Sodium in PDB 2xxr: Crystal Structure of the GLUK2 (GLUR6) Wild-Type Lbd Dimer in Complex with Glutamate

The structure of Crystal Structure of the GLUK2 (GLUR6) Wild-Type Lbd Dimer in Complex with Glutamate, PDB code: 2xxr 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)	19.44 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.326, 105.464, 114.278, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.5

The structure of Crystal Structure of the GLUK2 (GLUR6) Wild-Type 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) Wild-Type Lbd Dimer in Complex with Glutamate (pdb code 2xxr). 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) Wild-Type Lbd Dimer in Complex with Glutamate, PDB code: 2xxr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the GLUK2 (GLUR6) Wild-Type 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) Wild-Type Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:27.0 occ:0.90 O A:GLU524 2.4 20.1 1.0 OD1 A:ASP528 2.4 23.7 1.0 O A:HOH2104 2.4 30.6 0.8 O A:ILE527 2.4 17.6 1.0 OE1 A:GLU524 2.6 24.6 1.0 C A:ILE527 3.4 14.6 1.0 C A:GLU524 3.4 18.8 1.0 O A:HOH2099 3.4 26.4 1.0 CD A:GLU524 3.5 27.4 1.0 CG A:ASP528 3.5 26.1 1.0 CA A:ASP528 3.6 14.9 1.0 CG A:GLU524 3.7 35.9 1.0 SD A:MET770 3.8 56.4 1.0 CA A:GLU524 3.8 20.4 1.0 N A:ASP528 3.9 16.0 1.0 O B:HOH2193 3.9 23.5 1.0 CE A:MET770 4.1 52.1 1.0 CB A:ASP528 4.1 17.3 1.0 CB A:GLU524 4.3 24.9 1.0 OD2 A:ASP528 4.5 24.2 1.0 N A:LYS525 4.6 19.9 1.0 CA A:ILE527 4.6 16.8 1.0 OE2 A:GLU524 4.6 20.6 1.0 N A:ILE527 4.7 16.6 1.0 C A:ASP528 4.7 17.9 1.0 N A:PHE529 4.9 14.6 1.0 CA A:LYS525 5.0 24.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK2 (GLUR6) Wild-Type 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) Wild-Type Lbd Dimer in Complex with Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:36.4 occ:0.83 O B:HOH2084 2.4 38.9 0.8 O B:GLU524 2.4 22.1 1.0 O B:ILE527 2.4 19.8 1.0 OD1 B:ASP528 2.4 26.8 1.0 OE1 B:GLU524 2.8 24.5 1.0 C B:ILE527 3.4 20.1 1.0 C B:GLU524 3.4 20.4 1.0 SD B:MET770 3.5 46.8 1.0 O B:HOH2085 3.5 20.3 1.0 CG B:ASP528 3.5 23.9 1.0 CA B:ASP528 3.6 18.6 1.0 CE B:MET770 3.6 38.4 1.0 CA B:GLU524 3.8 17.4 1.0 N B:ASP528 3.9 16.5 1.0 O A:HOH2226 3.9 48.5 1.0 CD B:GLU524 4.0 25.0 1.0 O A:HOH2225 4.0 26.8 1.0 CB B:ASP528 4.2 17.8 1.0 CB B:GLU524 4.2 20.1 1.0 O A:HOH2027 4.2 48.1 1.0 OD2 B:ASP528 4.5 23.5 1.0 N B:LYS525 4.6 21.0 1.0 N B:ILE527 4.6 21.3 1.0 CA B:ILE527 4.6 17.2 1.0 CG B:GLU524 4.7 24.3 1.0 C B:ASP528 4.7 17.4 1.0 OE2 B:GLU524 4.9 20.9 1.0 O A:HOH2105 4.9 33.7 1.0 N B:PHE529 5.0 16.0 1.0 CA B:LYS525 5.0 24.4 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