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

Protein crystallography data

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

Other elements in 6gl4:

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

Sodium Binding Sites:

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 6gl4

Go back to Sodium Binding Sites List in 6gl4
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 6gl4

Go back to Sodium Binding Sites List in 6gl4
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

Reference:

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
Page generated: Tue Oct 8 09:01:52 2024

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