Sodium in PDB 6e7u: Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-31

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-31, PDB code: 6e7u 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 / 2.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.620, 59.595, 145.914, 90.00, 117.10, 90.00
R / Rfree (%)	20.2 / 23.7

The structure of Heterodimer of the GLUN1B-GLUN2B Nmda Receptor Amino-Terminal Domains Bound to Allosteric Inhibitor 93-31 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 93-31 (pdb code 6e7u). 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 93-31, PDB code: 6e7u:
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 93-31


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 93-31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:19.5 occ:1.00 O A:PHE137 2.1 19.4 1.0 O A:HOH677 2.2 10.2 1.0 O A:ASP364 2.3 22.4 1.0 O A:HOH654 2.4 17.7 1.0 O A:HOH697 2.6 22.0 1.0 C A:PHE137 3.3 19.1 1.0 O A:HOH678 3.4 26.1 1.0 C A:ASP364 3.4 23.4 1.0 O A:HOH680 3.8 29.6 1.0 O A:TYR128 3.8 20.1 1.0 CA A:GLY365 4.0 21.8 1.0 CA A:PHE137 4.1 19.3 1.0 CB A:PHE137 4.1 19.1 1.0 N A:GLY365 4.2 23.0 1.0 N A:LEU138 4.3 18.7 1.0 N A:PHE137 4.3 20.2 1.0 O A:HOH692 4.4 22.9 1.0 C A:GLY365 4.4 20.6 1.0 O A:HIS134 4.5 21.9 1.0 CA A:ASP364 4.5 25.1 1.0 CA A:LEU138 4.5 18.7 1.0 CD1 A:PHE137 4.5 18.6 1.0 O A:GLY365 4.6 19.7 1.0 CA A:SER129 4.6 21.6 1.0 OD1 A:ASP366 4.7 18.7 1.0 CB A:ASP364 4.8 25.1 1.0 CG A:PHE137 4.9 18.6 1.0 C A:SER129 4.9 22.5 1.0 C A:TYR128 4.9 20.3 1.0 O A:SER129 4.9 23.2 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 93-31


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 93-31 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:28.6 occ:1.00 O C:PHE137 2.2 26.8 1.0 O C:HOH613 2.3 23.3 1.0 O C:HOH649 2.4 25.8 1.0 O C:ASP364 2.4 28.3 1.0 O C:HOH640 2.4 21.8 1.0 C C:PHE137 3.3 26.4 1.0 O C:HOH624 3.4 22.5 1.0 C C:ASP364 3.5 29.5 1.0 O C:TYR128 3.7 22.4 1.0 CB C:PHE137 4.0 26.1 1.0 CA C:PHE137 4.1 26.5 1.0 CA C:GLY365 4.2 29.4 1.0 N C:PHE137 4.3 27.3 1.0 N C:GLY365 4.3 30.0 1.0 CD1 C:PHE137 4.3 25.6 1.0 O C:HIS134 4.3 26.8 1.0 O C:HOH667 4.4 26.5 1.0 N C:LEU138 4.4 26.0 1.0 CA C:SER129 4.5 23.3 1.0 C C:GLY365 4.5 28.6 1.0 CA C:ASP364 4.6 30.6 1.0 CA C:LEU138 4.6 25.9 1.0 CG C:PHE137 4.7 25.7 1.0 OD1 C:ASP366 4.7 26.3 1.0 C C:TYR128 4.8 22.4 1.0 C C:SER129 4.8 24.0 1.0 O C:GLY365 4.8 28.0 1.0 O C:SER129 4.8 24.8 1.0 CB C:ASP364 5.0 30.1 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