Chlorine in PDB 6v4s: A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain

The structure of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain, PDB code: 6v4s was solved by M.Delarue, H.D.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.04 / 3.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.406, 337.254, 111.812, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 26.8

The structure of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain also contains other interesting chemical elements:

Calcium	(Ca)	5 atoms
Sodium	(Na)	7 atoms

The binding sites of Chlorine atom in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain (pdb code 6v4s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain, PDB code: 6v4s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:0.9 occ:1.00 ND2 A:ASN560 2.8 0.1 1.0 CG A:ASN560 4.0 95.2 1.0 CE1 E:PHE559 4.3 86.5 1.0 OD1 A:ASN560 4.5 0.7 1.0 CG2 E:THR562 4.5 0.9 1.0 CD1 E:PHE559 4.6 80.1 1.0 O E:ARG521 4.7 64.0 1.0

Chlorine binding site 2 out of 5 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl702 b:0.4 occ:1.00 ND2 E:ASN560 3.1 92.7 1.0 CE1 D:PHE559 4.2 91.9 1.0 O D:ARG521 4.2 68.2 1.0 CG2 D:THR562 4.3 1.0 1.0 CG E:ASN560 4.4 85.3 1.0 CG D:ARG521 4.5 93.6 1.0 CD1 D:PHE559 4.7 85.0 1.0 OD1 E:ASN560 4.7 0.2 1.0 NH1 D:ARG521 4.8 0.5 1.0 CZ D:ARG521 4.9 0.5 1.0

Chlorine binding site 3 out of 5 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl702 b:0.1 occ:1.00 ND2 D:ASN560 2.9 1.0 1.0 CE1 C:PHE559 3.8 94.3 1.0 CD1 C:PHE559 4.0 86.9 1.0 CG D:ASN560 4.1 92.8 1.0 CG2 C:THR562 4.4 98.2 1.0 OD1 D:ASN560 4.7 96.6 1.0 O C:ARG521 4.8 78.9 1.0 CD1 D:PHE584 4.8 76.0 1.0 CG D:PHE584 4.9 80.3 1.0 CG C:PRO525 5.0 91.4 1.0

Chlorine binding site 4 out of 5 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl704 b:0.0 occ:1.00 ND2 C:ASN560 3.2 0.7 1.0 CE1 B:PHE559 4.0 0.2 1.0 CG C:ASN560 4.4 0.8 1.0 CD1 B:PHE559 4.4 98.9 1.0 O B:ARG521 4.5 65.5 1.0 CG B:PRO525 4.6 0.9 1.0 CG C:PHE584 4.7 75.6 1.0 CD1 C:PHE584 4.8 71.9 1.0 CB C:PHE584 4.8 90.4 1.0 OD1 C:ASN560 4.8 0.1 1.0 CB B:PRO525 4.9 91.2 1.0 CG2 B:THR562 5.0 0.3 1.0

Chlorine binding site 5 out of 5 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl703 b:0.4 occ:1.00 ND2 B:ASN560 3.1 0.8 1.0 CG B:ASN560 4.1 0.1 1.0 CE1 A:PHE559 4.3 95.1 1.0 CG B:PHE584 4.4 77.4 1.0 CB B:PHE584 4.5 87.3 1.0 CD1 B:PHE584 4.5 78.0 1.0 OD1 B:ASN560 4.5 0.0 1.0 CD1 A:PHE559 4.6 90.7 1.0 CG A:PRO525 4.7 94.7 1.0 O A:ARG521 4.9 83.6 1.0 O B:MET580 4.9 95.8 1.0 CD2 B:PHE584 5.0 76.3 1.0

H.Hu, R.Howard, U.Bastolla, E.Lindahl, M.Delarue. Structural Basis For Allosteric Transitions of A Multi-Domain Pentameric Ligand-Gated Ion Channel Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1922701117