Sodium in PDB 5ewj: Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil

The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil, PDB code: 5ewj was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.92 / 2.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.460, 60.100, 145.000, 90.00, 116.22, 90.00
R / Rfree (%)	17.4 / 21.1

The binding sites of Sodium atom in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil (pdb code 5ewj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil, PDB code: 5ewj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:65.5 occ:1.00 O A:ASP364 2.2 47.8 1.0 O A:PHE137 2.2 46.9 1.0 O A:HOH604 2.2 49.6 1.0 O A:HOH628 2.5 31.6 1.0 O A:HOH691 3.3 49.7 1.0 C A:ASP364 3.3 48.6 1.0 C A:PHE137 3.4 45.0 1.0 O A:TYR128 4.0 40.7 1.0 N A:GLY365 4.1 43.1 1.0 CA A:ASP364 4.2 44.7 1.0 CA A:PHE137 4.2 38.0 1.0 CA A:GLY365 4.3 39.3 1.0 CB A:PHE137 4.3 37.6 1.0 O A:HIS134 4.3 49.5 1.0 N A:LEU138 4.4 42.6 1.0 N A:PHE137 4.4 41.1 1.0 C A:GLY365 4.6 38.7 1.0 CA A:LEU138 4.6 42.1 1.0 CD1 A:PHE137 4.6 38.8 1.0 CB A:ASP364 4.6 46.5 1.0 CA A:SER129 4.7 42.0 1.0 O A:GLY365 4.7 36.6 1.0 O A:SER129 4.7 51.9 1.0 C A:SER129 4.9 49.0 1.0 CG A:PHE137 5.0 37.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ifenprodil within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:1.0 occ:1.00 O C:PHE137 2.3 62.5 1.0 O C:ASP364 2.6 71.2 1.0 O C:HOH612 3.0 54.0 1.0 O C:HOH625 3.2 51.7 1.0 C C:PHE137 3.5 62.5 1.0 C C:ASP364 3.7 72.0 1.0 O C:HIS134 3.7 64.3 1.0 O C:LEU135 3.8 80.1 1.0 O C:TYR128 3.9 65.8 1.0 CA C:PHE137 4.1 58.5 1.0 CB C:PHE137 4.1 59.0 1.0 N C:PHE137 4.2 61.0 1.0 N C:GLY365 4.5 68.7 1.0 CA C:GLY365 4.5 68.2 1.0 N C:LEU138 4.6 58.9 1.0 O C:SER129 4.6 63.5 1.0 CA C:ASP364 4.6 67.9 1.0 CA C:SER129 4.7 58.3 1.0 C C:SER129 4.7 62.3 1.0 CD1 C:PHE137 4.8 61.6 1.0 C C:HIS134 4.9 65.3 1.0 C C:LEU135 4.9 78.8 1.0 C C:TYR128 4.9 64.6 1.0 CG C:PHE137 5.0 59.9 1.0

D.Stroebel, D.L.Buhl, J.D.Knafels, P.K.Chanda, M.Green, S.Sciabola, L.Mony, P.Paoletti, J.Pandit. A Novel Binding Mode Reveals Two Distinct Classes of Nmda Receptor GLUN2B-Selective Antagonists. Mol.Pharmacol. V. 89 541 2016.
ISSN: ESSN 1521-0111
PubMed: 26912815
DOI: 10.1124/MOL.115.103036