Sodium in PDB 4il4: The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm

The structure of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm, PDB code: 4il4 was solved by L.Sauguet, L.Malherbe, P.J.Corringer, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.069, 132.491, 160.219, 90.00, 102.70, 90.00
R / Rfree (%)	19.5 / 20.9

The structure of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm (pdb code 4il4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm, PDB code: 4il4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:84.8 occ:1.00 O A:ILE71 2.6 91.9 1.0 O A:PRO68 3.2 0.3 1.0 N A:ILE73 3.6 85.1 1.0 C A:ILE71 3.7 91.7 1.0 CA A:TRP72 3.9 84.2 1.0 CG2 A:VAL5 4.0 0.7 1.0 C A:TRP72 4.2 90.3 1.0 CB A:ILE73 4.2 86.1 1.0 N A:TRP72 4.3 85.3 1.0 C A:PRO68 4.3 0.6 1.0 CG1 A:ILE73 4.4 85.9 1.0 CD1 A:ILE73 4.4 93.1 1.0 CA A:ILE73 4.5 83.3 1.0 O A:GLU69 4.6 0.7 1.0 CA A:GLU69 4.7 0.7 1.0 O A:ILE73 4.8 83.3 1.0 C A:GLU69 4.9 0.8 1.0 CA A:ILE71 4.9 91.6 1.0 N A:GLU69 4.9 0.2 1.0 N A:ILE71 5.0 93.6 1.0

Sodium binding site 2 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:0.7 occ:1.00 OG1 C:THR226 4.1 94.6 1.0 OG1 D:THR226 4.2 83.9 1.0 OG1 B:THR226 4.3 90.1 1.0 OG1 E:THR226 4.4 89.0 1.0 OG1 A:THR226 4.4 88.5 1.0

Sodium binding site 3 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:98.0 occ:1.00 O B:ILE71 2.4 84.2 1.0 N B:ILE73 3.3 75.7 1.0 O B:PRO68 3.4 95.0 1.0 C B:ILE71 3.5 83.9 1.0 CA B:TRP72 3.6 77.4 1.0 C B:TRP72 3.8 80.4 1.0 CG2 B:VAL5 3.8 0.7 1.0 N B:TRP72 4.0 78.8 1.0 CB B:ILE73 4.1 75.5 1.0 CA B:ILE73 4.2 73.4 1.0 CD1 B:ILE73 4.2 79.9 1.0 O B:ILE73 4.5 74.9 1.0 CG1 B:ILE73 4.5 75.1 1.0 C B:PRO68 4.6 94.8 1.0 CA B:ILE71 4.8 80.7 1.0 O B:GLU69 4.9 92.7 1.0 CB B:VAL5 4.9 0.8 1.0 C B:ILE73 4.9 75.7 1.0 O B:TRP72 4.9 79.1 1.0 CB B:TRP72 4.9 75.4 1.0

Sodium binding site 4 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:83.1 occ:1.00 O C:ILE71 2.8 95.5 1.0 N C:ILE73 3.4 85.8 1.0 O C:PRO68 3.6 0.4 1.0 CA C:TRP72 3.9 90.5 1.0 C C:ILE71 3.9 96.0 1.0 CB C:ILE73 4.0 85.5 1.0 C C:TRP72 4.0 93.2 1.0 CG2 C:VAL5 4.1 0.5 1.0 CA C:ILE73 4.2 83.3 1.0 CG1 C:ILE73 4.3 84.8 1.0 N C:TRP72 4.3 91.2 1.0 CD1 C:ILE73 4.4 90.6 1.0 O C:ILE73 4.4 85.8 1.0 C C:PRO68 4.7 0.1 1.0 C C:ILE73 4.8 85.4 1.0

Sodium binding site 5 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:99.9 occ:1.00 O D:ILE71 2.8 98.5 1.0 N D:ILE73 3.5 85.1 1.0 CG2 D:VAL5 3.7 0.5 1.0 O D:PRO68 3.8 0.2 1.0 CA D:TRP72 3.8 90.5 1.0 C D:ILE71 3.9 98.6 1.0 C D:TRP72 4.1 92.4 1.0 N D:TRP72 4.3 92.4 1.0 CB D:ILE73 4.3 84.7 1.0 CA D:ILE73 4.5 82.5 1.0 O D:ILE73 4.5 82.5 1.0 CG1 D:ILE73 4.7 85.1 1.0 CB D:VAL5 4.8 0.7 1.0 CD1 D:ILE73 4.9 97.4 1.0 C D:PRO68 4.9 0.5 1.0 O D:GLU69 5.0 0.3 1.0 CB D:TRP72 5.0 88.3 1.0

Sodium binding site 6 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ E:Na403 b:0.2 occ:1.00 O E:ILE71 2.5 96.9 1.0 O E:PRO68 3.2 0.1 1.0 N E:ILE73 3.5 83.2 1.0 C E:ILE71 3.7 95.9 1.0 CA E:TRP72 3.9 86.9 1.0 CG2 E:VAL5 4.1 0.2 1.0 C E:TRP72 4.1 89.1 1.0 CB E:ILE73 4.1 84.0 1.0 CG1 E:ILE73 4.2 83.2 1.0 CD1 E:ILE73 4.2 86.2 1.0 N E:TRP72 4.2 88.9 1.0 C E:PRO68 4.3 0.0 1.0 CA E:ILE73 4.4 81.3 1.0 O E:ILE73 4.8 82.5 1.0 O E:GLU69 4.8 0.3 1.0 CA E:GLU69 4.8 0.8 1.0 CA E:ILE71 4.9 94.2 1.0 N E:GLU69 5.0 0.6 1.0 C E:GLU69 5.0 0.1 1.0

L.Sauguet, F.Poitevin, S.Murail, C.Van Renterghem, G.Moraga-Cid, L.Malherbe, A.W.Thompson, P.Koehl, P.J.Corringer, M.Baaden, M.Delarue. Structural Basis For Ion Permeation Mechanism in Pentameric Ligand-Gated Ion Channels. Embo J. V. 32 728 2013.
ISSN: ISSN 0261-4189
PubMed: 23403925
DOI: 10.1038/EMBOJ.2013.17