Sodium in PDB 4pa7: Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound

The structure of Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound, PDB code: 4pa7 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)	45.20 / 3.02
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.810, 328.860, 79.920, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 26.5

The binding sites of Sodium atom in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound (pdb code 4pa7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound, PDB code: 4pa7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:27.6 occ:0.50 O A:HOH402 3.0 0.0 0.5 NA B:NA304 3.2 42.5 0.5 O A:THR176 4.1 66.0 1.0

Sodium binding site 2 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:12.4 occ:0.50 NA B:NA304 2.5 42.5 0.5 NA B:NA305 3.4 57.4 1.0 CA B:GLU178 3.9 54.2 1.0 CG B:GLU178 4.1 65.0 1.0 CA A:GLU178 4.4 49.5 1.0 O A:LEU177 4.4 57.7 1.0 CB B:GLU178 4.4 55.6 1.0 N B:GLU178 4.5 55.2 1.0 N A:SER179 4.6 47.6 1.0 C A:LEU177 4.7 57.0 1.0 N B:SER179 4.7 52.0 1.0 N A:GLU178 4.7 51.1 1.0 C B:LEU177 4.8 59.6 1.0 O B:LEU177 4.9 59.6 1.0 C B:GLU178 4.9 55.0 1.0

Sodium binding site 3 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:42.5 occ:0.50 NA B:NA303 2.5 12.4 0.5 NA A:NA303 3.2 27.6 0.5

Sodium binding site 4 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:57.4 occ:1.00 NA B:NA303 3.4 12.4 0.5 OE1 B:GLU178 3.8 56.0 1.0 OG B:SER179 3.9 66.5 1.0 OG A:SER179 4.0 61.6 1.0 N A:SER179 4.3 47.6 1.0 N B:SER179 4.3 52.0 1.0 CG B:GLU178 4.5 65.0 1.0 CD B:GLU178 4.5 76.6 1.0 OE1 A:GLU178 4.6 49.4 1.0 CA A:SER179 4.7 47.6 1.0 CA B:SER179 4.9 51.1 1.0 CB A:SER179 4.9 51.0 1.0 CB B:SER179 4.9 54.1 1.0

Sodium binding site 5 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:3.0 occ:0.50 NA D:NA302 3.8 3.0 0.5 OE1 C:GLU178 4.7 80.8 1.0 N C:SER179 4.8 54.0 1.0 CA C:GLU178 4.9 48.5 1.0 N D:SER179 4.9 54.0 1.0

Sodium binding site 6 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of 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 Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:3.0 occ:0.50 NA C:NA303 3.8 3.0 0.5 CB D:LEU177 4.4 54.1 1.0 O D:THR176 4.5 63.9 1.0 C D:LEU177 4.8 53.6 1.0 CB C:LEU177 5.0 50.2 1.0

Sodium binding site 7 out of 7 in the Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Navms Pore and C-Terminal Domain Crystallised in Presence of Channel Blocking Compound within 5.0Å range:

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