Chlorine 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:

Sodium

(Na)

6 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine where determined in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A, PDB code: 6hyv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl405 b:40.2 occ:1.00 N A:PHE78 3.2 31.1 1.0 NH1 A:ARG85 3.4 34.7 1.0 CD2 A:PHE78 3.6 42.1 1.0 N A:ARG85 3.7 46.6 1.0 CB A:PHE78 3.8 34.6 1.0 CG A:ARG85 3.8 42.0 1.0 CA A:ARG77 3.9 25.7 1.0 CA A:ALA84 4.0 45.9 1.0 CA A:PHE78 4.1 31.7 1.0 C A:ARG77 4.1 31.9 1.0 CG2 A:VAL81 4.1 28.4 1.0 CG A:PHE78 4.2 38.0 1.0 CB A:ARG85 4.2 43.4 1.0 CD A:ARG85 4.3 41.2 1.0 CB A:ARG77 4.3 23.7 1.0 O A:PHE78 4.3 35.1 1.0 C A:ALA84 4.4 52.2 1.0 CB A:ALA84 4.5 46.9 1.0 CZ A:ARG85 4.5 48.2 1.0 CA A:ARG85 4.6 45.5 1.0 CE2 A:PHE78 4.7 45.7 1.0 C A:PHE78 4.7 33.6 1.0 NE A:ARG85 4.8 41.5 1.0 CG A:ARG77 4.9 33.5 1.0 CG1 A:VAL81 5.0 29.1 1.0

Chlorine binding site 2 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl406 b:66.5 occ:1.00 OD1 A:ASN139 3.1 41.8 1.0 N A:LEU180 3.2 29.4 1.0 CB A:LEU180 3.8 26.8 1.0 CA A:ARG179 3.8 33.3 1.0 C A:ARG179 4.0 35.1 1.0 CG A:ASN139 4.0 52.3 1.0 CA A:LEU180 4.1 28.2 1.0 CB A:SER134 4.3 37.6 1.0 CD A:ARG179 4.5 36.8 1.0 CB A:ARG179 4.6 29.8 1.0 ND2 A:ASN139 4.7 53.1 1.0 N A:ARG179 4.7 36.0 1.0 OG A:SER134 4.7 48.2 1.0 O A:ASP178 4.8 43.3 1.0 CG A:ARG179 4.9 36.1 1.0

Chlorine binding site 3 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl407 b:61.5 occ:1.00 N A:ALA175 3.5 31.8 1.0 CB A:ALA175 4.0 32.8 1.0 CA A:PHE174 4.1 29.8 1.0 C A:PHE174 4.3 34.3 1.0 CA A:ALA175 4.4 31.5 1.0 CB A:PHE174 4.5 31.1 1.0 O A:ALA175 5.0 36.0 1.0

Chlorine binding site 4 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 B:Cl405 b:40.8 occ:1.00 N B:PHE78 3.2 30.2 1.0 NH1 B:ARG85 3.3 30.9 1.0 CD2 B:PHE78 3.5 40.3 1.0 N B:ARG85 3.7 46.5 1.0 CB B:PHE78 3.7 32.9 1.0 CG B:ARG85 3.8 37.0 1.0 CA B:ARG77 4.0 27.5 1.0 CA B:PHE78 4.0 30.5 1.0 C B:ARG77 4.0 31.8 1.0 CG2 B:VAL81 4.1 39.8 1.0 CG B:PHE78 4.1 36.2 1.0 CA B:ALA84 4.1 49.9 1.0 CB B:ARG85 4.2 40.6 1.0 CD B:ARG85 4.3 34.4 1.0 O B:PHE78 4.3 39.8 1.0 CB B:ARG77 4.4 24.6 1.0 CZ B:ARG85 4.4 37.0 1.0 C B:ALA84 4.5 53.9 1.0 CB B:ALA84 4.6 51.0 1.0 CA B:ARG85 4.6 44.8 1.0 CE2 B:PHE78 4.6 43.7 1.0 C B:PHE78 4.7 36.8 1.0 NE B:ARG85 4.8 27.2 1.0 CG B:ARG77 4.9 37.0 1.0 CG1 B:VAL81 5.0 38.1 1.0

Chlorine binding site 5 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 C:Cl406 b:42.8 occ:1.00 N C:PHE78 3.2 29.3 1.0 NH1 C:ARG85 3.4 39.3 1.0 CD2 C:PHE78 3.6 37.7 1.0 N C:ARG85 3.7 44.0 1.0 CB C:PHE78 3.7 31.2 1.0 CG C:ARG85 3.8 36.6 1.0 CA C:ARG77 3.9 26.8 1.0 CA C:PHE78 4.0 29.6 1.0 C C:ARG77 4.0 30.1 1.0 CG2 C:VAL81 4.1 34.7 1.0 CA C:ALA84 4.1 45.1 1.0 CG C:PHE78 4.1 33.6 1.0 CB C:ARG85 4.2 39.7 1.0 O C:PHE78 4.2 38.7 1.0 CB C:ARG77 4.3 21.5 1.0 CD C:ARG85 4.3 40.4 1.0 C C:ALA84 4.5 49.6 1.0 CZ C:ARG85 4.5 47.6 1.0 CB C:ALA84 4.6 46.2 1.0 CA C:ARG85 4.6 42.6 1.0 C C:PHE78 4.6 35.9 1.0 CE2 C:PHE78 4.7 40.5 1.0 CG C:ARG77 4.8 37.2 1.0 NE C:ARG85 4.8 37.0 1.0 CG1 C:VAL81 5.0 33.1 1.0

Chlorine binding site 6 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 D:Cl405 b:43.1 occ:1.00 N D:PHE78 3.2 30.7 1.0 NH1 D:ARG85 3.4 27.4 1.0 CD2 D:PHE78 3.6 38.9 1.0 N D:ARG85 3.7 38.5 1.0 CB D:PHE78 3.8 33.6 1.0 CG D:ARG85 3.8 38.6 1.0 CA D:ARG77 3.9 28.8 1.0 C D:ARG77 4.0 32.7 1.0 CA D:PHE78 4.0 31.2 1.0 CA D:ALA84 4.1 38.7 1.0 CG2 D:VAL81 4.1 28.4 1.0 CG D:PHE78 4.2 36.3 1.0 CB D:ARG85 4.2 36.0 1.0 CB D:ARG77 4.2 26.2 1.0 O D:PHE78 4.3 37.8 1.0 CD D:ARG85 4.3 40.5 1.0 C D:ALA84 4.4 44.0 1.0 CZ D:ARG85 4.5 45.9 1.0 CB D:ALA84 4.6 40.1 1.0 CA D:ARG85 4.6 37.4 1.0 C D:PHE78 4.7 35.1 1.0 CE2 D:PHE78 4.7 41.4 1.0 CG D:ARG77 4.8 31.4 1.0 NE D:ARG85 4.8 41.1 1.0

Chlorine binding site 7 out of 7 in the The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Glic Pentameric Ligand-Gated Ion Channel Mutant Y119A within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl405 b:49.0 occ:1.00 N E:PHE78 3.2 36.3 1.0 NH1 E:ARG85 3.4 30.7 1.0 CD2 E:PHE78 3.5 45.5 1.0 N E:ARG85 3.7 47.5 1.0 CB E:PHE78 3.7 39.4 1.0 CG E:ARG85 3.8 40.3 1.0 CA E:ARG77 4.0 33.2 1.0 CA E:PHE78 4.0 37.2 1.0 C E:ARG77 4.0 38.0 1.0 CG2 E:VAL81 4.1 39.7 1.0 CA E:ALA84 4.1 48.9 1.0 CG E:PHE78 4.1 41.9 1.0 CB E:ARG85 4.2 42.3 1.0 CD E:ARG85 4.3 34.1 1.0 O E:PHE78 4.3 42.7 1.0 CB E:ARG77 4.3 31.6 1.0 C E:ALA84 4.4 53.2 1.0 CZ E:ARG85 4.5 45.5 1.0 CB E:ALA84 4.5 49.9 1.0 CA E:ARG85 4.6 45.9 1.0 CE2 E:PHE78 4.6 48.8 1.0 C E:PHE78 4.7 40.7 1.0 NE E:ARG85 4.8 34.7 1.0 CG E:ARG77 4.9 46.5 1.0 CG1 E:VAL81 5.0 37.5 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