Sodium in PDB 6vea: Structure of the Glutamate-Like Receptor GLR3.2 Ligand-Binding Domain in Complex with Glycine

The structure of Structure of the Glutamate-Like Receptor GLR3.2 Ligand-Binding Domain in Complex with Glycine, PDB code: 6vea was solved by S.P.Gangwar, M.N.Green, J.B.Yoder, A.I.Sobolevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.23 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.389, 64.370, 75.933, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.4

The binding sites of Sodium atom in the Structure of the Glutamate-Like Receptor GLR3.2 Ligand-Binding Domain in Complex with Glycine (pdb code 6vea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Glutamate-Like Receptor GLR3.2 Ligand-Binding Domain in Complex with Glycine, PDB code: 6vea:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Glutamate-Like Receptor GLR3.2 Ligand-Binding Domain in Complex with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:27.2 occ:1.00 O A:HOH595 2.7 35.3 1.0 N A:LYS201 3.0 13.9 1.0 CD A:PRO200 3.4 14.9 1.0 CB A:SER199 3.5 14.8 1.0 CG A:PRO200 3.5 16.4 1.0 CG A:LYS201 3.5 25.4 1.0 CB A:LYS201 3.5 18.7 1.0 OG A:SER199 3.6 18.0 1.0 N A:PRO200 3.6 14.7 1.0 CA A:LYS201 3.8 15.3 1.0 CD A:LYS201 3.9 30.7 1.0 C A:PRO200 4.0 13.7 1.0 O A:HOH617 4.0 23.1 1.0 C A:SER199 4.1 14.4 1.0 CA A:PRO200 4.1 14.2 1.0 CB A:PRO200 4.2 16.0 1.0 CA A:SER199 4.3 14.4 1.0 O A:HOH503 4.8 31.0 1.0 CE A:LYS201 4.9 40.4 1.0 O A:SER199 4.9 13.5 1.0 OE1 A:GLU228 5.0 36.0 1.0 C A:LYS201 5.0 13.9 1.0 N A:GLU202 5.0 13.3 1.0

S.P.Gangwar, M.N.Green, E.Michard, A.A.Simon, J.A.Feijo, A.I.Sobolevsky. Structure of the Arabidopsis Glutamate Receptor-Like Channel GLR3.2 Ligand-Binding Domain. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 33027636
DOI: 10.1016/J.STR.2020.09.006