Sodium in PDB 4hfi: The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution

The structure of The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution, PDB code: 4hfi 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)	54.05 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.890, 133.200, 160.200, 90.00, 102.74, 90.00
R / Rfree (%)	20.5 / 21.6

The structure of The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution (pdb code 4hfi). 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 at 2.4 A Resolution, PDB code: 4hfi:
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 at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:78.1 occ:1.00 O A:ILE71 2.5 83.1 1.0 O A:PRO68 3.2 0.0 1.0 N A:ILE73 3.5 72.7 1.0 C A:ILE71 3.7 83.8 1.0 CA A:TRP72 3.8 76.5 1.0 C A:TRP72 4.0 78.2 1.0 CG2 A:VAL5 4.0 0.8 1.0 CB A:ILE73 4.1 73.8 1.0 N A:TRP72 4.2 78.2 1.0 C A:PRO68 4.3 0.8 1.0 CA A:ILE73 4.4 71.0 1.0 CG1 A:ILE73 4.4 74.6 1.0 CD1 A:ILE73 4.4 81.4 1.0 O A:ILE73 4.7 71.4 1.0 CA A:GLU69 4.8 95.5 1.0 O A:GLU69 4.8 96.7 1.0 CA A:ILE71 4.9 83.5 1.0 C A:GLU69 4.9 97.1 1.0 N A:GLU69 5.0 96.2 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:88.8 occ:1.00 O D:HOH535 3.3 85.9 1.0 O C:HOH511 3.4 83.0 1.0 O E:HOH520 3.6 72.3 1.0 O A:HOH518 3.7 76.0 1.0 O B:HOH524 3.8 76.0 1.0 OG1 C:THR226 4.1 59.4 1.0 OG1 D:THR226 4.2 54.4 1.0 OG1 B:THR226 4.4 56.2 1.0 OG1 E:THR226 4.4 61.1 1.0 OG1 A:THR226 4.5 61.0 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:79.9 occ:1.00 O B:ILE71 2.5 70.4 1.0 N B:ILE73 3.2 62.9 1.0 O B:PRO68 3.4 83.4 1.0 C B:ILE71 3.6 70.3 1.0 CA B:TRP72 3.6 64.3 1.0 C B:TRP72 3.8 67.1 1.0 CG2 B:VAL5 4.0 0.3 1.0 N B:TRP72 4.0 65.3 1.0 CB B:ILE73 4.1 64.3 1.0 CA B:ILE73 4.2 61.5 1.0 CD1 B:ILE73 4.2 71.1 1.0 O B:ILE73 4.5 64.8 1.0 C B:PRO68 4.5 84.5 1.0 CG1 B:ILE73 4.6 64.8 1.0 O B:TRP72 4.9 66.7 1.0 CA B:ILE71 4.9 68.5 1.0 C B:ILE73 4.9 64.7 1.0 O B:GLU69 4.9 83.2 1.0 CB B:TRP72 4.9 63.0 1.0 CB B:VAL5 5.0 0.7 1.0 CA B:GLU69 5.0 81.4 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:73.0 occ:1.00 O C:ILE71 2.9 80.0 1.0 N C:ILE73 3.3 69.1 1.0 O C:PRO68 3.7 95.3 1.0 CA C:TRP72 3.8 72.4 1.0 C C:TRP72 3.9 74.1 1.0 C C:ILE71 3.9 80.0 1.0 CB C:ILE73 4.0 69.8 1.0 CG2 C:VAL5 4.0 0.6 1.0 CA C:ILE73 4.1 67.2 1.0 N C:TRP72 4.3 73.9 1.0 O C:ILE73 4.3 69.8 1.0 CG1 C:ILE73 4.4 70.0 1.0 CD1 C:ILE73 4.5 77.2 1.0 C C:ILE73 4.8 69.9 1.0 C C:PRO68 4.8 96.4 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:86.3 occ:1.00 O D:ILE71 3.1 84.4 1.0 N D:ILE73 3.5 71.5 1.0 CG2 D:VAL5 3.7 0.3 1.0 CA D:TRP72 3.9 76.4 1.0 O D:PRO68 4.1 0.1 1.0 C D:TRP72 4.1 77.2 1.0 C D:ILE71 4.1 85.0 1.0 O D:ILE73 4.4 70.1 1.0 CB D:ILE73 4.4 72.4 1.0 CA D:ILE73 4.4 69.5 1.0 N D:TRP72 4.4 78.5 1.0 CB D:VAL5 4.8 0.7 1.0 CG1 D:ILE73 4.9 73.0 1.0 C D:ILE73 4.9 70.4 1.0 CB D:TRP72 5.0 74.9 1.0 CD1 D:TRP72 5.0 78.2 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel at 2.4 A Resolution


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 at 2.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:76.5 occ:1.00 O E:ILE71 2.5 78.1 1.0 O E:PRO68 3.1 90.8 1.0 N E:ILE73 3.6 69.8 1.0 C E:ILE71 3.6 78.5 1.0 CA E:TRP72 3.9 71.3 1.0 CG2 E:VAL5 4.0 0.4 1.0 C E:TRP72 4.1 73.6 1.0 CB E:ILE73 4.2 71.0 1.0 N E:TRP72 4.2 72.7 1.0 C E:PRO68 4.2 91.9 1.0 CD1 E:ILE73 4.3 80.2 1.0 CG1 E:ILE73 4.3 71.3 1.0 CA E:ILE73 4.5 68.3 1.0 CA E:GLU69 4.7 88.1 1.0 O E:GLU69 4.7 90.2 1.0 N E:GLU69 4.9 88.2 1.0 C E:GLU69 4.9 90.1 1.0 CA E:ILE71 4.9 77.9 1.0 O E:ILE73 4.9 72.2 1.0 N E:ILE71 5.0 79.7 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