Sodium in PDB 5bzb: Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain

The structure of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain, PDB code: 5bzb was solved by C.E.Naylor, C.Bagneris, B.A.Wallace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.81 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.340, 332.763, 80.380, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.4

The binding sites of Sodium atom in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain (pdb code 5bzb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain, PDB code: 5bzb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:67.4 occ:0.50 NA A:NA303 2.8 59.0 0.5 OG A:SER179 3.8 40.3 1.0 OG B:SER179 4.0 35.2 1.0 OE1 B:GLU178 4.4 31.2 1.0 OE1 A:GLU178 4.4 41.0 1.0 O B:HOH426 4.7 52.9 1.0 N A:SER179 4.8 26.7 1.0 N B:SER179 4.8 24.4 1.0 O A:HOH411 4.9 42.7 1.0 CB A:SER179 5.0 30.8 1.0

Sodium binding site 2 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:59.0 occ:0.50 O A:HOH443 2.5 55.0 0.5 NA A:NA302 2.8 67.4 0.5 O A:HOH431 3.2 96.9 0.5 O A:HOH429 4.0 21.6 0.5 N A:SER179 4.7 26.7 1.0 N B:SER179 4.7 24.4 1.0 CA A:GLU178 4.9 23.1 1.0 CA B:GLU178 4.9 23.4 1.0 OE1 B:GLU178 4.9 31.2 1.0 CG A:GLU178 4.9 29.1 1.0 O A:LEU177 4.9 31.8 1.0 O B:LEU177 5.0 30.1 1.0

Sodium binding site 3 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:62.2 occ:0.50 O B:HOH452 2.1 86.6 0.5 O B:HOH417 2.2 37.5 0.5 O A:HOH440 2.4 44.3 0.5 O A:HOH443 3.1 55.0 0.5 O A:HOH431 3.1 96.9 0.5 O A:HOH429 3.6 21.6 0.5 O B:HOH453 3.6 40.1 0.5 O B:THR176 4.8 35.2 1.0 O A:THR176 4.8 34.6 1.0

Sodium binding site 4 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:23.5 occ:0.50 O C:HOH417 2.1 22.6 0.5 O D:HOH415 2.1 20.8 0.5 NA D:NA303 3.1 70.6 0.5 O C:HOH437 3.3 33.8 0.5 O C:HOH435 3.5 41.4 0.5 O D:LEU177 4.7 30.5 1.0 N D:SER179 4.7 24.1 1.0 O C:LEU177 4.7 27.9 1.0 N C:SER179 4.8 24.0 1.0 CA D:GLU178 4.8 23.9 1.0 CA C:GLU178 4.9 23.4 1.0 OE1 C:GLU178 5.0 41.9 1.0 OE1 D:GLU178 5.0 40.6 1.0 NA C:NA303 5.0 47.2 0.5

Sodium binding site 5 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:47.2 occ:0.50 O D:HOH435 2.1 26.6 0.5 O C:HOH423 2.1 30.0 0.5 O C:HOH435 2.7 41.4 0.5 O C:HOH437 3.0 33.8 0.5 O D:HOH463 4.2 67.8 0.5 O D:HOH461 4.3 44.7 0.5 O D:THR176 4.7 30.6 1.0 O C:THR176 4.7 31.8 1.0 NA C:NA302 5.0 23.5 0.5

Sodium binding site 6 out of 6 in the Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Navms Voltage-Gated Sodium Channel Pore and C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:70.6 occ:0.50 O D:HOH415 2.7 20.8 0.5 O C:HOH417 3.1 22.6 0.5 NA C:NA302 3.1 23.5 0.5 OG D:SER179 3.8 46.5 1.0 OG C:SER179 3.9 45.3 1.0 OE1 C:GLU178 4.3 41.9 1.0 OE1 D:GLU178 4.3 40.6 1.0 N D:SER179 4.7 24.1 1.0 N C:SER179 4.8 24.0 1.0 CA D:SER179 4.9 24.1 1.0 CB D:SER179 4.9 28.9 1.0 CA C:SER179 5.0 24.1 1.0

C.E.Naylor, C.Bagneris, P.G.Decaen, A.Sula, A.Scaglione, D.E.Clapham, B.A.Wallace. Molecular Basis of Ion Permeability in A Voltage-Gated Sodium Channel. Embo J. V. 35 820 2016.
ISSN: ESSN 1460-2075
PubMed: 26873592
DOI: 10.15252/EMBJ.201593285