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

The structure of Crystal Structure of the GLUK2 (GLUR6) Wild-Type Lbd Dimer in Complex with Kainate, PDB code: 2xxt 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)	19.72 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.285, 105.915, 113.478, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The structure of Crystal Structure of the GLUK2 (GLUR6) Wild-Type Lbd Dimer in Complex with Kainate 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 Kainate (pdb code 2xxt). 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 Kainate, PDB code: 2xxt:
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 Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:35.2 occ:0.72 OD1 A:ASP528 2.4 30.8 1.0 O A:GLU524 2.4 21.2 1.0 O A:HOH2093 2.4 46.4 0.9 O A:ILE527 2.4 25.7 1.0 OE2 A:GLU524 3.2 37.7 1.0 C A:ILE527 3.3 23.4 1.0 CG A:ASP528 3.6 30.4 1.0 C A:GLU524 3.6 22.1 1.0 SD A:MET770 3.7 63.2 1.0 CA A:ASP528 3.8 22.8 1.0 N A:ASP528 3.8 23.6 1.0 CD A:GLU524 4.1 27.6 1.0 CG A:MET770 4.2 44.2 1.0 CG A:GLU524 4.2 34.7 1.0 O B:HOH2176 4.2 27.7 1.0 CB A:ASP528 4.3 17.8 1.0 CA A:GLU524 4.3 18.1 1.0 N A:ILE527 4.3 18.8 1.0 O A:HOH2092 4.3 37.9 1.0 CA A:ILE527 4.3 18.0 1.0 OD2 A:ASP528 4.5 29.1 1.0 N A:LYS525 4.6 21.2 1.0 C A:LYS525 4.7 29.1 1.0 N A:VAL526 4.7 23.9 1.0 CA A:LYS525 4.8 25.0 1.0 CB A:GLU524 4.8 26.5 1.0 C A:VAL526 4.9 26.2 1.0 CB A:MET770 4.9 35.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the GLUK2 (GLUR6) Wild-Type Lbd Dimer in Complex with Kainate


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 Kainate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:37.0 occ:0.71 O B:GLU524 2.4 28.0 1.0 O B:HOH2076 2.4 57.7 1.0 OD1 B:ASP528 2.4 33.8 1.0 O B:ILE527 2.4 24.9 1.0 OE2 B:GLU524 3.1 48.5 1.0 C B:ILE527 3.3 26.6 1.0 C B:GLU524 3.5 29.2 1.0 CG B:ASP528 3.6 35.2 1.0 CA B:ASP528 3.8 23.9 1.0 SD B:MET770 3.8 64.9 1.0 N B:ASP528 3.8 26.5 1.0 CG B:MET770 4.0 42.7 1.0 CD B:GLU524 4.1 31.8 1.0 CG B:GLU524 4.2 39.1 1.0 O A:HOH2188 4.2 33.2 1.0 CA B:GLU524 4.2 25.2 1.0 O B:HOH2077 4.3 35.6 1.0 CB B:ASP528 4.3 26.6 1.0 N B:ILE527 4.3 22.7 1.0 CA B:ILE527 4.3 26.1 1.0 OD2 B:ASP528 4.6 35.8 1.0 N B:LYS525 4.6 27.9 1.0 C B:LYS525 4.7 31.9 1.0 CA B:LYS525 4.8 28.4 1.0 N B:VAL526 4.8 23.3 1.0 CB B:GLU524 4.8 31.4 1.0 CB B:MET770 4.9 35.8 1.0 C B:VAL526 5.0 27.9 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