Sodium in PDB 6v8y: Structure of A Sodium Potassium Ion Channel

The structure of Structure of A Sodium Potassium Ion Channel, PDB code: 6v8y was solved by R.Roy, K.L.Weiss, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.32 / 1.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.716, 88.137, 49.848, 90, 90, 90
R / Rfree (%)	15.7 / 17.8

The structure of Structure of A Sodium Potassium Ion Channel also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Sodium atom in the Structure of A Sodium Potassium Ion Channel (pdb code 6v8y). 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 A Sodium Potassium Ion Channel, PDB code: 6v8y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of A Sodium Potassium Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Sodium Potassium Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:47.9 occ:0.44 O B:HOH327 2.6 27.9 1.0 O A:HOH524 2.6 27.9 1.0 K A:K407 2.9 13.9 0.5 O A:VAL64 3.1 16.8 1.0 O B:VAL64 3.1 16.4 1.0 HA3 A:GLY65 3.3 17.4 1.0 HA3 B:GLY65 3.4 20.6 1.0 C A:VAL64 4.2 18.2 1.0 CA A:GLY65 4.2 14.5 1.0 C B:VAL64 4.2 15.5 1.0 CA B:GLY65 4.3 17.1 1.0 N A:GLY65 4.6 13.3 1.0 C A:GLY65 4.6 17.4 1.0 N B:GLY65 4.7 15.4 1.0 C B:GLY65 4.7 21.0 1.0 O B:HOH302 4.8 39.2 1.0 HA2 A:GLY65 4.9 17.4 1.0 HA2 B:GLY65 4.9 20.6 1.0

Sodium binding site 2 out of 2 in the Structure of A Sodium Potassium Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Sodium Potassium Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:36.4 occ:1.00 O A:PHE69 2.3 22.2 0.6 O A:PHE69 2.3 22.2 0.5 O A:ASP66 2.6 28.7 1.0 OG A:SER70 2.8 44.5 1.0 HG A:SER70 3.2 53.4 1.0 C A:PHE69 3.3 23.1 0.6 C A:PHE69 3.4 23.2 0.5 HA A:SER70 3.5 30.8 1.0 HE1 A:PHE56 3.6 19.9 1.0 H A:ASP66 3.6 28.0 1.0 H A:PHE69 3.6 30.8 0.6 C A:ASP66 3.8 26.9 1.0 HB3 A:ASP66 3.8 25.6 1.0 CB A:SER70 3.9 29.8 1.0 CA A:SER70 3.9 25.6 1.0 N A:SER70 4.0 25.7 1.0 N A:PHE69 4.3 25.6 0.6 N A:ASP66 4.3 23.3 1.0 HB3 A:SER70 4.3 35.8 1.0 CA A:ASP66 4.4 24.5 1.0 CA A:PHE69 4.4 24.7 0.6 H A:PHE69 4.5 29.0 0.5 CE1 A:PHE56 4.5 16.6 1.0 O A:HOH519 4.5 21.2 0.6 N A:PHE69 4.5 24.1 0.5 CB A:ASP66 4.5 21.3 1.0 CA A:PHE69 4.5 23.2 0.5 HA2 A:GLY67 4.6 41.9 1.0 HB2 A:SER70 4.6 35.8 1.0 HZ A:PHE56 4.7 20.6 1.0 H A:SER70 4.7 30.9 1.0 O A:HOH519 4.7 25.4 0.4 N A:GLY67 4.8 29.6 1.0 H A:ASN68 4.8 33.8 0.6 H A:ASN68 4.9 33.8 0.5 HB3 A:PHE69 5.0 29.6 0.6

R.Roy, K.Hendriks, W.Kopec, S.Abdolvand, K.L.Weiss, B.L.De Groot, A.Lange, H.Sun, L.Coates. Structural Plasticity of the Selectivity Filter in A Nonselective Ion Channel Iucrj 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S205225252100213X