Sodium in PDB 6r85: Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate

The structure of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate, PDB code: 6r85 was solved by A.Alfieri, R.Pederzoli, A.Costa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.886, 61.280, 64.103, 75.19, 75.53, 90.02
R / Rfree (%)	20.7 / 26.2

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate (pdb code 6r85). 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 Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate, PDB code: 6r85:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:30.6 occ:1.00 OD1 A:ASP34 2.5 29.4 1.0 N A:GLY30 3.1 18.5 1.0 CA A:LYS29 3.5 19.6 1.0 CZ2 A:TRP237 3.5 22.3 1.0 O A:GLY30 3.6 17.1 1.0 CG A:ASP34 3.7 27.2 1.0 C A:LYS29 3.7 19.9 1.0 CB A:LYS29 3.7 20.6 1.0 CH2 A:TRP237 4.0 22.7 1.0 CG2 A:ILE33 4.1 17.5 1.0 CA A:GLY30 4.1 18.9 1.0 C A:GLY30 4.2 18.1 1.0 CB A:ILE33 4.2 18.4 1.0 N A:ASP34 4.3 18.8 1.0 CE2 A:TRP237 4.5 21.8 1.0 OD2 A:ASP34 4.5 30.4 1.0 CB A:ASP34 4.5 22.8 1.0 CA A:ASP34 4.7 19.2 1.0 O A:PHE28 4.7 18.9 1.0 C A:ILE33 4.7 17.6 1.0 N A:LYS29 4.8 19.2 1.0 O A:HOH440 4.8 34.6 1.0 NE1 A:TRP237 4.9 20.7 1.0 O A:LYS29 5.0 20.9 1.0

Sodium binding site 2 out of 2 in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:40.3 occ:1.00 O A:HOH539 3.8 39.1 1.0 CE1 A:TYR45 4.0 23.7 1.0 CZ A:TYR45 4.0 23.8 1.0 CD1 A:TYR45 4.0 23.6 1.0 CE2 A:TYR45 4.1 22.8 1.0 CG A:TYR45 4.1 23.4 1.0 CD2 A:TYR45 4.1 23.1 1.0 OH A:TYR45 4.6 23.3 1.0 CB A:TYR45 4.9 22.6 1.0

A.Alfieri, F.G.Doccula, R.Pederzoli, M.Grenzi, M.C.Bonza, L.Luoni, A.Candeo, N.Romano Armada, A.Barbiroli, G.Valentini, T.R.Schneider, A.Bassi, M.Bolognesi, M.Nardini, A.Costa. The Structural Bases For Agonist Diversity in An Arabidopsis Thaliana Glutamate Receptor-Like Channel Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1905142117