Sodium in PDB 4ntx: Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride

The structure of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride, PDB code: 4ntx was solved by I.Baconguis, C.J.Bohlen, A.Goehring, D.Julius, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.00 / 2.27
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	151.560, 151.560, 123.200, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.3

The structure of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride (pdb code 4ntx). 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 Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride, PDB code: 4ntx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:87.1 occ:1.00 CZ A:TYR68 4.1 69.3 1.0 OH A:TYR68 4.1 71.0 1.0 CE1 A:TYR68 4.2 63.5 1.0 CE2 A:TYR68 4.6 68.4 1.0 CD1 A:TYR68 4.7 67.2 1.0

Sodium binding site 2 out of 3 in the Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:57.6 occ:1.00 O A:THR240 2.8 44.5 1.0 O A:THR237 2.8 47.6 1.0 CA A:ASP238 3.7 43.5 1.0 O A:ASP238 3.8 47.6 1.0 C A:ASP238 3.8 48.5 1.0 C A:THR237 3.8 45.3 1.0 C A:THR240 4.0 43.4 1.0 N A:ASP238 4.3 42.0 1.0 N A:THR240 4.4 43.8 1.0 N A:GLU239 4.6 38.8 1.0 OG1 A:THR240 4.6 48.6 1.0 C18 A:P6G506 4.7 52.1 1.0 C17 A:P6G506 4.7 54.8 1.0 C11 A:P6G506 4.7 60.7 1.0 O16 A:P6G506 4.8 59.2 1.0 CA A:THR240 4.8 44.2 1.0 OD1 A:ASP238 4.8 50.1 1.0 CA A:SER241 5.0 47.1 1.0 N A:SER241 5.0 44.5 1.0 CB A:ASP238 5.0 44.2 1.0

Sodium binding site 3 out of 3 in the Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin and Amiloride within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:66.5 occ:1.00 O C:PHE68 2.8 47.7 1.0 CE1 C:PHE68 3.6 47.8 1.0 CZ C:PHE68 3.7 49.4 1.0 CD1 C:PHE68 3.8 48.1 1.0 O B:SER29 3.9 51.9 1.0 C C:PHE68 4.0 57.5 1.0 CE2 C:PHE68 4.0 51.7 1.0 CG C:PHE68 4.1 50.0 1.0 CD2 C:PHE68 4.2 46.6 1.0 N C:PHE68 4.4 53.7 1.0 CA C:PHE68 4.7 58.2 1.0 CA B:SER29 4.7 50.4 1.0 C B:SER29 4.7 47.0 1.0 OG B:SER29 4.8 51.9 1.0 N C:GLU69 5.0 57.8 1.0 O B:ARG28 5.0 43.2 1.0

I.Baconguis, C.J.Bohlen, A.Goehring, D.Julius, E.Gouaux. X-Ray Structure of Acid-Sensing Ion Channel 1-Snake Toxin Complex Reveals Open State of A Na(+)-Selective Channel. Cell(Cambridge,Mass.) V. 156 717 2014.
ISSN: ISSN 0092-8674
PubMed: 24507937
DOI: 10.1016/J.CELL.2014.01.011