Sodium in PDB 3c32: Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution

The structure of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution, PDB code: 3c32 was solved by M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.99 / 1.72
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.546, 70.546, 234.456, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.8

The structure of Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution (pdb code 3c32). 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 GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution, PDB code: 3c32:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution


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 GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:22.1 occ:1.00 O A:GLU96 2.3 14.4 1.0 O A:ILE99 2.3 13.0 1.0 O A:HOH403 2.3 28.1 1.0 OD1 A:ASP100 2.3 16.1 1.0 OE1 A:GLU96 2.4 22.9 1.0 C A:ILE99 3.3 13.1 1.0 C A:GLU96 3.3 12.8 1.0 CD A:GLU96 3.4 21.5 1.0 CA A:ASP100 3.5 14.5 1.0 CG A:ASP100 3.5 17.6 1.0 CG A:GLU96 3.6 16.3 1.0 O B:HOH459 3.6 37.7 1.0 CA A:GLU96 3.8 12.8 1.0 N A:ASP100 3.8 12.7 1.0 CB A:ASP100 4.1 15.8 1.0 O B:HOH552 4.2 46.2 1.0 CD1 A:ILE222 4.2 25.5 1.0 CG1 A:ILE222 4.2 20.6 1.0 CB A:GLU96 4.3 12.3 1.0 O A:HOH554 4.5 32.3 1.0 N A:ILE99 4.5 11.2 1.0 N A:LYS97 4.5 12.3 1.0 CA A:ILE99 4.5 11.9 1.0 OE2 A:GLU96 4.5 23.6 1.0 OD2 A:ASP100 4.5 18.4 1.0 C A:ASP100 4.6 16.8 1.0 N A:PHE101 4.7 14.2 1.0 C A:LYS97 4.8 13.3 1.0 CA A:LYS97 4.9 13.6 1.0 CD1 B:ILE232 5.0 13.4 1.0 N A:VAL98 5.0 11.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution


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 GLUR5 Ligand-Binding Core in Complex with Sodium at 1.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:22.6 occ:1.00 O B:GLU96 2.2 12.7 1.0 O B:HOH405 2.2 40.4 1.0 O B:ILE99 2.3 12.0 1.0 OE1 B:GLU96 2.4 27.9 1.0 OD1 B:ASP100 2.4 17.9 1.0 C B:ILE99 3.3 12.4 1.0 CD B:GLU96 3.3 22.4 1.0 C B:GLU96 3.4 12.1 1.0 CA B:ASP100 3.5 14.2 1.0 CG B:GLU96 3.6 16.4 1.0 CG B:ASP100 3.6 17.5 1.0 O A:HOH500 3.7 35.6 1.0 N B:ASP100 3.8 13.0 1.0 CA B:GLU96 3.9 12.2 1.0 O B:HOH532 3.9 37.6 1.0 CB B:ASP100 4.1 15.0 1.0 CB B:GLU96 4.3 14.1 1.0 CD1 B:ILE222 4.4 12.2 0.5 CG1 B:ILE222 4.5 12.0 0.5 CA B:ILE99 4.5 11.1 1.0 CG1 B:ILE222 4.5 11.6 0.5 N B:ILE99 4.5 11.2 1.0 OE2 B:GLU96 4.5 24.3 1.0 N B:LYS97 4.5 11.5 1.0 C B:ASP100 4.6 15.3 1.0 OD2 B:ASP100 4.6 18.3 1.0 NH1 B:ARG227 4.7 27.6 1.0 C B:LYS97 4.7 12.5 1.0 N B:PHE101 4.7 13.1 1.0 CA B:LYS97 4.8 11.9 1.0 O B:LYS97 4.9 14.3 1.0 N B:VAL98 4.9 12.2 1.0

A.J.Plested, R.Vijayan, P.C.Biggin, M.L.Mayer. Molecular Basis of Kainate Receptor Modulation By Sodium. Neuron V. 58 720 2008.
ISSN: ISSN 0896-6273
PubMed: 18549784
DOI: 10.1016/J.NEURON.2008.04.001