Sodium in PDB 8g18: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108, PDB code: 8g18 was solved by M.C.Regan, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.37 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	269.172, 60.076, 145.572, 90, 117.02, 90
R / Rfree (%)	17.4 / 24.6

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Sodium atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 (pdb code 8g18). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108, PDB code: 8g18:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:44.8 occ:0.00 O A:HOH630 1.3 15.3 1.0 O A:HOH617 2.1 20.6 1.0 O A:PHE137 2.1 27.5 1.0 O A:ASP364 2.1 32.7 1.0 C A:PHE137 3.3 23.9 1.0 C A:ASP364 3.4 33.5 1.0 O A:TYR128 3.8 26.9 1.0 CB A:PHE137 4.1 21.8 1.0 CA A:PHE137 4.1 22.8 1.0 N A:GLY365 4.2 27.7 1.0 CA A:GLY365 4.2 25.9 1.0 O A:HIS134 4.3 31.1 1.0 N A:LEU138 4.3 23.6 1.0 N A:PHE137 4.3 22.8 1.0 CA A:ASP364 4.4 37.0 1.0 CD1 A:PHE137 4.5 25.0 1.0 CA A:LEU138 4.5 25.9 1.0 C A:GLY365 4.6 25.0 1.0 CA A:SER129 4.7 28.5 1.0 OD1 A:ASP366 4.7 25.1 1.0 CB A:ASP364 4.8 38.0 1.0 CG A:PHE137 4.8 23.5 1.0 O A:GLY365 4.9 25.5 1.0 C A:TYR128 4.9 23.9 1.0

Sodium binding site 2 out of 2 in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-108 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:44.8 occ:0.00 O C:ASP364 1.9 51.2 1.0 O C:PHE137 2.6 44.6 1.0 C C:ASP364 3.2 56.9 1.0 O C:TYR128 3.6 34.5 1.0 C C:PHE137 3.8 38.4 1.0 CA C:ASP364 4.1 64.0 1.0 N C:GLY365 4.1 51.0 1.0 O C:HIS134 4.2 33.9 1.0 CA C:GLY365 4.3 50.4 1.0 CA C:SER129 4.4 36.3 1.0 CB C:ASP364 4.5 69.5 1.0 CB C:PHE137 4.5 32.5 1.0 CA C:PHE137 4.5 35.8 1.0 C C:SER129 4.6 38.8 1.0 C C:TYR128 4.6 36.2 1.0 CD1 C:PHE137 4.6 35.1 1.0 O C:SER129 4.7 43.0 1.0 N C:PHE137 4.7 37.5 1.0 C C:GLY365 4.7 49.3 1.0 N C:LEU138 4.8 39.6 1.0 OD1 C:ASP366 4.9 49.7 1.0 CA C:LEU138 5.0 41.3 1.0 O C:GLY365 5.0 52.4 1.0 N C:SER129 5.0 36.5 1.0

L.D.Harris, M.C.Regan, S.J.Myers, K.A.Nocilla, N.S.Akins, Y.A.Tahirovic, L.J.Wilson, R.Dingledine, H.Furukawa, S.F.Traynelis, D.C.Liotta. Novel GLUN2B-Selective Nmda Receptor Negative Allosteric Modulator Possesses Intrinsic Analgesic Properties and Enhances Analgesia of Morphine in A Rodent Tail Flick Pain Model. Acs Chem Neurosci 2023.
ISSN: ESSN 1948-7193
PubMed: 36779874
DOI: 10.1021/ACSCHEMNEURO.2C00779