Sodium in PDB 4hfh: The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform

The structure of The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform, PDB code: 4hfh was solved by L.Sauguet, R.J.Howard, L.Malherbe, U.S.Lee, P.J.Corringer, R.A.Harris, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.71 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.000, 132.650, 159.270, 90.00, 102.16, 90.00
R / Rfree (%)	20.2 / 21.3

The structure of The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform also contains other interesting chemical elements:

Bromine	(Br)	45 atoms
Chlorine	(Cl)	7 atoms

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

Sodium binding site 1 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform


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 (Wild-Type) Complexed to Bromoform within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:94.9 occ:1.00 O A:ILE71 2.6 80.1 1.0 O A:PRO68 3.2 94.3 1.0 N A:ILE73 3.6 71.1 1.0 C A:ILE71 3.7 81.1 1.0 CA A:TRP72 4.0 74.3 1.0 CG2 A:VAL5 4.0 0.7 1.0 C A:TRP72 4.2 76.5 1.0 CB A:ILE73 4.2 71.7 1.0 N A:TRP72 4.3 76.0 1.0 C A:PRO68 4.3 95.2 1.0 CG1 A:ILE73 4.4 72.7 1.0 CD1 A:ILE73 4.4 81.5 1.0 CA A:ILE73 4.5 69.2 1.0 O A:GLU69 4.7 92.3 1.0 CA A:GLU69 4.7 91.3 1.0 O A:ILE73 4.8 70.8 1.0 C A:GLU69 4.9 92.7 1.0 N A:GLU69 4.9 91.8 1.0 CA A:ILE71 5.0 80.9 1.0 N A:ILE71 5.0 82.8 1.0

Sodium binding site 2 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform


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 (Wild-Type) Complexed to Bromoform within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:89.4 occ:1.00 O B:ILE71 2.5 74.0 1.0 N B:ILE73 3.2 64.5 1.0 O B:PRO68 3.5 81.1 1.0 C B:ILE71 3.6 73.7 1.0 CA B:TRP72 3.6 67.4 1.0 C B:TRP72 3.8 69.3 1.0 CG2 B:VAL5 3.9 0.6 1.0 N B:TRP72 4.0 68.7 1.0 CB B:ILE73 4.1 65.0 1.0 CA B:ILE73 4.2 62.4 1.0 CD1 B:ILE73 4.2 73.3 1.0 O B:ILE73 4.5 65.1 1.0 CG1 B:ILE73 4.6 65.7 1.0 C B:PRO68 4.6 82.5 1.0 O B:TRP72 4.9 68.7 1.0 C B:ILE73 4.9 65.6 1.0 CA B:ILE71 4.9 71.4 1.0 CB B:TRP72 4.9 66.3 1.0 O B:GLU69 4.9 84.2 1.0 CB B:VAL5 4.9 0.9 1.0

Sodium binding site 3 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform


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 (Wild-Type) Complexed to Bromoform within 5.0Å range: probe atom residue distance (Å) B Occ C:Na407 b:81.7 occ:1.00 O C:ILE71 2.8 79.4 1.0 N C:ILE73 3.4 69.8 1.0 O C:PRO68 3.6 86.9 1.0 CA C:TRP72 3.8 73.2 1.0 C C:ILE71 3.9 79.5 1.0 CB C:ILE73 4.0 69.7 1.0 C C:TRP72 4.0 75.6 1.0 CG2 C:VAL5 4.0 0.5 1.0 CA C:ILE73 4.2 67.4 1.0 CG1 C:ILE73 4.3 70.5 1.0 N C:TRP72 4.3 74.3 1.0 O C:ILE73 4.4 70.8 1.0 CD1 C:ILE73 4.5 80.5 1.0 C C:PRO68 4.7 87.7 1.0 C C:ILE73 4.9 70.5 1.0

Sodium binding site 4 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform


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 (Wild-Type) Complexed to Bromoform within 5.0Å range: probe atom residue distance (Å) B Occ D:Na407 b:1.0 occ:1.00 O D:ILE71 2.9 78.5 1.0 N D:ILE73 3.5 70.5 1.0 CG2 D:VAL5 3.6 0.9 1.0 CA D:TRP72 3.8 74.1 1.0 O D:PRO68 3.9 92.5 1.0 C D:ILE71 4.0 79.8 1.0 C D:TRP72 4.1 76.1 1.0 N D:TRP72 4.3 75.7 1.0 CB D:ILE73 4.4 71.3 1.0 CA D:ILE73 4.5 68.4 1.0 O D:ILE73 4.5 70.0 1.0 CG1 D:ILE73 4.7 72.5 1.0 CB D:VAL5 4.8 0.5 1.0 CD1 D:ILE73 4.9 80.2 1.0 C D:PRO68 5.0 93.6 1.0

Sodium binding site 5 out of 5 in the The Glic Pentameric Ligand-Gated Ion Channel (Wild-Type) Complexed to Bromoform


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 (Wild-Type) Complexed to Bromoform within 5.0Å range: probe atom residue distance (Å) B Occ E:Na407 b:92.2 occ:1.00 O E:ILE71 2.6 78.0 1.0 O E:PRO68 3.2 87.8 1.0 N E:ILE73 3.5 70.8 1.0 C E:ILE71 3.7 78.8 1.0 CA E:TRP72 3.9 72.5 1.0 CB E:ILE73 4.0 71.8 1.0 C E:TRP72 4.1 75.0 1.0 CG2 E:VAL5 4.1 0.2 1.0 CG1 E:ILE73 4.2 72.9 1.0 CD1 E:ILE73 4.2 82.7 1.0 N E:TRP72 4.2 74.0 1.0 C E:PRO68 4.3 89.1 1.0 CA E:ILE73 4.4 69.0 1.0 O E:ILE73 4.8 71.8 1.0 CA E:GLU69 4.8 87.1 1.0 O E:GLU69 4.8 89.4 1.0 CA E:ILE71 5.0 77.8 1.0 N E:GLU69 5.0 86.6 1.0

L.Sauguet, R.J.Howard, L.Malherbe, U.S.Lee, P.J.Corringer, R.A.Harris, M.Delarue. Structural Basis For Potentiation By Alcohols and Anaesthetics in A Ligand-Gated Ion Channel. Nat Commun V. 4 1697 2013.
ISSN: ESSN 2041-1723
PubMed: 23591864
DOI: 10.1038/NCOMMS2682