Sodium in PDB 6e7w: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-115

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-115, PDB code: 6e7w 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 / 2.67
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.131, 59.590, 145.495, 90.00, 116.62, 90.00
R / Rfree (%)	19 / 23.2

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-115 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 93-115 (pdb code 6e7w). 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 93-115, PDB code: 6e7w:
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 93-115


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 93-115 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:24.4 occ:1.00 O A:PHE137 2.0 31.5 1.0 O A:HOH620 2.2 26.2 1.0 O A:ASP364 2.3 27.5 1.0 O A:HOH653 2.5 27.2 1.0 O A:HOH680 2.7 39.2 1.0 C A:PHE137 3.2 25.9 1.0 O A:HOH611 3.3 23.3 1.0 C A:ASP364 3.4 26.2 1.0 O A:TYR128 3.8 26.9 1.0 CA A:GLY365 4.0 27.2 1.0 O A:HOH603 4.0 31.0 1.0 CA A:PHE137 4.1 25.5 1.0 CB A:PHE137 4.1 25.6 1.0 N A:GLY365 4.2 26.5 1.0 N A:LEU138 4.2 25.6 1.0 N A:PHE137 4.4 25.4 1.0 C A:GLY365 4.4 24.0 1.0 CA A:LEU138 4.4 25.7 1.0 CD1 A:PHE137 4.4 28.2 1.0 CA A:ASP364 4.5 30.6 1.0 O A:HIS134 4.6 22.9 1.0 O A:GLY365 4.6 24.5 1.0 CA A:SER129 4.7 25.7 1.0 CE A:MET347 4.7 45.3 1.0 CG A:PHE137 4.8 27.0 1.0 O A:SER129 4.9 28.4 1.0 C A:TYR128 4.9 24.6 1.0 CB A:ASP364 4.9 31.8 1.0 N A:ASP366 4.9 24.6 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 93-115


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 93-115 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:42.5 occ:1.00 O C:HOH618 2.3 39.7 1.0 O C:HOH626 2.3 32.3 1.0 O C:PHE137 2.3 37.8 1.0 O C:ASP364 2.4 34.7 1.0 O C:HOH646 2.5 37.3 1.0 C C:PHE137 3.5 35.9 1.0 C C:ASP364 3.6 37.1 1.0 O C:TYR128 3.6 32.7 1.0 CB C:PHE137 4.0 37.0 1.0 O C:HOH647 4.1 34.1 1.0 CA C:PHE137 4.1 37.2 1.0 CA C:GLY365 4.3 36.9 1.0 O C:HIS134 4.3 34.0 1.0 N C:PHE137 4.4 40.2 1.0 N C:GLY365 4.4 37.2 1.0 CD1 C:PHE137 4.4 31.5 1.0 CA C:SER129 4.4 30.5 1.0 N C:LEU138 4.5 35.9 1.0 CA C:ASP364 4.6 39.3 1.0 O C:SER129 4.6 28.7 1.0 C C:SER129 4.7 30.4 1.0 C C:TYR128 4.7 32.7 1.0 C C:GLY365 4.7 35.8 1.0 CG C:PHE137 4.7 36.2 1.0 CA C:LEU138 4.8 38.0 1.0 CB C:ASP364 4.9 39.8 1.0 O C:GLY365 5.0 38.6 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