Sodium in PDB 6hyz: The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C, PDB code: 6hyz 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 / 3.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.220, 132.939, 159.951, 90.00, 101.98, 90.00
R / Rfree (%)	22.6 / 23.4

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C 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 K248C (pdb code 6hyz). 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 K248C, PDB code: 6hyz:
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 K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:93.9 occ:1.00 O A:ILE71 2.3 0.5 1.0 O A:PRO68 3.3 0.2 1.0 C A:ILE71 3.5 0.3 1.0 N A:ILE73 3.7 94.8 1.0 CA A:TRP72 4.0 99.9 1.0 CB A:ILE73 4.2 95.2 1.0 C A:TRP72 4.2 0.8 1.0 N A:TRP72 4.2 0.3 1.0 CG1 A:ILE73 4.3 95.8 1.0 O A:GLU69 4.4 0.2 1.0 C A:PRO68 4.4 1.0 1.0 CA A:ILE73 4.5 93.0 1.0 CD1 A:ILE73 4.6 0.4 1.0 C A:GLU69 4.7 0.2 1.0 CA A:ILE71 4.7 0.7 1.0 N A:ILE71 4.7 0.6 1.0 CA A:GLU69 4.8 0.6 1.0 O A:ILE73 4.8 94.5 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:0.2 occ:1.00 O B:ILE71 2.3 94.5 1.0 O B:PRO68 3.1 0.3 1.0 C B:ILE71 3.5 95.2 1.0 N B:ILE73 3.7 86.2 1.0 CB B:ILE73 4.1 87.1 1.0 CA B:TRP72 4.1 89.3 1.0 CG1 B:ILE73 4.1 87.5 1.0 C B:TRP72 4.2 91.0 1.0 N B:TRP72 4.2 90.4 1.0 C B:PRO68 4.2 0.3 1.0 O B:GLU69 4.4 0.7 1.0 CD1 B:ILE73 4.4 94.3 1.0 CA B:ILE73 4.5 84.5 1.0 C B:GLU69 4.6 0.5 1.0 N B:ILE71 4.6 95.0 1.0 CA B:ILE71 4.6 93.5 1.0 CA B:GLU69 4.7 0.0 1.0 O B:ILE73 4.8 88.1 1.0 N B:GLU69 4.9 0.6 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:94.1 occ:1.00 OG1 C:THR226 3.7 97.2 1.0 O D:HOH508 3.8 1.0 1.0 OG1 D:THR226 3.9 94.5 1.0 O B:HOH509 4.2 0.3 1.0 OG1 B:THR226 4.5 96.4 1.0 OG1 E:THR226 4.5 94.5 1.0 CG2 C:THR226 4.7 94.5 1.0 OG1 A:THR226 4.8 92.2 1.0 CB C:THR226 4.8 96.4 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:81.5 occ:1.00 O C:ILE71 2.4 0.5 1.0 O C:PRO68 2.9 0.1 1.0 C C:ILE71 3.6 0.2 1.0 N C:ILE73 4.0 93.8 1.0 C C:PRO68 4.0 0.7 1.0 O C:GLU69 4.2 0.7 1.0 CB C:ILE73 4.2 94.2 1.0 CG1 C:ILE73 4.2 94.6 1.0 CD1 C:ILE73 4.4 0.1 1.0 CA C:TRP72 4.4 98.7 1.0 CA C:GLU69 4.4 0.5 1.0 C C:GLU69 4.4 0.7 1.0 N C:TRP72 4.4 0.0 1.0 C C:TRP72 4.5 99.5 1.0 N C:ILE71 4.6 0.2 1.0 N C:GLU69 4.6 0.4 1.0 CA C:ILE73 4.7 91.7 1.0 CA C:ILE71 4.7 0.9 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:0.6 occ:1.00 O D:ILE71 2.3 0.1 1.0 O D:PRO68 3.2 0.7 1.0 C D:ILE71 3.5 0.1 1.0 N D:ILE73 3.6 0.8 1.0 CA D:TRP72 4.0 0.6 1.0 CB D:ILE73 4.1 0.4 1.0 C D:TRP72 4.1 0.9 1.0 CG1 D:ILE73 4.1 0.5 1.0 N D:TRP72 4.2 0.5 1.0 C D:PRO68 4.3 0.1 1.0 CA D:ILE73 4.4 99.6 1.0 O D:GLU69 4.4 1.0 1.0 CD1 D:ILE73 4.4 0.9 1.0 CA D:ILE71 4.6 0.5 1.0 N D:ILE71 4.7 0.1 1.0 C D:GLU69 4.7 0.2 1.0 CA D:GLU69 4.8 0.9 1.0 O D:ILE73 4.8 0.2 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant K248C


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 K248C within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:0.3 occ:1.00 O E:PRO68 2.4 0.9 1.0 O E:ILE71 2.4 0.6 1.0 C E:PRO68 3.5 0.5 1.0 C E:ILE71 3.7 0.2 1.0 O E:GLU69 3.8 0.8 1.0 CA E:GLU69 3.9 0.2 1.0 C E:GLU69 4.0 0.6 1.0 N E:GLU69 4.1 0.6 1.0 CD1 E:ILE73 4.2 0.4 1.0 CG1 E:ILE73 4.2 0.6 1.0 N E:ILE73 4.3 0.8 1.0 N E:ILE71 4.3 0.6 1.0 CB E:ILE73 4.4 0.1 1.0 CA E:ILE71 4.6 1.0 1.0 N E:TRP72 4.6 0.8 1.0 CA E:PRO68 4.6 0.2 1.0 CA E:TRP72 4.7 0.3 1.0 C E:TRP72 4.8 0.8 1.0 N E:ALA70 4.8 0.6 1.0 CA E:ILE73 5.0 98.4 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