Sodium in PDB 6hyv: The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A, PDB code: 6hyv was solved by H.D.Hu, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.810, 132.380, 159.650, 90.00, 102.22, 90.00
R / Rfree (%)	20.9 / 22.1

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A 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 Mutant Y119A (pdb code 6hyv). 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 Mutant Y119A, PDB code: 6hyv:
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 Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:47.6 occ:1.00 O A:ILE71 2.5 47.4 1.0 O A:PRO68 3.2 61.6 1.0 N A:ILE73 3.5 38.5 1.0 C A:ILE71 3.7 48.1 1.0 CB A:ILE73 4.0 36.8 1.0 CA A:TRP72 4.0 42.2 1.0 C A:TRP72 4.1 44.1 1.0 CG1 A:ILE73 4.1 37.7 1.0 CD1 A:ILE73 4.2 48.4 1.0 C A:PRO68 4.3 62.6 1.0 N A:TRP72 4.3 43.7 1.0 CA A:ILE73 4.3 35.5 1.0 CG2 A:VAL5 4.6 64.0 1.0 O A:ILE73 4.7 39.3 1.0 O A:GLU69 4.7 59.9 1.0 CA A:ILE71 4.9 45.9 1.0 CA A:GLU69 5.0 57.2 1.0 N A:GLU69 5.0 57.7 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:54.6 occ:1.00 OG1 C:THR226 4.1 45.1 1.0 OG1 B:THR226 4.2 40.8 1.0 OG1 A:THR226 4.2 42.2 1.0 OG1 E:THR226 4.3 46.3 1.0 OG1 D:THR226 4.3 47.7 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:42.6 occ:1.00 O B:ILE71 2.5 41.6 1.0 O B:PRO68 3.2 56.2 1.0 C B:ILE71 3.6 40.7 1.0 N B:ILE73 3.7 36.6 1.0 CA B:TRP72 4.0 37.2 1.0 C B:TRP72 4.2 43.9 1.0 N B:TRP72 4.2 37.0 1.0 C B:PRO68 4.2 57.0 1.0 CB B:ILE73 4.3 37.1 1.0 CG1 B:ILE73 4.4 39.0 1.0 CG2 B:VAL5 4.5 79.8 1.0 CD1 B:ILE73 4.5 52.9 1.0 O B:GLU69 4.5 59.1 1.0 CA B:ILE73 4.6 34.2 1.0 CA B:GLU69 4.7 55.4 1.0 C B:GLU69 4.8 57.3 1.0 CA B:ILE71 4.8 39.1 1.0 N B:ILE71 4.8 41.5 1.0 N B:GLU69 4.9 55.1 1.0 O B:ILE73 4.9 37.5 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na407 b:51.2 occ:1.00 O C:ILE71 2.5 49.5 1.0 O C:PRO68 3.1 61.0 1.0 C C:ILE71 3.7 51.4 1.0 N C:ILE73 3.8 43.4 1.0 CA C:TRP72 4.1 44.8 1.0 C C:PRO68 4.1 60.7 1.0 CB C:ILE73 4.1 41.1 1.0 CG1 C:ILE73 4.2 40.5 1.0 C C:TRP72 4.3 48.5 1.0 CD1 C:ILE73 4.3 45.8 1.0 N C:TRP72 4.3 47.0 1.0 CA C:ILE73 4.6 40.0 1.0 O C:GLU69 4.6 58.2 1.0 CG2 C:VAL5 4.6 70.0 1.0 CA C:GLU69 4.7 56.4 1.0 N C:GLU69 4.8 56.8 1.0 C C:GLU69 4.8 57.5 1.0 CA C:ILE71 4.9 49.9 1.0 O C:ILE73 4.9 45.0 1.0 N C:ILE71 4.9 50.8 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:80.2 occ:1.00 O D:ILE71 2.5 47.9 1.0 O D:PRO68 3.2 62.5 1.0 C D:ILE71 3.7 48.5 1.0 N D:ILE73 3.8 38.5 1.0 CA D:TRP72 4.1 42.5 1.0 C D:PRO68 4.2 62.9 1.0 CB D:ILE73 4.2 37.7 1.0 C D:TRP72 4.3 45.5 1.0 N D:TRP72 4.3 44.1 1.0 CG1 D:ILE73 4.4 37.9 1.0 CD1 D:ILE73 4.5 42.7 1.0 O D:GLU69 4.5 59.5 1.0 CG2 D:VAL5 4.5 76.3 1.0 CA D:ILE73 4.6 36.1 1.0 CA D:GLU69 4.7 58.5 1.0 C D:GLU69 4.8 59.6 1.0 N D:GLU69 4.8 59.4 1.0 CA D:ILE71 4.9 46.0 1.0 O D:ILE73 4.9 42.6 1.0 N D:ILE71 4.9 48.2 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


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 Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:54.1 occ:1.00 O E:ILE71 2.6 51.8 1.0 O E:PRO68 3.1 57.1 1.0 C E:ILE71 3.8 53.4 1.0 N E:ILE73 3.8 44.2 1.0 C E:PRO68 4.1 58.2 1.0 CB E:ILE73 4.1 44.2 1.0 CA E:TRP72 4.2 48.6 1.0 CG1 E:ILE73 4.2 44.3 1.0 CD1 E:ILE73 4.3 50.4 1.0 C E:TRP72 4.3 50.2 1.0 N E:TRP72 4.4 49.9 1.0 CA E:ILE73 4.6 41.7 1.0 O E:GLU69 4.6 61.4 1.0 CA E:GLU69 4.7 57.0 1.0 N E:GLU69 4.8 57.0 1.0 CG2 E:VAL5 4.8 67.2 1.0 C E:GLU69 4.9 60.0 1.0 O E:ILE73 4.9 43.3 1.0 CA E:ILE71 5.0 50.0 1.0 N E:ILE71 5.0 51.6 1.0

H.Hu, K.Ataka, A.Menny, Z.Fourati, L.Sauguet, P.J.Corringer, P.Koehl, J.Heberle, M.Delarue. Electrostatics, Proton Sensor, and Networks Governing the Gating Transition in Glic, A Proton-Gated Pentameric Ion Channel. Proc. Natl. Acad. Sci. V. 115 12172 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30541892
DOI: 10.1073/PNAS.1813378116