Sodium in PDB 6e7v: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88, PDB code: 6e7v 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 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.131, 59.612, 145.526, 90.00, 116.86, 90.00
R / Rfree (%)	19.1 / 23.3

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 also contains other interesting chemical elements:

Chlorine

(Cl)

15 atoms

The binding sites of Sodium atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-88 (pdb code 6e7v). 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 93-88, PDB code: 6e7v:
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 93-88


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 93-88 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:30.4 occ:1.00 O A:PHE137 2.2 32.7 1.0 O A:HOH629 2.3 28.5 1.0 O A:ASP364 2.4 33.9 1.0 O A:HOH636 2.7 33.2 1.0 O A:HOH658 3.3 38.9 1.0 C A:PHE137 3.4 31.0 1.0 O A:HOH690 3.4 17.4 1.0 C A:ASP364 3.5 33.2 1.0 O A:TYR128 3.9 27.6 1.0 CA A:GLY365 4.1 31.4 1.0 CA A:PHE137 4.1 30.3 1.0 CB A:PHE137 4.2 29.1 1.0 N A:GLY365 4.2 33.1 1.0 N A:PHE137 4.3 32.7 1.0 O A:HIS134 4.4 29.3 1.0 N A:LEU138 4.4 29.2 1.0 CA A:ASP364 4.5 34.4 1.0 C A:GLY365 4.5 28.5 1.0 CD1 A:PHE137 4.6 28.6 1.0 CA A:SER129 4.6 29.6 1.0 CA A:LEU138 4.7 29.4 1.0 O A:GLY365 4.8 25.8 1.0 O A:SER129 4.8 34.9 1.0 CG A:PHE137 4.9 30.1 1.0 C A:SER129 4.9 30.1 1.0 C A:TYR128 4.9 26.9 1.0 CB A:ASP364 5.0 34.0 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 93-88


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 93-88 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:37.2 occ:1.00 O C:PHE137 2.2 37.0 1.0 O C:ASP364 2.2 40.1 1.0 O C:HOH651 2.3 49.3 1.0 O C:HOH634 2.4 30.3 1.0 O C:HOH622 2.6 31.2 1.0 C C:ASP364 3.4 42.2 1.0 C C:PHE137 3.4 36.9 1.0 O C:HOH646 3.8 28.0 1.0 O C:TYR128 3.9 31.4 1.0 CA C:GLY365 4.0 39.0 1.0 N C:GLY365 4.1 40.2 1.0 CA C:PHE137 4.2 36.2 1.0 CB C:PHE137 4.2 34.3 1.0 N C:PHE137 4.3 38.6 1.0 C C:GLY365 4.4 36.9 1.0 O C:HIS134 4.4 33.5 1.0 CA C:ASP364 4.4 44.0 1.0 N C:LEU138 4.4 37.7 1.0 CD1 C:PHE137 4.6 31.7 1.0 CA C:LEU138 4.7 38.2 1.0 O C:GLY365 4.7 34.6 1.0 CA C:SER129 4.7 32.0 1.0 O C:SER129 4.9 32.0 1.0 C C:SER129 4.9 33.0 1.0 CB C:ASP364 4.9 45.5 1.0 OD1 C:ASP366 4.9 38.6 1.0 CG C:PHE137 5.0 33.3 1.0 C C:TYR128 5.0 32.0 1.0

M.C.Regan, H.Furukawa. Structural Elements of A pH-Sensitive Inhibitor Binding Site in Nmda Receptors Nat Commun V. 10 321 2019.
ISSN: ESSN 2041-1723