Sodium in PDB 4il9: The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide

The structure of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide, PDB code: 4il9 was solved by L.Sauguet, P.J.Corringer, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.77 / 2.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.520, 132.140, 159.960, 90.00, 102.16, 90.00
R / Rfree (%)	20.1 / 21.4

The structure of The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide also contains other interesting chemical elements:

Bromine

(Br)

12 atoms

The binding sites of Sodium atom in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide (pdb code 4il9). 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 A237F in Complex with Bromide, PDB code: 4il9:
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 A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:71.3 occ:1.00 OG1 C:THR226 4.0 55.4 1.0 OG1 B:THR226 4.2 53.4 1.0 OG1 D:THR226 4.4 58.6 1.0 OG1 A:THR226 4.6 56.5 1.0 OG1 E:THR226 4.6 58.3 1.0

Sodium binding site 2 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:64.9 occ:1.00 O A:ILE71 2.5 67.5 1.0 O A:PRO68 3.2 77.6 1.0 N A:ILE73 3.5 58.3 1.0 C A:ILE71 3.6 68.4 1.0 CA A:TRP72 3.9 61.3 1.0 CG2 A:VAL5 4.0 88.1 1.0 C A:TRP72 4.1 64.3 1.0 CB A:ILE73 4.1 57.8 1.0 N A:TRP72 4.2 63.3 1.0 C A:PRO68 4.3 78.5 1.0 CD1 A:ILE73 4.3 66.3 1.0 CG1 A:ILE73 4.3 59.2 1.0 CA A:ILE73 4.4 55.7 1.0 O A:GLU69 4.7 76.7 1.0 O A:ILE73 4.7 56.9 1.0 CA A:GLU69 4.8 74.7 1.0 CA A:ILE71 4.8 66.9 1.0 C A:GLU69 4.9 76.4 1.0 N A:GLU69 4.9 75.0 1.0 N A:ILE71 4.9 68.1 1.0

Sodium binding site 3 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na410 b:67.1 occ:1.00 O B:ILE71 2.4 59.1 1.0 O B:PRO68 3.3 69.3 1.0 N B:ILE73 3.4 51.9 1.0 C B:ILE71 3.5 57.6 1.0 CA B:TRP72 3.7 51.8 1.0 C B:TRP72 3.9 57.1 1.0 CG2 B:VAL5 3.9 0.7 1.0 N B:TRP72 4.0 52.2 1.0 CB B:ILE73 4.2 52.8 1.0 CA B:ILE73 4.3 49.9 1.0 CD1 B:ILE73 4.3 65.7 1.0 C B:PRO68 4.4 69.6 1.0 CG1 B:ILE73 4.5 54.8 1.0 O B:ILE73 4.7 53.7 1.0 O B:GLU69 4.7 70.6 1.0 CA B:ILE71 4.7 56.1 1.0 CA B:GLU69 4.9 67.0 1.0 N B:ILE71 4.9 57.9 1.0 CB B:VAL5 4.9 0.6 1.0 O B:TRP72 5.0 58.0 1.0 C B:GLU69 5.0 69.4 1.0 CB B:TRP72 5.0 51.1 1.0

Sodium binding site 4 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na411 b:66.8 occ:1.00 O C:ILE71 2.7 66.6 1.0 O C:PRO68 2.7 71.1 1.0 C C:PRO68 3.7 71.0 1.0 C C:ILE71 3.9 67.2 1.0 CA C:GLU69 4.1 67.4 1.0 CD1 C:ILE73 4.2 71.9 1.0 N C:ILE73 4.2 60.0 1.0 N C:GLU69 4.3 67.2 1.0 O C:GLU69 4.3 71.1 1.0 C C:GLU69 4.4 70.3 1.0 CB C:ILE73 4.4 59.4 1.0 CG1 C:ILE73 4.4 60.9 1.0 CA C:TRP72 4.5 60.6 1.0 N C:TRP72 4.6 62.1 1.0 C C:TRP72 4.7 65.3 1.0 CA C:PRO68 4.8 65.3 1.0 N C:ILE71 4.8 66.0 1.0 CG2 C:VAL5 4.9 0.0 1.0 CA C:ILE71 4.9 65.7 1.0 CA C:ILE73 5.0 57.0 1.0

Sodium binding site 5 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na411 b:80.9 occ:1.00 O D:ILE71 2.7 68.0 1.0 CG2 D:VAL5 3.6 93.3 1.0 N D:ILE73 3.7 61.8 1.0 O D:PRO68 3.7 77.7 1.0 C D:ILE71 3.7 69.2 1.0 CA D:TRP72 3.8 62.8 1.0 C D:TRP72 4.2 67.1 1.0 N D:TRP72 4.2 64.3 1.0 CB D:ILE73 4.5 62.2 1.0 CA D:ILE73 4.6 59.8 1.0 CB D:VAL5 4.7 94.2 1.0 O D:ILE73 4.7 64.1 1.0 O D:GLU69 4.7 77.1 1.0 C D:PRO68 4.8 78.2 1.0 CG1 D:ILE73 4.8 63.8 1.0 CD1 D:ILE73 4.9 76.1 1.0 CB D:TRP72 5.0 61.7 1.0

Sodium binding site 6 out of 6 in the The Pentameric Ligand-Gated Ion Channel Glic A237F in Complex with Bromide


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 A237F in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ E:Na410 b:71.1 occ:1.00 O E:ILE71 2.5 70.3 1.0 O E:PRO68 3.0 78.7 1.0 N E:ILE73 3.6 60.7 1.0 C E:ILE71 3.7 70.7 1.0 CB E:ILE73 4.0 59.4 1.0 CA E:TRP72 4.0 63.6 1.0 CD1 E:ILE73 4.0 64.2 1.0 C E:PRO68 4.1 79.0 1.0 CG1 E:ILE73 4.1 60.0 1.0 C E:TRP72 4.1 66.7 1.0 CG2 E:VAL5 4.2 0.2 1.0 N E:TRP72 4.3 65.5 1.0 CA E:ILE73 4.4 57.6 1.0 CA E:GLU69 4.7 77.2 1.0 O E:GLU69 4.7 77.9 1.0 N E:GLU69 4.8 77.0 1.0 O E:ILE73 4.8 60.9 1.0 CA E:ILE71 4.9 70.0 1.0 C E:GLU69 4.9 78.0 1.0 N E:ILE71 4.9 71.4 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