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

Protein crystallography data

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

Other elements in 6r88:

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

Sodium Binding Sites:

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 6r88

Go back to Sodium Binding Sites List in 6r88
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 6r88

Go back to Sodium Binding Sites List in 6r88
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 6r88

Go back to Sodium Binding Sites List in 6r88
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

Reference:

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
Page generated: Tue Dec 15 12:52:00 2020

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