Sodium in PDB 7lz2: Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine

The structure of Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine, PDB code: 7lz2 was solved by S.P.Gangwar, M.N.Green, A.I.Sobolevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.96 / 1.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.581, 74.581, 508.887, 90, 90, 120
R / Rfree (%)	18.5 / 20.9

The structure of Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine (pdb code 7lz2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine, PDB code: 7lz2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:31.9 occ:1.00 O A:HOH406 2.8 29.4 1.0 O A:HOH522 2.9 40.4 1.0 CG2 A:ILE88 3.8 16.4 1.0 CD1 A:ILE88 3.9 17.4 1.0 CB A:ILE88 4.1 15.2 1.0 N A:GLY209 4.4 20.3 1.0 CG1 A:ILE88 4.6 16.2 1.0 C A:THR208 4.7 22.7 1.0 CG A:PRO101 4.7 19.2 1.0 CA A:THR208 4.7 21.9 1.0 OG1 A:THR208 4.8 27.9 1.0 O A:ILE88 4.8 20.7 1.0 O A:HOH421 4.9 28.2 1.0

Sodium binding site 2 out of 2 in the Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:31.0 occ:1.00 OD1 A:ASP38 2.7 24.4 1.0 O A:HOH447 2.8 26.2 1.0 O A:HOH534 2.8 38.4 1.0 N A:GLY34 3.1 18.9 1.0 CA A:ARG33 3.4 20.8 1.0 CZ2 A:TRP244 3.4 23.4 1.0 CG A:ASP38 3.6 23.3 1.0 CB A:ARG33 3.6 23.4 1.0 C A:ARG33 3.7 19.9 1.0 O A:HOH459 3.8 44.8 1.0 O A:GLY34 3.8 20.2 1.0 CH2 A:TRP244 4.0 24.6 1.0 O A:HOH460 4.0 34.2 1.0 OD2 A:ASP38 4.1 24.0 1.0 CG2 A:ILE37 4.2 19.5 1.0 CA A:GLY34 4.2 20.9 1.0 CB A:ILE37 4.2 17.7 1.0 C A:GLY34 4.4 19.8 1.0 CE2 A:TRP244 4.4 22.6 1.0 O A:HOH535 4.5 32.4 1.0 N A:ASP38 4.5 19.2 1.0 O A:VAL32 4.6 21.8 1.0 CB A:ASP38 4.7 22.2 1.0 N A:ARG33 4.7 19.7 1.0 NE1 A:TRP244 4.9 23.6 1.0 CA A:ASP38 4.9 20.3 1.0 O A:ARG33 4.9 20.2 1.0 CG A:ARG33 5.0 26.2 1.0

M.N.Green, S.P.Gangwar, E.Michard, A.A.Simon, M.T.Portes, J.Barbosa-Caro, M.M.Wudick, M.A.Lizzio, O.Klykov, M.V.Yelshanskaya, J.A.Feijo, A.I.Sobolevsky. Structure of the Arabidopsis Thaliana Glutamate Receptor-Like Channel GLR3.4. Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34161757
DOI: 10.1016/J.MOLCEL.2021.05.025