Sodium in PDB 5b3j: Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil

The structure of Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil, PDB code: 5b3j was solved by N.Tajima, E.Karakas, T.Grant, N.Simorowski, R.Diaz-Avalos, N.Grigorieff, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.93 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.249, 79.903, 181.314, 90.00, 127.09, 90.00
R / Rfree (%)	27.3 / 30.2

The binding sites of Sodium atom in the Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil (pdb code 5b3j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil, PDB code: 5b3j:

Sodium binding site 1 out of 1 in the Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:52.1 occ:1.00 O B:ASP364 3.0 58.3 1.0 O B:PHE137 3.2 47.6 1.0 O B:HIS134 3.4 45.4 1.0 O B:TYR128 3.5 43.7 1.0 CB B:PHE137 4.0 44.1 1.0 CA B:LYS131 4.1 46.5 1.0 C B:PHE137 4.1 46.8 1.0 O B:SER129 4.2 51.6 1.0 C B:ASP364 4.2 57.5 1.0 N B:PHE137 4.2 43.3 1.0 CA B:PHE137 4.3 45.2 1.0 CB B:LYS131 4.4 49.0 1.0 C B:SER129 4.4 49.2 1.0 N B:LYS131 4.4 48.9 1.0 C B:HIS134 4.5 45.4 1.0 O B:ASP130 4.6 50.2 1.0 C B:ASP130 4.6 48.9 1.0 CA B:SER129 4.6 47.8 1.0 C B:TYR128 4.6 45.3 1.0 CB B:ASP364 4.7 56.8 1.0 CA B:ASP364 4.7 59.3 1.0 CB B:HIS134 4.8 43.0 1.0

N.Tajima, E.Karakas, T.Grant, N.Simorowski, R.Diaz-Avalos, N.Grigorieff, H.Furukawa. Activation of Nmda Receptors and the Mechanism of Inhibition By Ifenprodil Nature V. 534 63 2016.
ISSN: ESSN 1476-4687
PubMed: 27135925
DOI: 10.1038/NATURE17679