Sodium in PDB 4cbc: Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak

The structure of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak, PDB code: 4cbc was solved by C.Bagneris, C.E.Naylor, B.A.Wallace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.469 / 2.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.901, 331.704, 79.933, 90.00, 90.00, 90.00
R / Rfree (%)	27.6 / 29.94

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

Sodium binding site 1 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:89.0 occ:0.50 NA A:NA1302 2.2 91.7 0.5 OE2 B:GLU178 4.4 61.9 1.0 OE2 A:GLU178 4.4 58.0 1.0 N B:SER179 4.5 49.7 1.0 N A:SER179 4.5 38.7 1.0 OG A:SER179 4.5 54.4 1.0 OG B:SER179 4.5 46.0 1.0

Sodium binding site 2 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1302 b:91.7 occ:0.50 NA A:NA1301 2.2 89.0 0.5 OG A:SER179 3.8 54.4 1.0 OG B:SER179 3.8 46.0 1.0 O B:HOH2014 4.2 53.5 1.0 OE2 A:GLU178 4.5 58.0 1.0 OE2 B:GLU178 4.5 61.9 1.0 CB A:SER179 5.0 37.7 1.0

Sodium binding site 3 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range:

Sodium binding site 4 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1301 b:70.5 occ:0.50 NA C:NA1302 4.4 51.8 0.5 O D:THR176 4.8 45.3 1.0 O C:THR176 4.8 42.7 1.0 CD1 D:LEU177 4.9 40.9 1.0 CD1 C:LEU177 4.9 42.9 1.0 CB D:LEU177 4.9 38.0 1.0 CB C:LEU177 5.0 40.0 1.0

Sodium binding site 5 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1302 b:51.8 occ:0.50 NA C:NA1303 2.2 77.6 0.5 O D:LEU177 4.3 87.6 1.0 O C:LEU177 4.3 99.8 1.0 NA C:NA1301 4.4 70.5 0.5 CA D:GLU178 4.8 62.3 1.0 CA C:GLU178 4.8 66.2 1.0

Sodium binding site 6 out of 6 in the Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) After Thallium Soak within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1303 b:77.6 occ:0.50 NA C:NA1302 2.2 51.8 0.5 N C:SER179 4.4 37.6 1.0 N D:SER179 4.4 36.0 1.0 OE2 C:GLU178 4.5 77.0 1.0 OE2 D:GLU178 4.5 68.7 1.0 OG C:SER179 4.5 68.6 1.0 OG D:SER179 4.6 55.4 1.0 CA D:GLU178 4.9 62.3 1.0 CG D:GLU178 5.0 74.0 1.0 CA C:GLU178 5.0 66.2 1.0

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: ISSN 0027-8424
PubMed: 24850863
DOI: 10.1073/PNAS.1406855111