Sodium in PDB 6hyw: The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F, PDB code: 6hyw 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 (°)	183.000, 132.240, 161.480, 90.00, 103.25, 90.00
R / Rfree (%)	19.2 / 21.2

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F 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 Y119F (pdb code 6hyw). 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 Y119F, PDB code: 6hyw:
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 Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:66.5 occ:1.00 O A:ILE71 2.5 55.7 1.0 O A:PRO68 3.1 69.8 1.0 N A:ILE73 3.4 45.6 1.0 C A:ILE71 3.7 57.8 1.0 CA A:TRP72 3.8 50.5 1.0 C A:TRP72 4.0 53.4 1.0 CB A:ILE73 4.0 44.3 1.0 CG1 A:ILE73 4.1 43.9 1.0 CD1 A:ILE73 4.2 45.8 1.0 N A:TRP72 4.2 52.4 1.0 C A:PRO68 4.2 70.2 1.0 CG2 A:VAL5 4.2 70.5 1.0 CA A:ILE73 4.3 43.0 1.0 O A:ILE73 4.7 43.0 1.0 O A:GLU69 4.8 67.8 1.0 CA A:GLU69 4.9 66.2 1.0 CA A:ILE71 4.9 58.1 1.0 N A:GLU69 5.0 66.6 1.0 C A:GLU69 5.0 68.0 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:55.6 occ:1.00 OG1 A:THR226 4.0 41.9 1.0 OG1 B:THR226 4.1 39.7 1.0 OG1 E:THR226 4.1 39.3 1.0 OG1 C:THR226 4.2 45.9 1.0 OG1 D:THR226 4.2 43.5 1.0 CG2 A:THR226 4.8 34.5 1.0 CG2 E:THR226 4.8 28.0 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:63.7 occ:1.00 O B:ILE71 2.5 47.6 1.0 O B:PRO68 2.9 54.9 1.0 N B:ILE73 3.5 40.2 1.0 C B:ILE71 3.7 47.1 1.0 CA B:TRP72 4.0 41.8 1.0 CB B:ILE73 4.0 40.1 1.0 CD1 B:ILE73 4.1 47.5 1.0 C B:TRP72 4.1 46.9 1.0 C B:PRO68 4.1 56.9 1.0 CG1 B:ILE73 4.1 40.1 1.0 N B:TRP72 4.2 42.7 1.0 CA B:ILE73 4.3 38.0 1.0 CG2 B:VAL5 4.4 77.4 1.0 O B:ILE73 4.7 42.1 1.0 O B:GLU69 4.7 65.3 1.0 CA B:GLU69 4.8 57.7 1.0 N B:GLU69 4.8 56.5 1.0 CA B:ILE71 4.9 44.8 1.0 C B:GLU69 4.9 62.1 1.0 N B:ILE71 4.9 47.0 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:52.8 occ:1.00 O C:ILE71 2.7 55.7 1.0 O C:PRO68 3.1 63.1 1.0 N C:ILE73 3.6 44.3 1.0 C C:ILE71 3.9 57.2 1.0 CA C:TRP72 4.1 49.9 1.0 CB C:ILE73 4.1 43.8 1.0 C C:TRP72 4.2 51.0 1.0 CD1 C:ILE73 4.2 46.1 1.0 C C:PRO68 4.2 64.3 1.0 CG1 C:ILE73 4.3 44.2 1.0 CG2 C:VAL5 4.3 82.4 1.0 CA C:ILE73 4.4 41.9 1.0 N C:TRP72 4.4 51.8 1.0 O C:ILE73 4.7 45.6 1.0 O C:GLU69 4.8 65.0 1.0 CA C:GLU69 4.8 62.1 1.0 N C:GLU69 4.9 61.9 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:64.8 occ:1.00 O D:ILE71 2.7 56.7 1.0 O D:PRO68 3.0 79.3 1.0 N D:ILE73 3.7 46.9 1.0 C D:ILE71 3.9 58.0 1.0 CB D:ILE73 4.1 47.0 1.0 C D:PRO68 4.1 79.4 1.0 CA D:TRP72 4.1 51.5 1.0 CD1 D:ILE73 4.2 55.3 1.0 C D:TRP72 4.2 54.3 1.0 CG1 D:ILE73 4.2 47.1 1.0 CG2 D:VAL5 4.4 81.1 1.0 CA D:ILE73 4.4 44.6 1.0 N D:TRP72 4.5 53.0 1.0 CA D:GLU69 4.7 73.5 1.0 O D:ILE73 4.8 46.4 1.0 O D:GLU69 4.8 75.3 1.0 N D:GLU69 4.8 74.8 1.0 C D:GLU69 4.9 74.7 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119F


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 Y119F within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:61.8 occ:1.00 O E:ILE71 2.8 56.9 1.0 O E:PRO68 3.0 66.6 1.0 N E:ILE73 3.8 45.5 1.0 C E:ILE71 4.0 57.7 1.0 C E:PRO68 4.0 66.9 1.0 CD1 E:ILE73 4.2 46.2 1.0 CB E:ILE73 4.2 44.9 1.0 CA E:TRP72 4.3 49.6 1.0 CG1 E:ILE73 4.3 45.1 1.0 C E:TRP72 4.4 51.8 1.0 CG2 E:VAL5 4.5 79.0 1.0 N E:TRP72 4.6 51.4 1.0 CA E:ILE73 4.6 43.3 1.0 CA E:GLU69 4.6 64.3 1.0 O E:GLU69 4.7 66.3 1.0 N E:GLU69 4.7 64.4 1.0 C E:GLU69 4.9 66.0 1.0 O E:ILE73 4.9 48.4 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