Sodium in PDB 3qem: Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ro 25-6981

The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Ro 25-6981, PDB code: 3qem was solved by E.Karakas, N.Simorowski, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.029, 61.255, 144.423, 90.00, 116.32, 90.00
R / Rfree (%)	19.2 / 25

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 Ro 25-6981 (pdb code 3qem). 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 Ro 25-6981, PDB code: 3qem:
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 Ro 25-6981


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 Ro 25-6981 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:67.8 occ:1.00 O A:ASP364 2.5 70.4 1.0 O A:PHE137 2.6 52.1 1.0 O A:HIS134 3.3 44.4 1.0 O A:TYR128 3.5 47.4 1.0 C A:ASP364 3.6 61.5 1.0 C A:PHE137 3.7 49.2 1.0 CB A:PHE137 4.2 40.0 1.0 O A:LEU135 4.2 50.9 1.0 N A:PHE137 4.3 49.5 1.0 CA A:PHE137 4.3 46.4 1.0 CA A:ASP364 4.4 60.3 1.0 CG A:LYS131 4.4 77.7 1.0 O A:SER129 4.5 57.6 1.0 C A:HIS134 4.5 37.6 1.0 C A:SER129 4.5 52.0 1.0 N A:GLY365 4.6 42.9 1.0 C A:TYR128 4.6 41.9 1.0 CA A:SER129 4.6 42.6 1.0 CA A:GLY365 4.7 41.1 1.0 N A:LEU138 4.8 47.0 1.0 CB A:ASP364 4.8 63.6 1.0 CA A:LYS131 4.8 61.5 1.0 C A:LEU135 4.8 45.7 1.0 N A:LYS131 4.9 62.7 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 Ro 25-6981


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 Ro 25-6981 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:97.7 occ:1.00 O C:PHE137 2.1 74.3 1.0 O C:ASP364 2.4 94.2 1.0 C C:PHE137 3.3 73.6 1.0 O C:TYR128 3.4 71.1 1.0 C C:ASP364 3.6 90.8 1.0 O C:HIS134 3.8 59.1 1.0 CA C:PHE137 4.1 70.2 1.0 O C:SER129 4.2 76.4 1.0 CA C:GLY365 4.2 81.0 1.0 N C:PHE137 4.2 69.2 1.0 CB C:PHE137 4.2 70.8 1.0 N C:LEU138 4.3 67.2 1.0 N C:GLY365 4.4 79.4 1.0 O C:LEU135 4.4 72.4 1.0 CA C:LEU138 4.5 70.1 1.0 C C:TYR128 4.6 70.3 1.0 C C:SER129 4.6 71.6 1.0 CA C:SER129 4.6 69.2 1.0 CD2 C:PHE137 4.7 62.2 1.0 CA C:ASP364 4.7 88.2 1.0 C C:GLY365 4.7 76.1 1.0 OD1 C:ASP366 4.9 61.5 1.0 C C:HIS134 5.0 56.2 1.0 CG C:PHE137 5.0 65.6 1.0

E.Karakas, N.Simorowski, H.Furukawa. Subunit Arrangement and Phenylethanolamine Binding in GLUN1/GLUN2B Nmda Receptors. Nature V. 475 249 2011.
ISSN: ISSN 0028-0836
PubMed: 21677647
DOI: 10.1038/NATURE10180