NH1 A:ARG775 4.1 30.3 1.0 OE1 A:GLU524 4.1 31.6 1.0 C A:ILE527 4.1 32.3 1.0 CD1 D:ILE780 4.3 57.3 1.0 CA A:GLU524 4.3 31.6 1.0 CB A:ASP528 4.4 31.5 1.0 N A:ASP528 4.4 31.5 1.0 CB A:GLU524 4.5 31.6 1.0 NH2 A:ARG775 4.6 30.3 1.0 CZ A:ARG775 4.6 30.3 1.0 OD2 A:ASP528 4.7 31.5 1.0 N A:LYS525 4.8 32.2 1.0

Sodium binding site 5 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:138.5 occ:1.00 N B:GLY623 4.3 29.7 1.0 O C:GLN621 4.5 11.7 1.0 N C:GLY623 4.6 21.0 1.0 O B:GLN621 4.6 22.6 1.0 O A:GLN621 4.6 20.0 1.0 N D:GLY623 4.6 39.3 1.0 N A:GLY623 4.7 26.2 1.0 O D:GLN621 4.9 33.0 1.0 CA C:GLN622 4.9 14.6 1.0 CA B:GLN622 4.9 22.8 1.0

Sodium binding site 6 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1007 b:75.2 occ:1.00 OD1 B:ASP528 2.7 39.0 1.0 O B:GLU524 2.9 33.5 1.0 CD1 C:ILE780 3.2 14.5 1.0 CE B:MET770 3.6 53.0 1.0 OE2 B:GLU524 3.7 33.5 1.0 CG B:ASP528 3.9 39.0 1.0 C B:GLU524 4.1 33.5 1.0 CB C:ASP776 4.1 21.4 1.0 CG C:ASP776 4.2 21.4 1.0 SD B:MET770 4.2 53.0 1.0 O B:ILE527 4.3 36.3 1.0 OD1 C:ASP776 4.4 21.4 1.0 CD B:GLU524 4.4 33.5 1.0 OD2 B:ASP528 4.4 39.0 1.0 CG B:GLU524 4.5 33.5 1.0 OD2 C:ASP776 4.6 21.4 1.0 CG1 C:ILE780 4.6 14.5 1.0 CA B:LYS525 4.8 33.8 1.0 N B:LYS525 4.9 33.8 1.0 O C:ASP776 5.0 21.4 1.0 CA C:ASP776 5.0 21.4 1.0 NH1 B:ARG775 5.0 52.1 1.0

Sodium binding site 7 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


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 Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1010 b:101.4 occ:1.00 O C:GLU524 2.5 24.2 1.0 OD1 C:ASP528 2.5 25.2 1.0 OE2 C:GLU524 2.5 24.2 1.0 CD C:GLU524 3.2 24.2 1.0 O C:ILE527 3.2 24.6 1.0 C C:GLU524 3.6 24.2 1.0 CG C:GLU524 3.7 24.2 1.0 CG C:ASP528 3.7 25.2 1.0 CA C:ASP528 3.9 25.2 1.0 OE1 C:GLU524 4.1 24.2 1.0 CD1 B:ILE780 4.1 43.3 1.0 C C:ILE527 4.1 24.6 1.0 NH1 C:ARG775 4.1 23.2 1.0 CA C:GLU524 4.2 24.2 1.0 CB C:ASP528 4.3 25.2 1.0 N C:ASP528 4.4 25.2 1.0 CB C:GLU524 4.5 24.2 1.0 NH2 C:ARG775 4.6 23.2 1.0 CZ C:ARG775 4.6 23.2 1.0 OD2 C:ASP528 4.7 25.2 1.0 N C:LYS525 4.8 24.8 1.0 OD1 B:ASP776 4.8 51.7 1.0 CG B:ASP776 4.9 51.7 1.0 N C:PHE529 5.0 17.1 1.0

Sodium binding site 8 out of 8 in the Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Ligand-Binding and Transmembrane Domains of Kainate Receptor GLUK2 in Complex with the Positive Allosteric Modulator BPAM344 and Competitive Antagonist Dnqx within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1005 b:76.9 occ:1.00 OD1 D:ASP528 3.0 52.7 1.0 O D:GLU524 3.0 45.5 1.0 CD1 A:ILE780 3.2 21.8 1.0 OE2 D:GLU524 3.6 45.5 1.0 CE D:MET770 3.9 68.4 1.0 CG D:ASP528 4.1 52.7 1.0 C D:GLU524 4.1 45.5 1.0 CB A:ASP776 4.2 28.1 1.0 CD D:GLU524 4.3 45.5 1.0 CG A:ASP776 4.3 28.1 1.0 CG D:GLU524 4.3 45.5 1.0 CG1 A:ILE780 4.5 21.8 1.0 OD1 A:ASP776 4.5 28.1 1.0 O D:ILE527 4.5 48.7 1.0 SD D:MET770 4.6 68.4 1.0 OD2 D:ASP528 4.7 52.7 1.0 OD2 A:ASP776 4.7 28.1 1.0 CA D:LYS525 4.9 46.2 1.0 N D:LYS525 5.0 46.2 1.0 NH1 D:ARG775 5.0 67.1 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