Sodium in PDB 4ilc: The Glic Pentameric Ligand-Gated Ion Channel in Complex with Sulfates

The structure of The Glic Pentameric Ligand-Gated Ion Channel in Complex with Sulfates, PDB code: 4ilc 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)	34.53 / 2.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.328, 132.100, 161.137, 90.00, 103.02, 90.00
R / Rfree (%)	21.5 / 23.6

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

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel in Complex with Sulfates (pdb code 4ilc). 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 in Complex with Sulfates, PDB code: 4ilc:
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 in Complex with Sulfates


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:76.4 occ:1.00 O A:ILE71 2.6 69.7 1.0 N A:ILE73 3.3 58.5 1.0 O A:PRO68 3.6 78.8 1.0 CA A:TRP72 3.6 61.2 1.0 C A:ILE71 3.7 68.6 1.0 CG2 A:VAL5 3.8 87.8 1.0 C A:TRP72 3.9 64.9 1.0 CB A:ILE73 4.0 58.5 1.0 N A:TRP72 4.1 62.7 1.0 CA A:ILE73 4.2 56.2 1.0 CG1 A:ILE73 4.3 58.3 1.0 CD1 A:ILE73 4.5 64.9 1.0 O A:ILE73 4.5 60.1 1.0 C A:PRO68 4.7 80.1 1.0 CB A:VAL5 4.9 87.6 1.0 CB A:TRP72 4.9 58.7 1.0 C A:ILE73 4.9 59.2 1.0 O A:GLU69 5.0 76.1 1.0 CA A:ILE71 5.0 67.1 1.0 O A:TRP72 5.0 64.8 1.0

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


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ B:Na409 b:97.8 occ:1.00 O B:PRO68 2.6 78.0 1.0 O B:ILE71 2.7 64.6 1.0 CD1 B:ILE73 3.6 57.3 1.0 C B:PRO68 3.6 77.9 1.0 N B:ILE73 3.8 56.2 1.0 C B:ILE71 3.9 64.0 1.0 CB B:ILE73 4.0 56.3 1.0 CA B:GLU69 4.3 75.3 1.0 CG1 B:ILE73 4.3 56.5 1.0 N B:GLU69 4.3 75.1 1.0 CA B:TRP72 4.4 57.0 1.0 C B:TRP72 4.4 63.4 1.0 O B:GLU69 4.5 79.2 1.0 CA B:ILE73 4.5 54.2 1.0 C B:GLU69 4.6 78.4 1.0 N B:TRP72 4.6 57.9 1.0 CG2 B:VAL5 4.7 0.3 1.0 CA B:PRO68 4.7 71.9 1.0 N B:ILE71 4.9 64.2 1.0 CA B:ILE71 5.0 62.6 1.0

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


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ C:Na409 b:83.6 occ:1.00 OG1 C:THR226 3.9 72.0 1.0 OG1 B:THR226 4.2 67.5 1.0 OG1 D:THR226 4.2 63.5 1.0 OG1 A:THR226 4.4 69.3 1.0 OG1 E:THR226 4.4 76.5 1.0 CG2 C:THR226 4.9 61.0 1.0

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


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ C:Na410 b:83.8 occ:1.00 O C:ILE71 2.6 70.2 1.0 O C:PRO68 3.2 77.5 1.0 C C:ILE71 3.7 69.6 1.0 CG2 C:VAL5 3.8 0.7 1.0 N C:ILE73 4.0 63.8 1.0 CA C:TRP72 4.1 61.1 1.0 C C:PRO68 4.2 77.4 1.0 O C:GLU69 4.3 77.4 1.0 N C:TRP72 4.3 62.7 1.0 C C:TRP72 4.4 68.2 1.0 CA C:GLU69 4.5 73.7 1.0 CB C:ILE73 4.6 64.3 1.0 CD1 C:ILE73 4.6 69.7 1.0 C C:GLU69 4.6 77.3 1.0 CG1 C:ILE73 4.6 64.3 1.0 N C:GLU69 4.8 74.0 1.0 N C:ILE71 4.9 70.3 1.0 CA C:ILE71 4.9 68.7 1.0 CB C:VAL5 4.9 0.9 1.0 CA C:ILE73 4.9 61.8 1.0

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


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ D:Na409 b:88.0 occ:1.00 O D:ILE71 2.6 74.0 1.0 CG2 D:VAL5 3.5 96.6 1.0 O D:PRO68 3.6 81.4 1.0 C D:ILE71 3.6 73.6 1.0 N D:ILE73 3.6 62.2 1.0 CA D:TRP72 3.7 65.9 1.0 C D:TRP72 4.1 68.8 1.0 N D:TRP72 4.1 67.5 1.0 CB D:ILE73 4.4 62.4 1.0 CA D:ILE73 4.6 60.3 1.0 CG1 D:ILE73 4.6 62.2 1.0 CB D:VAL5 4.6 96.8 1.0 C D:PRO68 4.6 82.6 1.0 O D:GLU69 4.7 78.4 1.0 CD1 D:ILE73 4.8 71.1 1.0 O D:ILE73 4.8 63.8 1.0 CA D:GLU69 4.9 78.2 1.0 CA D:ILE71 4.9 73.3 1.0 CB D:TRP72 5.0 63.6 1.0 C D:GLU69 5.0 79.9 1.0

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


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 in Complex with Sulfates within 5.0Å range: probe atom residue distance (Å) B Occ E:Na409 b:79.1 occ:1.00 O E:ILE71 2.5 70.3 1.0 O E:PRO68 3.1 75.9 1.0 C E:ILE71 3.6 69.0 1.0 N E:ILE73 3.6 58.4 1.0 CA E:TRP72 3.9 60.0 1.0 CG2 E:VAL5 4.0 90.5 1.0 C E:TRP72 4.1 65.0 1.0 CB E:ILE73 4.1 58.8 1.0 CG1 E:ILE73 4.1 57.8 1.0 CD1 E:ILE73 4.1 59.3 1.0 N E:TRP72 4.2 61.0 1.0 C E:PRO68 4.2 77.3 1.0 CA E:ILE73 4.5 56.9 1.0 O E:GLU69 4.7 79.7 1.0 CA E:GLU69 4.7 75.5 1.0 CA E:ILE71 4.8 69.2 1.0 C E:GLU69 4.9 79.7 1.0 O E:ILE73 4.9 64.6 1.0 N E:GLU69 4.9 75.4 1.0 N E:ILE71 4.9 71.0 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