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

The structure of Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin, PDB code: 4ntw 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)	28.00 / 2.07
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	151.930, 151.930, 123.790, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.6

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of Acid-Sensing Ion Channel in Complex with Snake Toxin (pdb code 4ntw). 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, PDB code: 4ntw:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:86.8 occ:1.00 CZ A:TYR68 4.1 69.1 1.0 OH A:TYR68 4.2 70.1 1.0 CE1 A:TYR68 4.3 67.5 1.0 CE2 A:TYR68 4.5 68.0 1.0 CD1 A:TYR68 4.8 67.2 1.0 CD2 A:TYR68 4.9 70.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:44.5 occ:1.00 O A:HOH737 2.4 49.9 1.0 O A:HOH694 2.5 48.7 1.0 O A:HOH665 2.5 45.2 1.0 O A:THR237 2.5 33.9 1.0 O A:HOH754 2.5 48.5 1.0 O A:THR240 2.6 33.5 1.0 C A:THR237 3.6 36.5 1.0 C A:THR240 3.8 35.4 1.0 CA A:ASP238 4.0 34.1 1.0 O A:HOH812 4.1 43.6 1.0 C A:ASP238 4.2 38.5 1.0 O A:HOH745 4.3 50.1 1.0 N A:ASP238 4.3 34.2 1.0 O A:ASP238 4.3 36.5 1.0 N A:THR240 4.4 36.8 1.0 O A:HOH659 4.5 43.7 1.0 N A:THR237 4.5 37.3 1.0 CA A:SER241 4.5 37.5 1.0 N A:SER241 4.6 33.5 1.0 CA A:THR240 4.7 40.1 1.0 CA A:THR237 4.8 36.1 1.0 N A:GLU239 4.8 34.3 1.0 CB A:SER241 4.8 41.7 1.0 OG1 A:THR240 4.9 38.7 1.0 OD1 A:ASP238 4.9 38.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:54.6 occ:1.00 O C:PHE68 2.7 39.8 1.0 O C:HOH309 2.8 47.2 1.0 O B:HOH117 3.1 51.0 1.0 CE1 C:PHE68 3.3 43.2 1.0 CZ C:PHE68 3.3 43.7 1.0 O B:HOH107 3.4 45.1 1.0 CD1 C:PHE68 3.6 43.2 1.0 CE2 C:PHE68 3.6 41.7 1.0 C C:PHE68 3.7 47.8 1.0 CD2 C:PHE68 3.8 42.9 1.0 CG C:PHE68 3.8 44.0 1.0 O A:HOH629 4.2 42.9 1.0 O A:HOH833 4.2 49.3 1.0 O B:SER29 4.2 44.1 1.0 N C:PHE68 4.4 47.2 1.0 O C:HOH306 4.5 45.5 1.0 CA C:PHE68 4.5 46.2 1.0 N C:GLU69 4.6 45.5 1.0 CA C:GLU69 4.7 44.5 1.0 N C:CYS70 4.7 42.9 1.0 CB C:PHE68 4.8 41.9 1.0 CA B:SER29 4.9 40.1 1.0 O B:ARG28 4.9 36.0 1.0 CD1 B:ILE31 4.9 49.8 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