Sodium in PDB 4pa3: Structure of Navms in Complex with Channel Blocking Compound

The structure of Structure of Navms in Complex with Channel Blocking Compound, PDB code: 4pa3 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)	45.54 / 3.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.030, 331.950, 80.200, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23

The structure of Structure of Navms in Complex with Channel Blocking Compound also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Sodium atom in the Structure of Navms in Complex with Channel Blocking Compound (pdb code 4pa3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Navms in Complex with Channel Blocking Compound, PDB code: 4pa3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:37.0 occ:0.50 OG A:SER179 3.9 53.8 1.0 OE1 A:GLU178 4.1 59.1 1.0 OE1 B:GLU178 4.3 56.9 1.0 OG B:SER179 4.4 58.7 1.0 N A:SER179 4.7 39.5 1.0

Sodium binding site 2 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:65.9 occ:0.50 NA B:NA303 2.8 30.9 0.5 O A:THR176 4.6 55.0 1.0 CB A:LEU177 4.7 45.7 1.0 C A:LEU177 4.8 47.1 1.0 O A:LEU177 4.8 47.2 1.0 N A:GLU178 4.9 42.3 1.0

Sodium binding site 3 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:30.9 occ:0.50 NA A:NA304 2.8 65.9 0.5 O B:THR176 4.5 53.6 1.0 CD1 B:LEU177 4.8 52.5 1.0

Sodium binding site 4 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:11.3 occ:0.50 NA C:NA304 3.6 32.8 0.5 N D:SER179 4.6 44.0 1.0 N C:SER179 4.6 44.8 1.0 CA D:GLU178 4.8 43.9 1.0 CA C:GLU178 4.8 42.9 1.0 OE1 C:GLU178 4.8 84.1 1.0

Sodium binding site 5 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:32.8 occ:0.50 NA C:NA303 3.6 11.3 0.5 NA C:NA305 4.9 0.6 0.5

Sodium binding site 6 out of 6 in the Structure of Navms in Complex with Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Navms in Complex with Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:0.6 occ:0.50 O D:HOH403 4.2 38.7 1.0 O C:HOH403 4.8 27.1 1.0 NA C:NA304 4.9 32.8 0.5

C.Bagneris, P.G.Decaen, C.E.Naylor, D.C.Pryde, I.Nobeli, D.E.Clapham, B.A.Wallace. Prokaryotic Navms Channel As A Structural and Functional Model For Eukaryotic Sodium Channel Antagonism. Proc.Natl.Acad.Sci.Usa V. 111 8428 2014.
ISSN: ESSN 1091-6490
PubMed: 24850863
DOI: 10.1073/PNAS.1406855111