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Sodium in PDB 6r89: Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Cysteine

Protein crystallography data

The structure of Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Cysteine, PDB code: 6r89 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) 49.40 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.661, 98.544, 114.154, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.8

Other elements in 6r89:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Cysteine (pdb code 6r89). 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-Cysteine, PDB code: 6r89:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6r89

Go back to Sodium Binding Sites List in 6r89
Sodium binding site 1 out of 2 in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Cysteine


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-Cysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:41.3
occ:1.00
OE1 A:GLN231 3.2 58.0 1.0
CD2 A:HIS234 4.2 51.6 1.0
NE2 A:HIS234 4.2 56.2 1.0
CD A:GLN231 4.3 54.1 1.0
CG A:HIS234 4.3 51.1 1.0
CE1 A:HIS234 4.4 54.9 1.0
ND1 A:HIS234 4.5 51.6 1.0
NE2 A:GLN231 4.5 60.1 1.0

Sodium binding site 2 out of 2 in 6r89

Go back to Sodium Binding Sites List in 6r89
Sodium binding site 2 out of 2 in the Structure of Arabidopsis Thaliana GLR3.3 Ligand-Binding Domain in Complex with L-Cysteine


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-Cysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:36.7
occ:1.00
O A:LYS236 4.0 38.5 1.0
CZ3 A:TRP237 4.4 27.2 1.0
CE3 A:TRP237 4.5 26.9 1.0
CH2 A:TRP237 4.8 26.8 1.0
CD2 A:TRP237 5.0 27.3 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 Oct 8 13:05:59 2024

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