Sodium in PDB 6hyx: The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C, PDB code: 6hyx 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 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.810, 134.230, 160.300, 90.00, 102.09, 90.00
R / Rfree (%)	20.9 / 22.4

The structure of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C (pdb code 6hyx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C, PDB code: 6hyx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:36.1 occ:1.00 NH2 A:ARG85 3.3 72.8 1.0 O A:PRO74 3.8 66.5 1.0 O A:ILE76 4.0 53.3 1.0 N A:ILE76 4.1 52.9 1.0 OH A:TYR102 4.3 61.8 1.0 OE1 A:GLU104 4.4 70.6 1.0 CZ A:ARG85 4.6 80.7 1.0 CG2 A:ILE73 4.6 75.0 1.0 CA A:GLU75 4.8 58.6 1.0 CB A:ILE76 4.8 52.8 1.0 CZ A:TYR102 4.8 63.1 1.0 CA A:ILE76 4.8 50.7 1.0 C A:ILE76 4.8 52.9 1.0 C A:PRO74 4.9 68.2 1.0 C A:GLU75 4.9 59.0 1.0

Sodium binding site 2 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:52.2 occ:1.00 C12 B:LMT401 4.9 26.4 1.0

Sodium binding site 3 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:24.0 occ:1.00 NH2 B:ARG85 3.2 60.6 1.0 O B:PRO74 3.5 46.8 1.0 O B:ILE76 3.9 45.6 1.0 N B:ILE76 4.0 38.2 1.0 OH B:TYR102 4.3 47.7 1.0 OE1 B:GLU104 4.5 54.5 1.0 CG2 B:ILE73 4.5 51.6 1.0 CZ B:ARG85 4.6 71.4 1.0 CB B:ILE76 4.6 39.4 1.0 CA B:ILE76 4.7 37.3 1.0 C B:PRO74 4.7 48.3 1.0 CA B:GLU75 4.7 42.8 1.0 C B:ILE76 4.7 43.4 1.0 CZ B:TYR102 4.8 48.2 1.0 CD1 B:LEU45 4.8 49.9 1.0 C B:GLU75 4.9 43.4 1.0 CG1 B:ILE76 4.9 41.0 1.0

Sodium binding site 4 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:21.6 occ:1.00 O C:PRO74 3.4 66.3 1.0 NH2 C:ARG85 3.6 86.1 1.0 N C:ILE76 4.0 54.2 1.0 O C:ILE76 4.1 58.4 1.0 CG2 C:ILE73 4.2 66.8 1.0 OH C:TYR102 4.3 68.2 1.0 C C:PRO74 4.5 66.8 1.0 CA C:GLU75 4.6 59.9 1.0 OE1 C:GLU104 4.6 62.5 1.0 CB C:ILE76 4.7 56.2 1.0 CA C:ILE76 4.8 53.8 1.0 CZ C:TYR102 4.8 67.0 1.0 C C:GLU75 4.8 59.8 1.0 CD1 C:LEU45 4.9 55.4 1.0 C C:ILE76 4.9 58.1 1.0 CZ C:ARG85 4.9 85.9 1.0 CG1 C:ILE76 5.0 59.0 1.0

Sodium binding site 5 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:69.0 occ:1.00 OG1 D:THR226 4.1 53.7 1.0 CG2 D:THR226 4.3 46.8 1.0 OG1 E:THR226 4.5 59.1 1.0 CG2 C:THR226 4.5 57.5 1.0 OG1 C:THR226 4.5 62.8 1.0 CG2 E:THR226 4.8 48.3 1.0 CB D:THR226 4.9 47.8 1.0

Sodium binding site 6 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


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 Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:37.6 occ:1.00 NH2 D:ARG85 3.4 68.8 1.0 O D:PRO74 3.5 73.8 1.0 O D:ILE76 3.9 61.8 1.0 N D:ILE76 3.9 60.8 1.0 OH D:TYR102 4.4 71.4 1.0 OE1 D:GLU104 4.5 65.7 1.0 CG2 D:ILE73 4.5 84.9 1.0 CA D:GLU75 4.6 67.2 1.0 CB D:ILE76 4.6 62.4 1.0 CA D:ILE76 4.6 59.5 1.0 C D:PRO74 4.6 74.9 1.0 CZ D:ARG85 4.7 80.7 1.0 C D:ILE76 4.7 61.5 1.0 C D:GLU75 4.7 66.1 1.0 CZ D:TYR102 4.9 75.0 1.0 CG1 D:ILE76 4.9 64.5 1.0 CD1 D:LEU45 4.9 67.9 1.0

Sodium binding site 7 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y197F-P250C within 5.0Å range: probe atom residue distance (Å) B Occ E:Na402 b:31.1 occ:1.00 NH2 E:ARG85 3.5 91.2 1.0 O E:PRO74 3.6 74.6 1.0 N E:ILE76 4.2 63.1 1.0 O E:ILE76 4.2 62.0 1.0 OH E:TYR102 4.2 69.0 1.0 CG2 E:ILE73 4.4 75.9 1.0 OE1 E:GLU104 4.4 64.0 1.0 C E:PRO74 4.7 76.6 1.0 CZ E:TYR102 4.7 66.8 1.0 CA E:GLU75 4.8 71.5 1.0 CZ E:ARG85 4.8 90.8 1.0 CB E:ILE76 4.8 62.3 1.0 CA E:ILE76 4.9 60.8 1.0 CD1 E:LEU45 4.9 56.4 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