Sodium in PDB 2xxu: Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate

The structure of Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate, PDB code: 2xxu was solved by N.Nayeem, O.Mayans, T.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.266, 104.781, 114.204, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 18.9

The structure of Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate (pdb code 2xxu). 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 the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate, PDB code: 2xxu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate


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 the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:17.1 occ:0.39 NZ A:LYS770 1.4 25.1 0.6 O A:GLU524 2.4 19.2 1.0 OD1 A:ASP528 2.4 22.9 1.0 O A:ILE527 2.4 15.2 1.0 OE2 A:GLU524 2.7 33.3 1.0 CE A:LYS770 2.8 32.7 0.6 C A:ILE527 3.4 14.6 1.0 C A:GLU524 3.4 16.2 1.0 O A:HOH2100 3.5 22.8 1.0 CD A:LYS770 3.5 30.7 0.6 CG A:ASP528 3.5 21.2 1.0 CD A:GLU524 3.6 27.8 1.0 CA A:ASP528 3.6 13.9 1.0 CD A:LYS770 3.6 30.4 0.4 CG A:GLU524 3.7 29.9 1.0 N A:ASP528 3.8 14.7 1.0 CA A:GLU524 3.9 17.0 1.0 O B:HOH2205 4.0 26.8 1.0 CB A:ASP528 4.1 16.5 1.0 CE A:LYS770 4.2 36.0 0.4 CB A:GLU524 4.3 21.0 1.0 NZ A:LYS770 4.4 41.2 0.4 OD2 A:ASP528 4.5 22.9 1.0 N A:ILE527 4.6 13.8 1.0 CA A:ILE527 4.6 13.6 1.0 N A:LYS525 4.6 16.3 1.0 O B:HOH2206 4.7 49.2 1.0 C A:ASP528 4.7 15.1 1.0 OE1 A:GLU524 4.7 22.7 1.0 CG A:LYS770 4.8 28.9 0.6 N A:PHE529 4.9 12.5 1.0 CA A:LYS525 4.9 20.6 1.0 C A:LYS525 5.0 19.3 1.0 CG A:LYS770 5.0 26.8 0.4

Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate


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 the GLUK2 (GLUR6) M770K Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:15.8 occ:0.24 NZ B:LYS770 1.3 25.3 0.8 O B:GLU524 2.4 22.2 1.0 OD1 B:ASP528 2.4 24.6 1.0 O B:ILE527 2.4 16.4 1.0 CE B:LYS770 2.7 36.1 0.8 OE1 B:GLU524 2.8 39.8 1.0 CD B:LYS770 3.3 34.0 0.8 O B:HOH2199 3.4 48.7 1.0 C B:ILE527 3.4 15.5 1.0 C B:GLU524 3.4 19.1 1.0 CG B:ASP528 3.5 21.5 1.0 O B:HOH2100 3.5 21.4 1.0 CA B:ASP528 3.6 15.8 1.0 CD B:GLU524 3.7 31.8 1.0 CD B:LYS770 3.7 34.4 0.2 CG B:GLU524 3.8 33.0 1.0 CA B:GLU524 3.9 19.2 1.0 N B:ASP528 3.9 15.3 1.0 NZ B:LYS770 3.9 37.7 0.2 CE B:LYS770 4.1 37.0 0.2 O A:HOH2231 4.2 51.8 1.0 CB B:ASP528 4.2 18.9 1.0 O A:HOH2230 4.2 32.0 1.0 CB B:GLU524 4.4 22.7 1.0 OD2 B:ASP528 4.5 21.1 1.0 N B:ILE527 4.6 17.1 1.0 N B:LYS525 4.6 19.4 1.0 CA B:ILE527 4.6 16.6 1.0 CG B:LYS770 4.7 32.9 0.8 C B:ASP528 4.8 16.9 1.0 OE2 B:GLU524 4.8 24.8 1.0 C B:LYS525 4.9 24.1 1.0 CG B:LYS770 5.0 31.2 0.2 CA B:LYS525 5.0 22.8 1.0

N.Nayeem, O.Mayans, T.Green. Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization J.Neurosci. V. 31 2916 2011.
ISSN: ISSN 0270-6474
PubMed: 21414913
DOI: 10.1523/JNEUROSCI.4771-10.2011