Sodium in PDB 6e7t: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-6

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-6, PDB code: 6e7t 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 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.594, 59.835, 146.015, 90.00, 116.86, 90.00
R / Rfree (%)	19.4 / 22.5

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-6 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 93-6 (pdb code 6e7t). 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 93-6, PDB code: 6e7t:
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 93-6


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 93-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:27.5 occ:1.00 O A:PHE137 2.2 20.8 1.0 O A:HOH656 2.3 16.8 1.0 O A:ASP364 2.3 23.9 1.0 O A:HOH662 2.5 24.6 1.0 O A:HOH642 3.3 18.3 1.0 C A:PHE137 3.4 20.9 1.0 O A:HOH712 3.4 22.4 1.0 C A:ASP364 3.4 22.8 1.0 O A:HOH658 3.7 28.1 1.0 O A:TYR128 3.8 19.1 1.0 CA A:GLY365 4.1 21.3 1.0 CB A:PHE137 4.1 21.3 1.0 CA A:PHE137 4.1 21.0 1.0 N A:GLY365 4.1 21.5 1.0 N A:PHE137 4.3 24.0 1.0 N A:LEU138 4.4 20.2 1.0 CA A:ASP364 4.4 25.3 1.0 O A:HIS134 4.4 19.3 1.0 C A:GLY365 4.5 20.4 1.0 CD1 A:PHE137 4.6 20.2 1.0 CA A:SER129 4.6 24.0 1.0 CA A:LEU138 4.6 21.2 1.0 CB A:ASP364 4.8 27.2 1.0 O A:GLY365 4.8 20.2 1.0 CG A:PHE137 4.9 20.5 1.0 OD1 A:ASP366 4.9 16.7 1.0 C A:SER129 4.9 22.7 1.0 C A:TYR128 4.9 21.3 1.0 O A:SER129 4.9 23.4 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 93-6


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 93-6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:31.1 occ:1.00 O C:PHE137 2.2 29.6 1.0 O C:HOH630 2.3 25.6 1.0 O C:ASP364 2.3 29.7 1.0 O C:HOH657 2.5 29.3 1.0 O C:HOH633 2.5 21.1 1.0 O C:HOH659 3.2 28.5 1.0 C C:PHE137 3.3 31.3 1.0 C C:ASP364 3.4 32.9 1.0 O C:HOH651 3.8 37.0 1.0 O C:TYR128 3.9 28.2 1.0 CA C:GLY365 3.9 34.9 1.0 N C:GLY365 4.1 34.0 1.0 CA C:PHE137 4.1 31.2 1.0 CB C:PHE137 4.2 29.9 1.0 O C:HOH634 4.2 36.0 1.0 N C:PHE137 4.3 32.3 1.0 C C:GLY365 4.4 33.6 1.0 N C:LEU138 4.4 30.7 1.0 CA C:ASP364 4.5 35.9 1.0 CD1 C:PHE137 4.5 33.1 1.0 CA C:LEU138 4.6 32.1 1.0 O C:GLY365 4.6 34.9 1.0 O C:HIS134 4.6 33.0 1.0 CA C:SER129 4.7 28.8 1.0 OD1 C:ASP366 4.9 31.1 1.0 CG C:PHE137 4.9 30.8 1.0 CB C:ASP364 5.0 38.8 1.0 O C:SER129 5.0 30.3 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