Sodium in PDB 6e7s: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-5

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-5, PDB code: 6e7s 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 / 2.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.430, 60.633, 145.391, 90.00, 116.42, 90.00
R / Rfree (%)	18.9 / 23.4

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-5 also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-5 (pdb code 6e7s). 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 93-5, PDB code: 6e7s:
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 93-5


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 93-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:48.4 occ:1.00 O A:PHE137 2.2 47.2 1.0 O A:ASP364 2.3 48.0 1.0 O A:HOH656 2.5 53.4 1.0 O A:HOH648 2.7 43.5 1.0 O A:HOH654 2.9 59.6 1.0 C A:PHE137 3.4 49.0 1.0 C A:ASP364 3.4 43.6 1.0 O A:HOH676 3.4 29.2 1.0 O A:TYR128 3.9 45.9 1.0 CA A:GLY365 4.0 46.1 1.0 N A:GLY365 4.1 48.3 1.0 CB A:PHE137 4.1 45.1 1.0 CA A:PHE137 4.1 52.8 1.0 N A:PHE137 4.3 55.4 1.0 N A:LEU138 4.4 39.0 1.0 C A:GLY365 4.4 43.3 1.0 CA A:ASP364 4.5 44.9 1.0 O A:HIS134 4.6 39.8 1.0 CD1 A:PHE137 4.6 51.8 1.0 CA A:LEU138 4.7 41.8 1.0 O A:GLY365 4.7 36.0 1.0 CA A:SER129 4.8 41.8 1.0 CG A:PHE137 4.9 42.0 1.0 CB A:ASP364 5.0 50.0 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 93-5


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 93-5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:60.9 occ:1.00 O C:PHE137 1.9 70.6 1.0 O C:ASP364 2.4 61.2 1.0 O C:HOH623 2.4 61.9 1.0 O C:HOH628 2.5 65.6 1.0 O C:HOH619 2.8 56.0 1.0 C C:PHE137 3.1 75.7 1.0 C C:ASP364 3.5 63.2 1.0 CA C:GLY365 3.8 69.6 1.0 O C:HOH624 3.8 64.7 1.0 CA C:PHE137 4.0 77.1 1.0 N C:GLY365 4.0 64.9 1.0 CB C:PHE137 4.1 78.1 1.0 N C:LEU138 4.1 75.1 1.0 N C:PHE137 4.2 71.0 1.0 O C:TYR128 4.2 59.0 1.0 C C:GLY365 4.3 65.0 1.0 CA C:LEU138 4.4 77.7 1.0 O C:HIS134 4.6 59.4 1.0 O C:GLY365 4.6 59.0 1.0 CD1 C:PHE137 4.6 66.1 1.0 CA C:ASP364 4.6 67.6 1.0 CG C:PHE137 4.9 73.7 1.0 O C:LEU135 4.9 91.0 1.0 O C:SER129 5.0 57.2 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