Sodium in PDB 6r88: Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine

The structure of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine, PDB code: 6r88 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)	49.27 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.972, 98.239, 114.256, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.1

The structure of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine (pdb code 6r88). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine, PDB code: 6r88:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Arabidopsis Thaliana GLR3.3 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 Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:23.9 occ:1.00 O A:HOH682 2.8 16.2 1.0 O A:THR95 2.8 13.1 1.0 O A:HOH690 2.8 34.6 1.0 O A:HOH652 3.3 37.4 1.0 C A:THR95 3.6 12.5 1.0 CA A:GLN96 3.6 13.4 1.0 N A:GLN96 3.8 13.2 1.0 CD1 A:ILE84 3.8 13.6 1.0 CG2 A:ILE84 3.8 13.2 1.0 O A:PHE94 4.1 13.8 1.0 CD A:PRO97 4.2 14.2 1.0 CB A:PHE94 4.2 13.2 1.0 CD A:GLN96 4.3 15.7 1.0 C A:GLN96 4.3 12.4 1.0 OE1 A:GLN96 4.4 15.8 1.0 O A:HOH483 4.4 16.1 1.0 NE2 A:GLN96 4.4 18.4 1.0 CG1 A:ILE84 4.5 13.3 1.0 C A:PHE94 4.5 13.3 1.0 N A:PRO97 4.5 13.8 1.0 O A:HOH681 4.6 46.8 1.0 CG A:GLN96 4.7 14.4 1.0 CB A:ILE84 4.7 13.2 1.0 CB A:GLN96 4.7 14.1 1.0 CA A:THR95 4.9 12.0 1.0 O A:HOH557 5.0 23.2 1.0 N A:THR95 5.0 13.2 1.0 CA A:PHE94 5.0 12.8 1.0

Sodium binding site 2 out of 3 in the Structure of Arabidopsis Thaliana GLR3.3 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 2 of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:47.8 occ:1.00 CZ3 B:TRP237 3.9 17.0 1.0 CH2 B:TRP237 3.9 16.2 1.0 O B:LYS236 4.1 20.7 1.0 CE B:LYS236 4.1 28.5 1.0 CE3 B:TRP237 4.1 16.7 1.0 CZ2 B:TRP237 4.2 17.2 1.0 CG B:LYS236 4.2 23.2 1.0 O B:HOH518 4.2 41.2 1.0 CD2 B:TRP237 4.4 15.7 1.0 CE2 B:TRP237 4.4 15.1 1.0 CD B:LYS236 4.8 25.7 1.0 O B:HOH536 4.9 39.1 1.0 C B:LYS236 5.0 20.9 1.0

Sodium binding site 3 out of 3 in the Structure of Arabidopsis Thaliana GLR3.3 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 3 of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with Glycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:55.9 occ:1.00 CE C:LYS236 4.0 29.7 1.0 CH2 C:TRP237 4.0 21.2 1.0 CZ3 C:TRP237 4.1 20.7 1.0 O C:LYS236 4.2 20.6 1.0 CZ2 C:TRP237 4.2 19.3 1.0 CE3 C:TRP237 4.3 19.9 1.0 CG C:LYS236 4.3 25.1 1.0 O C:HOH527 4.4 38.7 1.0 O A:HOH485 4.4 36.7 1.0 CE2 C:TRP237 4.4 18.0 1.0 CD2 C:TRP237 4.4 17.2 1.0 O A:HOH656 4.7 39.1 1.0 CD C:LYS236 4.8 27.6 1.0 O A:HOH438 4.8 29.7 1.0 O C:HOH461 4.9 35.2 1.0 O A:HOH541 4.9 31.3 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