Chlorine in PDB 3wtm: Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid

The structure of Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid, PDB code: 3wtm 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)	17.97 / 2.48
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	74.812, 74.812, 351.402, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 26.2

The binding sites of Chlorine atom in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid (pdb code 3wtm). 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid, PDB code: 3wtm:
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 Q55R Mutant 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:8.0 occ:1.00 CL A:N1Y301 0.0 8.0 1.0 C1 A:N1Y301 1.7 18.2 1.0 N1 A:N1Y301 2.6 20.2 1.0 C6 A:N1Y301 2.7 21.8 1.0 O A:LEU112 2.8 29.2 1.0 O E:HOH460 3.3 27.5 1.0 C A:LEU112 3.5 28.6 1.0 CB A:ARG104 3.6 28.7 1.0 N A:ARG104 3.7 28.9 1.0 CG A:LEU112 3.7 32.9 1.0 N A:MET114 3.8 27.4 1.0 C2 A:N1Y301 3.9 21.3 1.0 CG2 E:THR144 3.9 20.6 1.0 CA A:TYR113 3.9 27.3 1.0 C5 A:N1Y301 4.0 22.1 1.0 N A:TYR113 4.0 28.2 1.0 O A:LEU102 4.1 22.6 1.0 C A:ALA103 4.1 27.4 1.0 CA A:ALA103 4.2 25.7 1.0 CD2 A:LEU112 4.3 29.1 1.0 C A:TYR113 4.3 27.2 1.0 CA A:ARG104 4.3 28.6 1.0 CB A:LEU112 4.3 28.2 1.0 C3 A:N1Y301 4.5 26.4 1.0 CB A:MET114 4.6 30.3 1.0 CA A:LEU112 4.6 28.6 1.0 CD1 A:LEU112 4.7 27.9 1.0 CG A:ARG104 4.7 29.4 1.0 CA A:MET114 4.8 27.3 1.0 CB E:THR144 4.8 19.9 1.0 O A:ALA103 4.9 27.5 1.0 C A:LEU102 5.0 23.9 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:11.0 occ:1.00 CL B:N1Y301 0.0 11.0 1.0 C1 B:N1Y301 1.7 21.8 1.0 N1 B:N1Y301 2.6 24.2 1.0 C6 B:N1Y301 2.7 25.9 1.0 O B:LEU112 3.1 23.9 1.0 O B:HOH402 3.2 16.5 1.0 C B:LEU112 3.5 24.3 1.0 N B:MET114 3.5 27.4 1.0 N B:ARG104 3.6 25.1 1.0 CA B:TYR113 3.6 23.5 1.0 N B:TYR113 3.8 23.4 1.0 CB B:ARG104 3.8 28.8 1.0 CG B:LEU112 3.8 29.6 1.0 O B:LEU102 3.9 22.1 1.0 C2 B:N1Y301 3.9 27.0 1.0 C B:TYR113 4.0 23.8 1.0 C5 B:N1Y301 4.0 26.2 1.0 CA B:ALA103 4.0 22.4 1.0 C B:ALA103 4.1 23.4 1.0 CG2 A:THR144 4.2 24.5 1.0 CA B:ARG104 4.3 26.3 1.0 CB B:LEU112 4.4 25.9 1.0 CD2 B:LEU112 4.4 28.6 1.0 C3 B:N1Y301 4.5 29.9 1.0 CB B:MET114 4.6 35.3 1.0 CA B:LEU112 4.6 25.9 1.0 CA B:MET114 4.6 30.3 1.0 C B:LEU102 4.7 23.0 1.0 N B:ALA103 4.8 23.7 1.0 CD1 B:LEU112 4.9 31.6 1.0 CB B:TYR113 4.9 21.7 1.0 CD1 B:TYR113 4.9 20.6 1.0 CG B:ARG104 4.9 27.7 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:3.8 occ:1.00 CL C:N1Y301 0.0 3.8 1.0 C1 C:N1Y301 1.7 18.1 1.0 N1 C:N1Y301 2.6 21.0 1.0 C6 C:N1Y301 2.7 21.3 1.0 O C:LEU112 3.0 28.0 1.0 O B:HOH404 3.3 24.9 1.0 N C:ARG104 3.6 25.1 1.0 CB C:ARG104 3.6 25.4 1.0 C C:LEU112 3.6 27.1 1.0 CG C:LEU112 3.8 29.8 1.0 CA C:TYR113 3.8 23.6 1.0 N C:MET114 3.8 24.3 1.0 C2 C:N1Y301 3.9 19.7 1.0 O C:LEU102 3.9 23.1 1.0 C5 C:N1Y301 4.0 21.0 1.0 N C:TYR113 4.0 24.2 1.0 C C:ALA103 4.0 25.6 1.0 CA C:ALA103 4.0 25.1 1.0 CD2 C:LEU112 4.2 29.8 1.0 CA C:ARG104 4.2 23.0 1.0 C C:TYR113 4.2 24.6 1.0 CG2 B:THR144 4.3 22.7 1.0 CB C:LEU112 4.3 27.4 1.0 C3 C:N1Y301 4.5 22.5 1.0 CA C:LEU112 4.6 27.9 1.0 CG C:ARG104 4.8 26.5 1.0 CB C:MET114 4.8 29.9 1.0 C C:LEU102 4.8 24.5 1.0 CA C:MET114 4.9 26.1 1.0 CD1 C:LEU112 4.9 29.2 1.0 N C:ALA103 4.9 25.9 1.0 O C:ALA103 4.9 23.9 1.0 CB B:THR144 4.9 23.3 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:4.9 occ:1.00 CL D:N1Y301 0.0 4.9 1.0 C1 D:N1Y301 1.7 15.6 1.0 N1 D:N1Y301 2.6 20.2 1.0 C6 D:N1Y301 2.7 20.4 1.0 O D:LEU112 2.8 24.1 1.0 C D:LEU112 3.4 24.2 1.0 N D:ARG104 3.4 23.6 1.0 CB D:ARG104 3.5 22.6 1.0 O D:HOH401 3.5 9.1 1.0 CA D:TYR113 3.7 22.9 1.0 N D:TYR113 3.8 21.7 1.0 N D:MET114 3.9 24.6 1.0 C2 D:N1Y301 3.9 19.9 1.0 C D:ALA103 3.9 23.7 1.0 C5 D:N1Y301 4.0 21.6 1.0 CA D:ALA103 4.0 22.7 1.0 O D:LEU102 4.1 25.4 1.0 CA D:ARG104 4.1 22.1 1.0 CB D:LEU112 4.1 26.3 1.0 C D:TYR113 4.2 24.1 1.0 CA D:LEU112 4.4 25.5 1.0 CG2 C:THR144 4.4 24.9 1.0 C3 D:N1Y301 4.5 22.2 1.0 CB D:MET114 4.6 29.6 1.0 CG D:ARG104 4.6 25.3 1.0 O D:ALA103 4.8 25.2 1.0 C D:LEU102 4.9 23.6 1.0 CA D:MET114 4.9 27.3 1.0 N D:ALA103 4.9 23.6 1.0 CB D:TYR113 5.0 22.6 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant 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 Q55R Mutant Complexed with Nitromethylene Analogue of Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl301 b:5.1 occ:1.00 CL E:N1Y301 0.0 5.1 1.0 C1 E:N1Y301 1.7 15.2 1.0 N1 E:N1Y301 2.6 20.6 1.0 C6 E:N1Y301 2.7 19.6 1.0 O E:LEU112 2.8 30.3 1.0 O E:HOH407 3.1 24.8 1.0 C E:LEU112 3.5 29.9 1.0 N E:ARG104 3.5 30.2 1.0 CB E:ARG104 3.7 31.7 1.0 CA E:TYR113 3.7 26.0 1.0 N E:MET114 3.8 26.7 1.0 CG E:LEU112 3.8 31.2 1.0 O E:LEU102 3.8 23.7 1.0 C2 E:N1Y301 3.9 18.8 1.0 N E:TYR113 3.9 28.0 1.0 C E:ALA103 3.9 28.7 1.0 C5 E:N1Y301 4.0 22.2 1.0 CA E:ALA103 4.0 26.8 1.0 CG2 D:THR144 4.1 21.7 1.0 C E:TYR113 4.2 26.3 1.0 CA E:ARG104 4.2 30.4 1.0 CD2 E:LEU112 4.4 28.6 1.0 CB E:LEU112 4.4 29.7 1.0 C3 E:N1Y301 4.5 23.0 1.0 CA E:LEU112 4.6 29.8 1.0 CG E:ARG104 4.6 34.4 1.0 CD E:ARG104 4.6 36.3 1.0 C E:LEU102 4.7 24.1 1.0 O E:ALA103 4.7 28.4 1.0 CD1 E:LEU112 4.7 29.2 1.0 CB E:MET114 4.7 30.6 1.0 N E:ALA103 4.8 24.9 1.0 CA E:MET114 4.8 27.2 1.0 CD1 E:TYR113 4.9 23.0 1.0 CB D:THR144 4.9 23.4 1.0 CB E:TYR113 4.9 22.5 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