Sodium in PDB 8r32: Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution

The structure of Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution, PDB code: 8r32 was solved by Y.Bay, M.E.Jeppesen, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.197, 100.746, 48.16, 90, 90, 90
R / Rfree (%)	15.3 / 17.9

The structure of Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution (pdb code 8r32). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution, PDB code: 8r32:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:17.8 occ:1.00 O A:HOH1209 2.2 18.8 1.0 O A:GLU524 2.3 11.6 1.0 OD1 A:ASP528 2.3 15.2 1.0 O A:ILE527 2.3 10.7 1.0 OE1 A:GLU524 2.4 19.0 1.0 HA A:ASP528 2.9 10.8 1.0 HA A:GLU524 3.1 11.7 1.0 HE1 A:MET770 3.2 19.4 0.4 C A:GLU524 3.2 10.8 1.0 C A:ILE527 3.4 9.1 1.0 HG3 A:MET770 3.5 27.3 0.4 CG A:ASP528 3.5 16.6 1.0 HB3 A:GLU524 3.5 12.9 1.0 CA A:GLU524 3.6 9.7 1.0 CD A:GLU524 3.6 16.3 1.0 CA A:ASP528 3.7 9.0 1.0 HG3 A:MET770 3.8 25.7 0.6 N A:ASP528 3.9 9.7 1.0 CB A:GLU524 4.0 10.7 1.0 CE A:MET770 4.2 16.1 0.4 CB A:ASP528 4.2 12.2 1.0 H A:ILE527 4.2 13.4 1.0 CG A:GLU524 4.4 16.4 1.0 CG A:MET770 4.4 22.8 0.4 N A:LYS525 4.5 9.3 1.0 N A:ILE527 4.5 11.1 1.0 HE2 A:MET770 4.5 19.4 0.4 CA A:ILE527 4.5 9.7 1.0 OD2 A:ASP528 4.5 15.6 1.0 OE2 A:GLU524 4.6 22.1 1.0 CG A:MET770 4.6 21.4 0.6 HB3 A:ASP528 4.6 14.7 1.0 SD A:MET770 4.6 35.5 0.6 HA A:LYS525 4.6 14.5 1.0 H A:ASP528 4.7 11.6 1.0 H A:PHE529 4.7 13.0 1.0 O A:HOH1275 4.7 26.9 1.0 HE3 A:MET770 4.7 19.4 0.4 HH12 A:ARG775 4.7 24.2 1.0 HG2 A:GLU524 4.8 19.8 1.0 H A:VAL526 4.8 13.7 1.0 O A:ARG523 4.8 10.3 1.0 HB2 A:GLU524 4.9 12.9 1.0 CA A:LYS525 4.9 12.0 1.0 C A:LYS525 4.9 12.9 1.0 HA A:ILE527 4.9 11.7 1.0 HG2 A:MET770 4.9 27.3 0.4 HB2 A:MET770 4.9 21.7 0.6 C A:ASP528 4.9 10.3 1.0 HA A:MET770 4.9 21.3 0.6 N A:VAL526 4.9 11.4 1.0 HA A:MET770 4.9 21.3 0.4 SD A:MET770 4.9 20.6 0.4 HB2 A:ASP528 5.0 14.7 1.0 N A:GLU524 5.0 9.2 1.0 HB2 A:MET770 5.0 21.7 0.4

Sodium binding site 2 out of 3 in the Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na905 b:18.1 occ:1.00 HE1 B:MET770 2.0 18.7 0.7 O B:GLU524 2.2 12.0 1.0 HE2 B:MET770 2.3 18.7 0.7 O B:HOH1193 2.3 21.0 1.0 O B:ILE527 2.3 12.0 1.0 OD1 B:ASP528 2.3 15.5 1.0 CE B:MET770 2.5 15.7 0.7 HA B:ASP528 3.0 10.5 1.0 OE2 B:GLU524 3.1 24.9 0.7 HE3 B:MET770 3.1 18.7 0.7 C B:ILE527 3.2 13.1 1.0 C B:GLU524 3.3 11.6 1.0 HG3 B:GLU524 3.4 24.1 0.7 HA B:GLU524 3.5 12.0 1.0 HG3 B:GLU524 3.5 24.6 0.3 CG B:ASP528 3.5 15.4 1.0 SD B:MET770 3.6 18.6 0.3 CA B:ASP528 3.7 8.8 1.0 HG3 B:MET770 3.8 25.3 0.7 N B:ASP528 3.8 11.0 1.0 OE1 B:GLU524 3.8 29.0 0.3 CD B:GLU524 3.9 24.2 0.3 CA B:GLU524 3.9 9.9 0.3 CA B:GLU524 3.9 9.7 0.7 SD B:MET770 4.0 36.1 0.7 O B:HOH1147 4.0 27.1 1.0 HG3 B:MET770 4.0 25.0 0.3 CD B:GLU524 4.0 23.9 0.7 H B:ILE527 4.0 13.7 1.0 CG B:GLU524 4.1 20.1 0.7 CG B:GLU524 4.1 20.4 0.3 N B:ILE527 4.1 11.4 1.0 O B:HOH1191 4.2 20.8 1.0 HA B:LYS525 4.2 13.9 1.0 CB B:ASP528 4.2 13.7 1.0 CA B:ILE527 4.3 11.1 1.0 CG B:MET770 4.3 21.1 0.7 N B:LYS525 4.3 10.8 1.0 O B:HOH1242 4.4 27.4 1.0 CG B:MET770 4.4 20.8 0.3 HB2 B:MET770 4.4 19.2 0.3 HB2 B:MET770 4.4 19.4 0.7 C B:LYS525 4.4 13.0 1.0 OD2 B:ASP528 4.5 16.1 1.0 N B:VAL526 4.5 10.4 1.0 OE2 B:GLU524 4.5 10.9 0.3 H B:VAL526 4.5 12.5 1.0 HA B:MET770 4.5 16.1 1.0 CA B:LYS525 4.6 11.6 1.0 H B:ASP528 4.6 13.3 1.0 HA B:ILE527 4.6 13.3 1.0 CB B:GLU524 4.6 13.4 0.3 CB B:GLU524 4.6 13.3 0.7 HH12 B:ARG775 4.6 45.8 1.0 C B:VAL526 4.7 12.5 1.0 HB3 B:ASP528 4.8 16.4 1.0 H B:PHE529 4.8 13.4 1.0 CB B:MET770 4.8 16.1 0.7 O B:LYS525 4.8 17.5 1.0 O B:ARG523 4.8 10.7 1.0 CB B:MET770 4.9 16.0 0.3 HG2 B:GLU524 4.9 24.1 0.7 HB2 B:ASP528 5.0 16.4 1.0 HG2 B:GLU524 5.0 24.6 0.3 HH22 B:ARG775 5.0 41.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the GLUK2 Ligand-Binding Domain in Complex with L-Glutamate and BPAM344 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na906 b:27.3 occ:1.00 OE1 B:GLN784 2.2 15.4 0.6 OE1 B:GLN784 2.6 14.5 0.4 HA B:ALA781 2.7 10.1 1.0 O B:HOH1245 2.8 15.8 1.0 HB2 B:GLN784 3.0 17.5 0.4 HG22 B:ILE780 3.1 15.2 0.2 HB3 B:GLN784 3.1 17.5 0.6 HG21 B:ILE473 3.1 19.1 1.0 HB2 B:GLN784 3.1 17.5 0.6 HG22 B:ILE780 3.2 15.2 0.8 HB3 B:GLN784 3.2 17.5 0.4 CD B:GLN784 3.3 18.2 0.6 CD B:GLN784 3.5 11.9 0.4 CB B:GLN784 3.5 14.5 0.6 CB B:GLN784 3.5 14.6 0.4 CA B:ALA781 3.6 8.3 1.0 O B:ILE780 3.8 11.1 1.0 HG23 B:ILE473 3.8 19.1 1.0 CG2 B:ILE473 3.8 15.9 1.0 CG B:GLN784 3.9 22.3 0.4 HG2 B:GLN784 3.9 26.8 0.4 CG2 B:ILE780 3.9 12.6 0.2 CG B:GLN784 3.9 13.9 0.6 HG23 B:ILE780 4.0 15.2 0.2 N B:ALA781 4.0 8.2 1.0 HB2 B:ALA781 4.0 14.4 1.0 CG2 B:ILE780 4.0 12.6 0.8 HD13 B:ILE473 4.1 27.8 1.0 C B:ILE780 4.1 11.1 1.0 HG22 B:ILE473 4.1 19.1 1.0 HG23 B:ILE780 4.2 15.2 0.8 CB B:ALA781 4.3 11.9 1.0 HG3 B:GLN784 4.4 16.8 0.6 NE2 B:GLN784 4.4 22.9 0.6 HG21 B:ILE780 4.4 15.2 0.2 HB1 B:ALA781 4.4 14.4 1.0 HG21 B:ILE780 4.5 15.2 0.8 HE22 B:GLN784 4.5 27.5 0.6 H B:GLN784 4.5 10.7 1.0 H B:ALA781 4.5 9.9 1.0 C B:ALA781 4.6 8.7 1.0 NE2 B:GLN784 4.6 10.0 0.4 O B:ALA781 4.6 7.7 1.0 O B:HOH1157 4.7 15.6 1.0 HG2 B:GLN784 4.7 16.8 0.6 HE21 B:GLN784 4.8 11.9 0.4 HG3 B:GLN784 4.8 26.8 0.4 CA B:GLN784 4.9 9.5 0.6 CA B:GLN784 4.9 9.6 0.4 HG12 B:ILE473 5.0 26.4 1.0 CD1 B:ILE473 5.0 23.2 1.0

Y.Bay, M.Egeberg Jeppesen, K.Frydenvang, P.Francotte, B.Pirotte, D.S.Pickering, A.S.Kristensen, J.S.Kastrup. The Positive Allosteric Modulator BPAM344 and L-Glutamate Introduce An Active-Like Structure of the Ligand-Binding Domain of GLUK2. Febs Lett. V. 598 743 2024.
ISSN: ISSN 0014-5793
PubMed: 38369668
DOI: 10.1002/1873-3468.14824