Chlorine in PDB 3wtl: Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid

The structure of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid, PDB code: 3wtl was solved by T.Okajima, M.Ihara, A.Yamashita, T.Oda, K.Matsuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.59 / 2.30
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	74.741, 74.741, 351.003, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 26.5

The binding sites of Chlorine atom in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid (pdb code 3wtl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid, PDB code: 3wtl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:19.0 occ:1.00 CL A:N1Y301 0.0 19.0 1.0 C1 A:N1Y301 1.7 31.7 1.0 N1 A:N1Y301 2.6 32.3 1.0 C6 A:N1Y301 2.7 33.5 1.0 O B:LEU112 3.0 30.8 1.0 O A:HOH481 3.3 21.1 1.0 N B:ARG104 3.5 31.4 1.0 C B:LEU112 3.6 32.8 1.0 N B:MET114 3.7 33.5 1.0 CA B:TYR113 3.7 32.3 1.0 CG B:LEU112 3.7 40.3 1.0 CB B:ARG104 3.8 34.0 1.0 O B:LEU102 3.8 23.1 1.0 C2 A:N1Y301 3.9 35.5 1.0 N B:TYR113 3.9 32.2 1.0 CA B:ALA103 3.9 28.2 1.0 C5 A:N1Y301 4.0 35.1 1.0 C B:ALA103 4.0 29.1 1.0 C B:TYR113 4.1 31.5 1.0 CG2 A:THR144 4.2 28.4 1.0 CA B:ARG104 4.3 32.6 1.0 CD2 B:LEU112 4.4 40.0 1.0 CB B:LEU112 4.4 37.4 1.0 C3 A:N1Y301 4.5 36.6 1.0 CD1 B:LEU112 4.6 39.6 1.0 CB B:MET114 4.6 39.7 1.0 CA B:LEU112 4.7 34.5 1.0 C B:LEU102 4.7 25.2 1.0 CA B:MET114 4.7 34.8 1.0 N B:ALA103 4.8 25.6 1.0 CB B:ALA103 4.9 26.9 1.0 CB A:THR144 5.0 29.1 1.0 O B:ALA103 5.0 30.0 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:7.7 occ:1.00 CL B:N1Y301 0.0 7.7 1.0 C1 B:N1Y301 1.7 22.8 1.0 N1 B:N1Y301 2.6 23.2 1.0 C6 B:N1Y301 2.7 26.0 1.0 O C:LEU112 3.0 30.8 1.0 O B:HOH487 3.2 22.2 1.0 C C:LEU112 3.6 32.2 1.0 N C:ARG104 3.6 29.4 1.0 CB C:ARG104 3.6 31.2 1.0 CG C:LEU112 3.7 33.7 1.0 CA C:TYR113 3.7 29.2 1.0 N C:MET114 3.8 28.8 1.0 C2 B:N1Y301 3.9 24.7 1.0 O C:LEU102 3.9 25.7 1.0 N C:TYR113 3.9 29.8 1.0 C5 B:N1Y301 4.0 26.2 1.0 C C:ALA103 4.1 29.3 1.0 CA C:ALA103 4.1 27.8 1.0 C C:TYR113 4.2 28.1 1.0 CA C:ARG104 4.3 29.3 1.0 CD2 C:LEU112 4.3 34.2 1.0 CG2 B:THR144 4.4 19.9 1.0 CB C:LEU112 4.4 31.0 1.0 C3 B:N1Y301 4.5 28.5 1.0 CD1 C:LEU112 4.6 34.4 1.0 CA C:LEU112 4.7 33.0 1.0 CB C:MET114 4.7 35.7 1.0 CG C:ARG104 4.7 33.9 1.0 C C:LEU102 4.8 26.9 1.0 CA C:MET114 4.8 30.9 1.0 N C:ALA103 4.9 27.1 1.0 O C:ALA103 4.9 28.3 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:4.5 occ:1.00 CL C:N1Y301 0.0 4.5 1.0 C1 C:N1Y301 1.7 20.4 1.0 N1 C:N1Y301 2.6 25.4 1.0 C6 C:N1Y301 2.7 24.6 1.0 O D:LEU112 2.9 24.0 1.0 N D:ARG104 3.4 26.4 1.0 C D:LEU112 3.4 24.8 1.0 O C:HOH490 3.4 15.7 1.0 CB D:ARG104 3.4 26.4 1.0 CA D:TYR113 3.7 24.8 1.0 N D:TYR113 3.8 23.3 1.0 N D:MET114 3.9 26.5 1.0 C2 C:N1Y301 3.9 25.2 1.0 C D:ALA103 3.9 25.1 1.0 CA D:ALA103 4.0 23.1 1.0 C5 C:N1Y301 4.0 27.5 1.0 CB D:LEU112 4.1 27.9 1.0 CA D:ARG104 4.1 25.2 1.0 O D:LEU102 4.1 25.7 1.0 C D:TYR113 4.2 24.8 1.0 CA D:LEU112 4.4 25.0 1.0 C3 C:N1Y301 4.5 28.6 1.0 CG D:ARG104 4.6 30.4 1.0 CG2 C:THR144 4.6 24.6 1.0 CB D:MET114 4.7 34.2 1.0 O D:ALA103 4.8 24.2 1.0 CG D:MET114 4.8 41.4 1.0 C D:LEU102 4.9 24.3 1.0 N D:ALA103 4.9 22.6 1.0 CA D:MET114 4.9 31.3 1.0 CB D:ALA103 4.9 16.7 1.0 CE D:MET114 5.0 49.8 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:5.9 occ:1.00 CL D:N1Y301 0.0 5.9 1.0 C1 D:N1Y301 1.7 18.3 1.0 N1 D:N1Y301 2.6 24.0 1.0 C6 D:N1Y301 2.7 24.8 1.0 O E:LEU112 2.9 33.1 1.0 O D:HOH498 3.3 17.8 1.0 N E:ARG104 3.5 28.0 1.0 C E:LEU112 3.5 32.1 1.0 CB E:ARG104 3.6 31.9 1.0 CG E:LEU112 3.7 32.2 1.0 CA E:TYR113 3.7 25.7 1.0 N E:MET114 3.7 26.2 1.0 O E:LEU102 3.8 24.6 1.0 N E:TYR113 3.9 28.5 1.0 C2 D:N1Y301 3.9 25.2 1.0 C5 D:N1Y301 4.0 25.2 1.0 CA E:ALA103 4.0 26.2 1.0 C E:ALA103 4.1 29.3 1.0 CG2 D:THR144 4.1 24.2 1.0 C E:TYR113 4.2 24.9 1.0 CA E:ARG104 4.2 29.5 1.0 CD2 E:LEU112 4.2 31.4 1.0 CB E:LEU112 4.3 30.7 1.0 C3 D:N1Y301 4.5 27.0 1.0 CA E:LEU112 4.6 31.3 1.0 CD1 E:LEU112 4.7 31.3 1.0 C E:LEU102 4.7 25.0 1.0 CB E:MET114 4.7 31.0 1.0 CG E:ARG104 4.8 37.0 1.0 CB D:THR144 4.8 24.4 1.0 CA E:MET114 4.8 26.3 1.0 N E:ALA103 4.9 24.7 1.0 CB E:TYR113 5.0 22.2 1.0 CD1 E:TYR113 5.0 27.3 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl301 b:11.2 occ:1.00 CL E:N1Y301 0.0 11.2 1.0 C1 E:N1Y301 1.7 23.2 1.0 N1 E:N1Y301 2.6 25.4 1.0 C6 E:N1Y301 2.7 26.9 1.0 O A:LEU112 2.9 30.9 1.0 O A:HOH482 3.2 22.6 1.0 N A:ARG104 3.6 33.5 1.0 CB A:ARG104 3.6 33.5 1.0 C A:LEU112 3.6 31.9 1.0 CG A:LEU112 3.7 36.6 1.0 C2 E:N1Y301 3.9 27.6 1.0 N A:MET114 3.9 30.3 1.0 CA A:TYR113 3.9 30.1 1.0 C5 E:N1Y301 4.0 29.2 1.0 O A:LEU102 4.0 27.9 1.0 CG2 E:THR144 4.1 24.4 1.0 C A:ALA103 4.1 32.2 1.0 N A:TYR113 4.1 31.1 1.0 CA A:ALA103 4.1 31.1 1.0 CA A:ARG104 4.2 32.6 1.0 CD2 A:LEU112 4.3 37.7 1.0 C A:TYR113 4.3 29.3 1.0 CB A:LEU112 4.4 34.6 1.0 C3 E:N1Y301 4.5 30.5 1.0 CB A:MET114 4.6 35.2 1.0 CA A:LEU112 4.7 33.2 1.0 CD1 A:LEU112 4.7 36.7 1.0 CG A:ARG104 4.7 37.4 1.0 CB E:THR144 4.7 23.9 1.0 C A:LEU102 4.8 29.3 1.0 CA A:MET114 4.9 31.6 1.0 O A:ALA103 5.0 33.0 1.0 N A:ALA103 5.0 30.9 1.0

M.Ihara, T.Okajima, A.Yamashita, T.Oda, T.Asano, M.Matsui, D.B.Sattelle, K.Matsuda. Studies on An Acetylcholine Binding Protein Identify A Basic Residue in Loop G on the Beta 1 Strand As A New Structural Determinant of Neonicotinoid Actions Mol.Pharmacol. V. 86 736 2014.
ISSN: ISSN 0026-895X
PubMed: 25267717
DOI: 10.1124/MOL.114.094698