Sodium in PDB 3zjz: Open-Form Navms Sodium Channel Pore (with C-Terminal Domain)

The structure of Open-Form Navms Sodium Channel Pore (with C-Terminal Domain), PDB code: 3zjz 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)	45.77 / 2.92
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.150, 334.380, 80.210, 90.00, 90.00, 90.00
R / Rfree (%)	25.72 / 28.71

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

Sodium binding site 1 out of 5 in the Open-Form Navms Sodium Channel Pore (with 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 Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1400 b:41.6 occ:0.50 OG B:SER54 3.2 41.1 1.0 N B:SER54 3.5 28.6 1.0 OE2 B:GLU53 3.5 38.6 1.0 CA B:SER54 3.8 28.4 1.0 CB B:SER54 4.1 32.2 1.0 NA A:NA1401 4.4 49.9 0.5 C B:GLU53 4.6 31.4 1.0 CD B:GLU53 4.6 54.9 1.0 OG A:SER54 4.6 40.4 1.0 CA B:GLU53 4.8 31.7 1.0 N A:SER54 4.9 27.1 1.0 CG B:GLU53 5.0 43.1 1.0

Sodium binding site 2 out of 5 in the Open-Form Navms Sodium Channel Pore (with 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 Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1401 b:49.9 occ:0.50 NA A:NA1400 4.4 41.6 0.5 NA A:NA1402 4.8 52.7 0.5 CA A:GLU53 4.8 29.0 1.0 O A:LEU52 4.8 33.9 1.0 CA B:GLU53 5.0 31.7 1.0

Sodium binding site 3 out of 5 in the Open-Form Navms Sodium Channel Pore (with 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 Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1402 b:52.7 occ:0.50 O B:THR51 3.6 43.9 1.0 CD1 A:LEU52 3.9 41.3 1.0 CB A:LEU52 4.5 33.9 1.0 CD1 B:LEU52 4.5 44.0 1.0 CB B:LEU52 4.6 36.3 1.0 O A:THR51 4.7 42.2 1.0 NA A:NA1401 4.8 49.9 0.5 CG A:LEU52 4.8 39.0 1.0 C B:THR51 4.8 43.9 1.0 O B:HOH3020 4.9 36.6 1.0

Sodium binding site 4 out of 5 in the Open-Form Navms Sodium Channel Pore (with 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 Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1400 b:21.7 occ:0.50 N C:SER54 4.5 29.6 1.0 N D:SER54 4.5 32.1 1.0 OE2 C:GLU53 4.7 47.5 1.0 OE2 D:GLU53 4.8 52.2 1.0 CA C:GLU53 4.9 26.9 1.0 CA D:GLU53 4.9 31.2 1.0

Sodium binding site 5 out of 5 in the Open-Form Navms Sodium Channel Pore (with 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 Open-Form Navms Sodium Channel Pore (with C-Terminal Domain) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1401 b:24.7 occ:0.50 O C:THR51 3.6 39.3 1.0 CB C:LEU52 4.1 27.7 1.0 CD1 C:LEU52 4.4 32.6 1.0 C C:THR51 4.7 37.5 1.0 O D:THR51 4.8 43.7 1.0 CG C:LEU52 4.8 32.0 1.0 CA C:LEU52 5.0 27.6 1.0

C.Bagneris, P.G.Decaen, B.A.Hall, C.E.Naylor, D.E.Clapham, C.W.M.Kay, B.A.Wallace. Role of the C-Terminal Domain in the Structure and Function of Tetrameric Sodium Channels. Nat.Commun. V. 4 2465 2013.
ISSN: ISSN 2041-1723
PubMed: 24051986
DOI: 10.1038/NCOMMS3465