Sodium in PDB 6e7r: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-4

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-4, PDB code: 6e7r 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)	25.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	267.953, 59.898, 145.286, 90.00, 116.69, 90.00
R / Rfree (%)	18.9 / 21.8

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-4 also contains other interesting chemical elements:

Chlorine

(Cl)

16 atoms

The binding sites of Sodium atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-4 (pdb code 6e7r). 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 93-4, PDB code: 6e7r:
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 93-4


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 93-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:18.1 occ:1.00 O A:ASP364 2.2 16.1 1.0 O A:PHE137 2.2 12.0 1.0 O A:HOH670 2.3 8.5 1.0 O A:HOH666 2.4 13.2 1.0 C A:ASP364 3.3 16.3 1.0 C A:PHE137 3.4 12.8 1.0 O A:HOH671 3.7 12.1 1.0 O A:TYR128 3.7 12.9 1.0 CA A:GLY365 3.9 14.4 1.0 O A:HOH627 3.9 24.9 1.0 O A:HOH704 4.0 23.1 1.0 N A:GLY365 4.0 15.1 1.0 CB A:PHE137 4.2 13.7 1.0 CA A:PHE137 4.2 13.3 1.0 C A:GLY365 4.3 13.4 1.0 N A:LEU138 4.4 12.2 1.0 CA A:ASP364 4.4 19.1 1.0 N A:PHE137 4.4 15.6 1.0 CD1 A:PHE137 4.4 15.1 1.0 CA A:SER129 4.5 14.5 1.0 CA A:LEU138 4.5 12.6 1.0 O A:HIS134 4.6 13.2 1.0 O A:GLY365 4.6 12.4 1.0 OD1 A:ASP366 4.7 15.9 1.0 O A:SER129 4.8 15.2 1.0 CB A:ASP364 4.8 20.9 1.0 C A:SER129 4.8 14.8 1.0 C A:TYR128 4.8 13.0 1.0 CG A:PHE137 4.8 13.8 1.0 N A:ASP366 4.9 14.1 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 93-4


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 93-4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:25.9 occ:1.00 O C:HOH642 2.2 16.4 1.0 O C:PHE137 2.3 21.6 1.0 O C:HOH637 2.3 19.5 1.0 O C:ASP364 2.3 23.7 1.0 C C:ASP364 3.4 24.7 1.0 C C:PHE137 3.4 23.4 1.0 O C:HOH644 3.6 19.5 1.0 O C:TYR128 3.7 19.7 1.0 O C:HOH664 4.0 32.4 1.0 CA C:GLY365 4.0 25.5 1.0 N C:GLY365 4.1 24.5 1.0 CB C:PHE137 4.2 22.6 1.0 CA C:PHE137 4.2 22.8 1.0 N C:PHE137 4.4 24.6 1.0 C C:GLY365 4.4 23.9 1.0 CD1 C:PHE137 4.4 21.6 1.0 N C:LEU138 4.4 20.8 1.0 CA C:ASP364 4.5 26.9 1.0 CA C:SER129 4.5 22.2 1.0 O C:HIS134 4.5 21.5 1.0 O C:GLY365 4.6 24.7 1.0 CA C:LEU138 4.6 22.2 1.0 OD1 C:ASP366 4.7 22.8 1.0 C C:TYR128 4.8 21.3 1.0 C C:SER129 4.8 22.6 1.0 CG C:PHE137 4.8 21.4 1.0 O C:SER129 4.9 22.4 1.0 CB C:ASP364 4.9 29.1 1.0

M.C.Regan, Z.Zhu, H.Yuan, S.J.Myers, D.S.Menaldino, Y.A.Tahirovic, D.C.Liotta, S.F.Traynelis, H.Furukawa. Structural Elements of A pH-Sensitive Inhibitor Binding Site in Nmda Receptors Nat Commun V. 10 321 2019.
ISSN: ESSN 2041-1723