Sodium in PDB 6hz1: The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C, PDB code: 6hz1 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 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.900, 132.950, 160.060, 90.00, 102.41, 90.00
R / Rfree (%)	20.5 / 21.6

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C 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 E243C (pdb code 6hz1). 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 E243C, PDB code: 6hz1:
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 E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:69.1 occ:1.00 O A:ILE71 2.6 64.0 1.0 N A:ILE73 3.2 52.3 1.0 CA A:TRP72 3.6 56.8 1.0 O A:PRO68 3.7 90.3 1.0 C A:ILE71 3.7 65.7 1.0 C A:TRP72 3.8 58.9 1.0 CB A:ILE73 3.9 52.6 1.0 CG2 A:VAL5 4.0 95.4 1.0 CA A:ILE73 4.1 50.1 1.0 N A:TRP72 4.1 59.1 1.0 O A:ILE73 4.3 50.0 1.0 CG1 A:ILE73 4.3 53.1 1.0 CD1 A:ILE73 4.5 60.1 1.0 C A:ILE73 4.7 51.1 1.0 C A:PRO68 4.8 90.9 1.0 O A:TRP72 4.8 59.7 1.0 CB A:TRP72 4.9 54.7 1.0

Sodium binding site 2 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:77.1 occ:1.00 OG1 B:THR226 4.0 31.9 1.0 OG1 C:THR226 4.2 36.0 1.0 OG1 A:THR226 4.2 37.3 1.0 OG1 D:THR226 4.5 37.2 1.0 OG1 E:THR226 4.6 35.2 1.0 CG2 B:THR226 4.9 26.8 1.0 CG2 A:THR226 5.0 28.8 1.0

Sodium binding site 3 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:54.8 occ:1.00 O B:ILE71 2.7 48.6 1.0 N B:ILE73 3.4 45.5 1.0 O B:PRO68 3.6 61.7 1.0 C B:ILE71 3.8 48.4 1.0 CA B:TRP72 3.8 43.4 1.0 CG2 B:VAL5 3.9 88.8 1.0 C B:TRP72 4.0 48.4 1.0 CB B:ILE73 4.2 47.9 1.0 N B:TRP72 4.2 44.0 1.0 CA B:ILE73 4.3 44.6 1.0 O B:ILE73 4.5 48.4 1.0 CD1 B:ILE73 4.6 59.4 1.0 CG1 B:ILE73 4.7 49.3 1.0 C B:PRO68 4.7 63.2 1.0 C B:ILE73 5.0 48.2 1.0 O B:GLU69 5.0 62.8 1.0 CB B:VAL5 5.0 89.1 1.0

Sodium binding site 4 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na405 b:57.7 occ:1.00 O C:ILE71 2.7 56.5 1.0 N C:ILE73 3.4 47.6 1.0 O C:PRO68 3.6 76.2 1.0 C C:ILE71 3.8 57.5 1.0 CA C:TRP72 3.8 50.2 1.0 CG2 C:VAL5 3.9 94.5 1.0 C C:TRP72 4.0 53.4 1.0 CB C:ILE73 4.2 48.5 1.0 N C:TRP72 4.2 51.7 1.0 CA C:ILE73 4.3 45.8 1.0 CG1 C:ILE73 4.6 49.0 1.0 O C:ILE73 4.6 48.8 1.0 CD1 C:ILE73 4.6 55.4 1.0 C C:PRO68 4.7 76.8 1.0 O C:GLU69 5.0 72.5 1.0

Sodium binding site 5 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:83.7 occ:1.00 O D:ILE71 2.7 68.4 1.0 N D:ILE73 3.4 55.1 1.0 O D:PRO68 3.6 91.6 1.0 C D:ILE71 3.8 69.1 1.0 CA D:TRP72 3.8 60.4 1.0 CG2 D:VAL5 3.9 94.1 1.0 C D:TRP72 4.0 62.2 1.0 CB D:ILE73 4.2 56.0 1.0 N D:TRP72 4.2 62.5 1.0 CA D:ILE73 4.3 52.8 1.0 O D:ILE73 4.5 52.3 1.0 CG1 D:ILE73 4.6 57.1 1.0 CD1 D:ILE73 4.6 64.5 1.0 C D:PRO68 4.7 92.5 1.0 O D:GLU69 5.0 86.0 1.0 CB D:VAL5 5.0 94.6 1.0 C D:ILE73 5.0 52.8 1.0

Sodium binding site 6 out of 6 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant E243C


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 E243C within 5.0Å range: probe atom residue distance (Å) B Occ E:Na406 b:71.9 occ:1.00 O E:ILE71 2.7 61.2 1.0 N E:ILE73 3.4 54.0 1.0 O E:PRO68 3.6 77.8 1.0 C E:ILE71 3.8 62.5 1.0 CA E:TRP72 3.8 56.9 1.0 CG2 E:VAL5 3.9 0.5 1.0 C E:TRP72 4.0 60.0 1.0 CB E:ILE73 4.2 55.2 1.0 N E:TRP72 4.2 57.9 1.0 CA E:ILE73 4.3 52.2 1.0 CG1 E:ILE73 4.5 56.0 1.0 O E:ILE73 4.6 52.5 1.0 CD1 E:ILE73 4.6 63.8 1.0 C E:PRO68 4.7 78.5 1.0 O E:GLU69 5.0 76.4 1.0 CB E:VAL5 5.0 1.0 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