Chlorine in PDB 4il4: The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm

The structure of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm, PDB code: 4il4 was solved by L.Sauguet, L.Malherbe, P.J.Corringer, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.069, 132.491, 160.219, 90.00, 102.70, 90.00
R / Rfree (%)	19.5 / 20.9

The structure of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

The binding sites of Chlorine atom in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm (pdb code 4il4). 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 Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm, PDB code: 4il4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:79.1 occ:1.00 N A:PHE78 3.3 72.0 1.0 N A:ARG85 3.6 90.4 1.0 NH1 A:ARG85 3.6 80.7 1.0 CD2 A:PHE78 3.8 81.9 1.0 CB A:PHE78 3.9 75.4 1.0 CA A:ALA84 3.9 91.0 1.0 CA A:ARG77 4.0 66.9 1.0 CG2 A:VAL81 4.0 69.7 1.0 C A:ARG77 4.1 74.4 1.0 CA A:PHE78 4.2 72.3 1.0 CG A:ARG85 4.2 85.1 1.0 O A:PHE78 4.2 75.9 1.0 CB A:ARG85 4.2 86.5 1.0 C A:ALA84 4.3 95.1 1.0 CB A:ARG77 4.3 66.1 1.0 CG A:PHE78 4.3 78.5 1.0 CD A:ARG85 4.4 87.0 1.0 CB A:ALA84 4.4 91.8 1.0 CA A:ARG85 4.5 90.2 1.0 CG A:ARG77 4.6 76.9 1.0 CZ A:ARG85 4.7 98.3 1.0 C A:PHE78 4.7 74.1 1.0 CE2 A:PHE78 4.8 85.4 1.0 NE A:ARG85 5.0 93.3 1.0

Chlorine binding site 2 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:0.3 occ:1.00 N A:LEU180 3.3 77.3 1.0 OD1 A:ASN139 3.3 93.4 1.0 CA A:ARG179 3.8 76.8 1.0 CB A:LEU180 3.9 77.0 1.0 C A:ARG179 4.0 81.1 1.0 CA A:LEU180 4.2 77.2 1.0 O A:ASP178 4.2 89.5 1.0 CG A:ASN139 4.4 0.8 1.0 CD A:ARG179 4.5 89.9 1.0 CB A:ARG179 4.6 71.1 1.0 CB A:SER134 4.6 84.0 1.0 N A:ARG179 4.7 79.1 1.0 C A:ASP178 4.8 87.5 1.0 CG A:ARG179 4.9 77.4 1.0

Chlorine binding site 3 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:0.5 occ:1.00 N A:ALA175 3.6 75.5 1.0 CB A:ALA175 4.0 77.1 1.0 CA A:PHE174 4.2 73.2 1.0 C A:PHE174 4.4 76.8 1.0 CB A:PHE174 4.4 74.9 1.0 CA A:ALA175 4.4 76.5 1.0 O A:ALA175 4.9 84.7 1.0

Chlorine binding site 4 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:92.2 occ:1.00 N B:PHE78 3.2 75.9 1.0 NH1 B:ARG85 3.5 69.1 1.0 CD2 B:PHE78 3.5 84.7 1.0 N B:ARG85 3.6 91.4 1.0 CB B:PHE78 3.7 79.1 1.0 CA B:ARG77 4.0 72.1 1.0 CG2 B:VAL81 4.0 78.0 1.0 CA B:PHE78 4.0 76.6 1.0 CG B:ARG85 4.1 88.2 1.0 C B:ARG77 4.1 77.6 1.0 CA B:ALA84 4.1 94.5 1.0 CG B:PHE78 4.1 82.1 1.0 CB B:ARG85 4.1 85.4 1.0 O B:PHE78 4.2 81.5 1.0 CD B:ARG85 4.2 89.9 1.0 CB B:ARG77 4.3 70.7 1.0 C B:ALA84 4.4 97.0 1.0 CA B:ARG85 4.5 90.1 1.0 CE2 B:PHE78 4.6 88.4 1.0 CB B:ALA84 4.6 95.5 1.0 CZ B:ARG85 4.6 91.9 1.0 C B:PHE78 4.6 80.8 1.0 CG B:ARG77 4.7 80.4 1.0 NE B:ARG85 4.9 91.2 1.0

Chlorine binding site 5 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:81.8 occ:1.00 N C:PHE78 3.4 74.7 1.0 NH1 C:ARG85 3.5 80.2 1.0 N C:ARG85 3.5 91.5 1.0 CD2 C:PHE78 3.7 82.6 1.0 CB C:PHE78 3.9 76.8 1.0 CA C:ALA84 4.0 92.3 1.0 CG C:ARG85 4.0 88.5 1.0 CA C:ARG77 4.1 71.7 1.0 CG2 C:VAL81 4.1 84.7 1.0 CB C:ARG85 4.1 87.5 1.0 C C:ARG77 4.2 77.3 1.0 CA C:PHE78 4.2 74.6 1.0 CD C:ARG85 4.2 87.4 1.0 CG C:PHE78 4.3 79.9 1.0 C C:ALA84 4.3 95.9 1.0 CB C:ARG77 4.3 70.7 1.0 O C:PHE78 4.4 81.8 1.0 CA C:ARG85 4.5 90.4 1.0 CB C:ALA84 4.5 93.1 1.0 CZ C:ARG85 4.6 95.2 1.0 CG C:ARG77 4.6 84.8 1.0 CE2 C:PHE78 4.7 85.8 1.0 C C:PHE78 4.8 79.0 1.0 NE C:ARG85 4.8 84.6 1.0

Chlorine binding site 6 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl402 b:86.9 occ:1.00 N D:PHE78 3.3 69.3 1.0 NH1 D:ARG85 3.4 67.5 1.0 N D:ARG85 3.5 89.8 1.0 CD2 D:PHE78 3.5 78.8 1.0 CB D:PHE78 3.8 72.8 1.0 CG D:ARG85 4.0 86.3 1.0 CA D:ARG77 4.0 65.2 1.0 CB D:ARG85 4.1 85.8 1.0 CA D:ALA84 4.1 91.4 1.0 C D:ARG77 4.1 71.9 1.0 CA D:PHE78 4.1 69.9 1.0 CG D:PHE78 4.1 75.7 1.0 CG2 D:VAL81 4.1 75.1 1.0 CD D:ARG85 4.1 82.2 1.0 C D:ALA84 4.3 95.1 1.0 O D:PHE78 4.3 76.6 1.0 CB D:ARG77 4.3 63.2 1.0 CA D:ARG85 4.4 89.5 1.0 CZ D:ARG85 4.5 91.5 1.0 CE2 D:PHE78 4.6 82.4 1.0 CB D:ALA84 4.6 92.4 1.0 C D:PHE78 4.7 74.6 1.0 CG D:ARG77 4.7 73.0 1.0 NE D:ARG85 4.8 84.1 1.0 O D:ILE76 5.0 71.9 1.0

Chlorine binding site 7 out of 7 in the The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Pentameric Ligand-Gated Ion Channel Glic in Complex with Se-Ddm within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl402 b:84.4 occ:1.00 N E:PHE78 3.2 74.9 1.0 NH1 E:ARG85 3.5 70.6 1.0 N E:ARG85 3.6 91.8 1.0 CD2 E:PHE78 3.7 85.0 1.0 CB E:PHE78 3.8 78.9 1.0 CA E:ARG77 3.9 70.2 1.0 CA E:ALA84 4.1 95.9 1.0 C E:ARG77 4.1 75.8 1.0 CG2 E:VAL81 4.1 86.3 1.0 CA E:PHE78 4.1 76.0 1.0 CG E:ARG85 4.2 84.0 1.0 CB E:ARG77 4.2 70.2 1.0 CG E:PHE78 4.2 82.1 1.0 O E:PHE78 4.2 80.9 1.0 CB E:ARG85 4.2 84.5 1.0 CD E:ARG85 4.3 82.4 1.0 C E:ALA84 4.4 98.1 1.0 CB E:ALA84 4.5 96.8 1.0 CA E:ARG85 4.6 90.1 1.0 CG E:ARG77 4.6 84.1 1.0 CZ E:ARG85 4.6 89.0 1.0 C E:PHE78 4.7 79.6 1.0 CE2 E:PHE78 4.7 88.3 1.0 NE E:ARG85 4.9 82.1 1.0 O E:ILE76 5.0 76.5 1.0

L.Sauguet, F.Poitevin, S.Murail, C.Van Renterghem, G.Moraga-Cid, L.Malherbe, A.W.Thompson, P.Koehl, P.J.Corringer, M.Baaden, M.Delarue. Structural Basis For Ion Permeation Mechanism in Pentameric Ligand-Gated Ion Channels. Embo J. V. 32 728 2013.
ISSN: ISSN 0261-4189
PubMed: 23403925
DOI: 10.1038/EMBOJ.2013.17