Sodium in PDB 4zzc: The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon

The structure of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon, PDB code: 4zzc was solved by L.Sauguet, Z.Fourati, T.Prange, M.Delarue, N.Colloc'h, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.000, 132.820, 159.150, 90.00, 101.88, 90.00
R / Rfree (%)	20.8 / 22.8

The structure of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon also contains other interesting chemical elements:

Xenon	(Xe)	35 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon (pdb code 4zzc). 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 Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon, PDB code: 4zzc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:94.7 occ:1.00 O A:ILE71 2.4 0.1 1.0 O A:PRO68 3.2 0.2 1.0 N A:ILE73 3.3 99.4 1.0 C A:ILE71 3.5 0.1 1.0 CA A:TRP72 3.7 0.9 1.0 C A:TRP72 3.9 0.9 1.0 CG2 A:VAL5 4.0 0.9 1.0 CB A:ILE73 4.0 96.5 1.0 N A:TRP72 4.1 0.7 1.0 CD1 A:ILE73 4.1 97.1 1.0 CA A:ILE73 4.2 95.3 1.0 C A:PRO68 4.3 0.1 1.0 CG1 A:ILE73 4.5 96.5 1.0 O A:ILE73 4.6 95.5 1.0 O A:GLU69 4.6 0.2 1.0 CA A:ILE71 4.8 0.7 1.0 CA A:GLU69 4.8 0.6 1.0 C A:GLU69 4.9 0.6 1.0 N A:ILE71 4.9 0.4 1.0 C A:ILE73 4.9 95.9 1.0 O A:TRP72 5.0 0.3 1.0 N A:GLU69 5.0 0.4 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:84.1 occ:1.00 O B:ILE71 2.2 92.1 1.0 O B:PRO68 2.6 0.1 1.0 C B:ILE71 3.4 93.3 1.0 N B:ILE73 3.6 85.2 1.0 C B:PRO68 3.8 0.2 1.0 CA B:TRP72 4.0 90.1 1.0 CD1 B:ILE73 4.0 91.8 1.0 C B:TRP72 4.1 92.2 1.0 CG2 B:VAL5 4.1 0.1 1.0 CB B:ILE73 4.1 83.9 1.0 N B:TRP72 4.1 90.4 1.0 CG1 B:ILE73 4.2 84.2 1.0 O B:GLU69 4.4 0.3 1.0 CA B:GLU69 4.4 1.0 1.0 CA B:ILE73 4.5 82.4 1.0 C B:GLU69 4.5 0.9 1.0 N B:GLU69 4.5 0.7 1.0 N B:ILE71 4.6 92.1 1.0 CA B:ILE71 4.6 90.8 1.0 CA B:PRO68 4.8 100.0 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ C:Na405 b:98.4 occ:1.00 O C:ILE71 2.4 0.4 1.0 O C:PRO68 2.7 0.4 1.0 C C:ILE71 3.6 0.2 1.0 O C:GLU69 3.7 0.1 1.0 CG2 C:VAL5 3.8 0.4 1.0 C C:PRO68 3.8 0.1 1.0 CA C:GLU69 4.0 0.3 1.0 C C:GLU69 4.0 1.0 1.0 N C:ILE73 4.2 94.7 1.0 CA C:TRP72 4.2 99.8 1.0 N C:GLU69 4.3 0.8 1.0 N C:TRP72 4.3 1.0 1.0 CD1 C:ILE73 4.5 0.4 1.0 N C:ILE71 4.5 0.5 1.0 C C:TRP72 4.6 0.1 1.0 CA C:ILE71 4.6 0.1 1.0 CB C:ILE73 4.7 93.2 1.0 N C:ALA70 4.9 0.2 1.0 CB C:VAL5 4.9 0.8 1.0 CG1 C:ILE73 4.9 93.5 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:59.3 occ:1.00 OG1 C:THR226 4.0 71.5 1.0 OG1 D:THR226 4.1 72.4 1.0 OG1 B:THR226 4.2 71.6 1.0 OG1 E:THR226 4.2 73.5 1.0 OG1 A:THR226 4.3 71.7 1.0 CG2 C:THR226 4.9 70.5 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:96.7 occ:1.00 O D:ILE71 2.8 0.2 1.0 O D:PRO68 3.4 0.6 1.0 N D:ILE73 3.7 99.9 1.0 CG2 D:VAL5 3.7 0.1 1.0 C D:ILE71 3.8 0.0 1.0 CA D:TRP72 4.0 0.8 1.0 C D:TRP72 4.3 0.7 1.0 CB D:ILE73 4.3 97.5 1.0 N D:TRP72 4.4 0.1 1.0 C D:PRO68 4.5 0.4 1.0 O D:GLU69 4.5 0.9 1.0 CA D:ILE73 4.5 96.0 1.0 CD1 D:ILE73 4.6 0.6 1.0 CA D:GLU69 4.7 0.5 1.0 O D:ILE73 4.8 98.3 1.0 C D:GLU69 4.8 0.1 1.0 CB D:VAL5 4.9 0.7 1.0 CG1 D:ILE73 4.9 98.0 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Glic Pentameric Ligand-Gated Ion Channel Open Form Complexed to Xenon within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:98.6 occ:1.00 O E:PRO68 2.8 0.7 1.0 O E:ILE71 2.8 0.0 1.0 C E:PRO68 3.8 0.0 1.0 C E:ILE71 3.9 1.0 1.0 O E:GLU69 4.0 0.9 1.0 CA E:GLU69 4.0 0.1 1.0 CG2 E:VAL5 4.1 0.9 1.0 C E:GLU69 4.2 0.6 1.0 N E:GLU69 4.3 0.4 1.0 N E:ILE73 4.3 0.4 1.0 CD1 E:ILE73 4.4 0.7 1.0 CA E:TRP72 4.5 0.3 1.0 CB E:ILE73 4.7 98.5 1.0 N E:TRP72 4.7 0.8 1.0 C E:TRP72 4.8 0.2 1.0 N E:ILE71 4.8 0.6 1.0 CA E:PRO68 5.0 0.8 1.0

L.Sauguet, Z.Fourati, T.Prange, M.Delarue, N.Colloc'h. Structural Basis For Xenon Inhibition in A Cationic Pentameric Ligand-Gated Ion Channel. Plos One V. 11 49795 2016.
ISSN: ESSN 1932-6203
PubMed: 26910105
DOI: 10.1371/JOURNAL.PONE.0149795