Sodium in PDB 6gl4: Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution

The structure of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution, PDB code: 6gl4 was solved by R.Venskutonyte, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.62 / 1.95
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.717, 47.715, 116.713, 90.00, 93.79, 90.00
R / Rfree (%)	16.3 / 19.9

The structure of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution also contains other interesting chemical elements:

Bromine

(Br)

6 atoms

The binding sites of Sodium atom in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution (pdb code 6gl4). 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 GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution, PDB code: 6gl4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:28.5 occ:1.00 O B:HOH484 2.1 25.2 1.0 O B:ARG203 2.3 19.0 1.0 O B:ILE200 2.3 16.1 1.0 O B:PRO205 2.5 30.3 1.0 O B:HOH434 3.4 26.5 1.0 C B:ARG203 3.5 19.0 1.0 C B:ILE200 3.5 17.7 1.0 C B:PRO205 3.5 29.4 1.0 NH2 B:ARG182 3.6 30.1 1.0 CA B:CYS206 3.8 25.6 1.0 N B:ARG203 4.0 18.0 1.0 CG2 B:ILE200 4.0 21.8 1.0 N B:CYS206 4.0 31.6 1.0 OG1 B:THR208 4.1 21.8 1.0 N B:ASP207 4.1 18.3 1.0 CA B:GLU201 4.1 22.4 1.0 C B:GLU201 4.2 20.8 1.0 O B:GLU201 4.2 24.0 1.0 CA B:ARG203 4.2 19.7 1.0 N B:GLU201 4.2 21.2 1.0 C B:CYS206 4.4 22.8 1.0 OD1 B:ASP207 4.4 22.4 1.0 C B:LYS204 4.4 24.3 1.0 N B:PRO205 4.5 23.2 1.0 N B:LYS204 4.5 20.7 1.0 CA B:ILE200 4.5 14.1 1.0 SG B:CYS261 4.6 23.4 1.0 N B:THR208 4.6 16.9 1.0 CA B:PRO205 4.6 24.2 1.0 CB B:ARG203 4.7 25.7 1.0 CA B:LYS204 4.7 22.9 1.0 N B:GLN202 4.7 24.1 1.0 O B:LYS204 4.7 28.3 1.0 CZ B:ARG182 4.8 28.0 1.0 CB B:CYS206 4.9 27.3 1.0 CB B:ILE200 4.9 15.4 1.0

Sodium binding site 2 out of 2 in the Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of GLUA2O Ligand-Binding Domain (S1S2J) in Complex with Glutamate and Sodium Bromide at 1.95 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:28.1 occ:1.00 OD1 B:ASN242 2.1 27.4 1.0 O B:HOH499 2.3 19.2 1.0 O B:HOH424 2.3 31.4 1.0 O B:HOH573 2.6 15.6 0.3 CG B:ASN242 3.0 22.9 1.0 ND2 B:ASN242 3.3 30.2 1.0 O B:HOH529 4.0 20.2 1.0 OD1 B:ASP248 4.1 29.7 1.0 OD2 B:ASP248 4.3 30.1 1.0 O B:HOH489 4.4 22.1 1.0 CB B:ASN242 4.4 17.2 1.0 CG B:ASP248 4.5 28.8 1.0 O B:HOH573 4.7 30.8 0.7 O B:HOH443 4.7 20.0 1.0 O B:ASN242 4.8 15.8 1.0 CA B:ASN242 4.9 16.0 1.0

G.B.Dawe, M.F.Kadir, R.Venskutonyte, A.M.Perozzo, Y.Yan, R.P.D.Alexander, C.Navarrete, E.A.Santander, M.Arsenault, C.Fuentes, M.R.P.Aurousseau, K.Frydenvang, N.P.Barrera, J.S.Kastrup, J.M.Edwardson, D.Bowie. Nanoscale Mobility of the Apo State and Tarp Stoichiometry Dictate the Gating Behavior of Alternatively Spliced Ampa Receptors. Neuron V. 102 976 2019.
ISSN: ISSN 0896-6273
PubMed: 31053408
DOI: 10.1016/J.NEURON.2019.03.046