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

Protein crystallography data

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

Sodium Binding Sites:

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 6r85

Go back to Sodium Binding Sites List in 6r85
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 6r85

Go back to Sodium Binding Sites List in 6r85
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

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 12:51:56 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy