Sodium in PDB 4x89: Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate

The structure of Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate, PDB code: 4x89 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)	45.25 / 2.62
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.000, 329.240, 80.020, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 24.5

The structure of Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate also contains other interesting chemical elements:

Silver

(Ag)

1 atom

The binding sites of Sodium atom in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate (pdb code 4x89). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate, PDB code: 4x89:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:37.8 occ:0.50 NA A:NA304 2.6 82.0 0.5 OG A:SER179 3.8 28.6 1.0 OG B:SER179 3.8 32.5 1.0 O A:HOH424 4.3 47.7 1.0 OE2 B:GLU178 4.3 49.1 1.0 OE2 A:GLU178 4.3 50.2 1.0

Sodium binding site 2 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:82.0 occ:0.50 NA A:NA303 2.6 37.8 0.5 NA A:NA305 3.0 51.4 0.5 OE2 B:GLU178 4.6 49.1 1.0 N A:SER179 4.6 21.3 1.0 OE2 A:GLU178 4.6 50.2 1.0 N B:SER179 4.6 21.1 1.0

Sodium binding site 3 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:51.4 occ:0.50 NA A:NA304 3.0 82.0 0.5 NA A:NA306 4.5 90.2 0.5 O B:LEU177 4.6 28.1 1.0 O A:LEU177 4.6 27.0 1.0

Sodium binding site 4 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:90.2 occ:0.50 NA A:NA305 4.5 51.4 0.5 O A:THR176 4.9 31.0 1.0 O B:THR176 5.0 34.5 1.0

Sodium binding site 5 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:81.2 occ:0.50 NA C:NA304 2.4 43.0 0.5 OG D:SER179 4.1 41.9 1.0 OG C:SER179 4.1 42.8 1.0 OE2 D:GLU178 4.2 44.0 1.0 OE2 C:GLU178 4.2 50.3 1.0 N C:SER179 4.5 25.9 1.0 N D:SER179 4.5 23.8 1.0 CA C:SER179 4.9 25.9 1.0 CA D:SER179 5.0 24.0 1.0

Sodium binding site 6 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


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 Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:43.0 occ:0.50 NA C:NA303 2.4 81.2 0.5 O C:HOH428 3.4 48.6 1.0 O D:HOH438 3.4 38.5 1.0 O C:LEU177 4.5 30.1 1.0 O D:LEU177 4.5 28.2 1.0 N C:SER179 4.7 25.9 1.0 N D:SER179 4.8 23.8 1.0 CA D:GLU178 4.8 23.4 1.0 CA C:GLU178 4.8 24.9 1.0

Sodium binding site 7 out of 7 in the Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Navms Voltage-Gated Sodium Channal Pore and C-Terminal Domain Soaked with Silver Nitrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:53.1 occ:0.50 O C:HOH428 3.0 48.6 1.0 O D:HOH438 3.0 38.5 1.0 O D:HOH462 3.8 65.2 1.0 O C:HOH461 4.3 70.1 1.0 O D:THR176 4.7 32.0 1.0 O C:THR176 4.7 31.9 1.0 CB D:LEU177 5.0 22.6 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