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Chlorine in PDB 3wto: Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid

Protein crystallography data

The structure of Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid, PDB code: 3wto 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) 20.78 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.056, 120.742, 139.346, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid (pdb code 3wto). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid, PDB code: 3wto:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3wto

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Chlorine binding site 1 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-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 Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:12.3
occ:1.00
 CL1 A:N2Y301 0.0 12.3 1.0
C4 A:N2Y301 1.7 26.7 1.0
N6 A:N2Y301 2.6 30.8 1.0
C8 A:N2Y301 2.8 27.1 1.0
CG B:ARG104 3.3 34.1 1.0
O B:LEU112 3.3 28.3 1.0
N B:ARG104 3.5 31.4 1.0
CG B:LEU112 3.7 35.3 1.0
CB B:ARG104 3.7 34.6 1.0
O B:HOH401 3.8 28.9 1.0
CD2 B:LEU112 3.9 35.2 1.0
C5 A:N2Y301 3.9 34.1 1.0
C B:LEU112 3.9 30.8 1.0
C B:ALA103 4.0 30.9 1.0
CA B:ALA103 4.0 31.0 1.0
C7 A:N2Y301 4.1 30.1 1.0
CG2 A:THR144 4.1 25.5 1.0
O B:LEU102 4.2 26.6 1.0
CA B:ARG104 4.2 32.9 1.0
CB B:LEU112 4.3 32.1 1.0
N B:MET114 4.4 28.3 1.0
CA B:TYR113 4.4 28.2 1.0
N B:TYR113 4.4 29.6 1.0
C6 A:N2Y301 4.6 33.4 1.0
CD B:ARG104 4.6 35.4 1.0
CB A:THR144 4.6 26.9 1.0
CA B:LEU112 4.8 31.4 1.0
C B:TYR113 4.9 26.8 1.0
C B:LEU102 4.9 28.8 1.0
CD1 B:LEU112 4.9 33.6 1.0
N B:ALA103 4.9 29.6 1.0
O B:ALA103 5.0 29.9 1.0

Chlorine binding site 2 out of 6 in 3wto

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Chlorine binding site 2 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-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 Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:4.2
occ:1.00
 CL1 B:N2Y301 0.0 4.2 1.0
C4 B:N2Y301 1.7 21.1 1.0
N6 B:N2Y301 2.6 26.7 1.0
C8 B:N2Y301 2.8 25.9 1.0
O C:LEU112 3.1 29.4 1.0
CG C:ARG104 3.4 30.9 1.0
N C:ARG104 3.6 29.4 1.0
O C:HOH401 3.6 23.0 1.0
CB C:ARG104 3.8 28.0 1.0
CG C:LEU112 3.8 32.9 1.0
C C:LEU112 3.9 29.1 1.0
C5 B:N2Y301 3.9 29.6 1.0
CD2 C:LEU112 4.1 32.0 1.0
O C:LEU102 4.1 25.9 1.0
C7 B:N2Y301 4.1 28.1 1.0
C C:ALA103 4.1 29.7 1.0
CA C:ALA103 4.2 29.5 1.0
CA C:ARG104 4.3 28.7 1.0
CG2 B:THR144 4.3 23.3 1.0
N C:MET114 4.3 25.8 1.0
CB C:LEU112 4.4 27.2 1.0
CA C:TYR113 4.4 27.2 1.0
N C:TYR113 4.5 29.4 1.0
C6 B:N2Y301 4.5 30.9 1.0
CB B:THR144 4.7 22.7 1.0
CA C:LEU112 4.8 28.7 1.0
CD C:ARG104 4.8 30.0 1.0
C C:TYR113 4.8 27.6 1.0
C C:LEU102 4.9 26.7 1.0
CB C:MET114 4.9 28.3 1.0
N C:ALA103 5.0 27.6 1.0

Chlorine binding site 3 out of 6 in 3wto

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Chlorine binding site 3 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-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 Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:2.9
occ:1.00
 CL1 C:N2Y301 0.0 2.9 1.0
C4 C:N2Y301 1.7 18.4 1.0
N6 C:N2Y301 2.6 23.3 1.0
C8 C:N2Y301 2.8 24.1 1.0
O D:LEU112 3.1 27.1 1.0
CB D:ARG104 3.4 32.4 1.0
N D:ARG104 3.5 30.1 1.0
CG D:LEU112 3.6 32.1 1.0
CD2 D:LEU112 3.7 34.2 1.0
C D:LEU112 3.8 28.1 1.0
O D:HOH401 3.9 25.4 1.0
C5 C:N2Y301 3.9 26.6 1.0
C7 C:N2Y301 4.1 25.6 1.0
C D:ALA103 4.1 30.1 1.0
CA D:ARG104 4.1 30.4 1.0
O D:LEU102 4.2 30.2 1.0
CA D:ALA103 4.2 29.8 1.0
CB D:LEU112 4.2 30.6 1.0
CG2 C:THR144 4.4 21.1 1.0
N D:MET114 4.4 28.0 1.0
CA D:TYR113 4.4 27.6 1.0
N D:TYR113 4.4 27.7 1.0
CG D:ARG104 4.5 36.3 1.0
C6 C:N2Y301 4.5 26.8 1.0
CA D:LEU112 4.7 29.6 1.0
C D:TYR113 4.8 27.7 1.0
CD1 D:LEU112 4.8 31.2 1.0
CB C:THR144 4.8 22.6 1.0
C D:LEU102 5.0 28.2 1.0
O D:ALA103 5.0 31.4 1.0
CD D:ARG104 5.0 36.9 1.0

Chlorine binding site 4 out of 6 in 3wto

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Chlorine binding site 4 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-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 Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:11.5
occ:1.00
 CL1 D:N2Y301 0.0 11.5 1.0
C4 D:N2Y301 1.7 25.7 1.0
N6 D:N2Y301 2.7 28.5 1.0
C8 D:N2Y301 2.7 29.9 1.0
O E:LEU112 3.1 30.3 1.0
O E:HOH401 3.3 26.0 1.0
N E:ARG104 3.6 32.9 1.0
C E:LEU112 3.7 31.8 1.0
CG E:LEU112 3.7 33.4 1.0
CB E:ARG104 3.8 33.2 1.0
O E:LEU102 3.9 30.6 1.0
C5 D:N2Y301 3.9 29.9 1.0
CA E:TYR113 3.9 32.4 1.0
N E:MET114 3.9 32.8 1.0
CA E:ALA103 4.0 31.0 1.0
C7 D:N2Y301 4.0 32.1 1.0
C E:ALA103 4.0 32.5 1.0
CG2 D:THR144 4.1 31.5 1.0
N E:TYR113 4.1 30.4 1.0
CD2 E:LEU112 4.1 35.0 1.0
CA E:ARG104 4.3 32.8 1.0
CB E:LEU112 4.4 33.0 1.0
C E:TYR113 4.4 32.1 1.0
C6 D:N2Y301 4.5 31.5 1.0
CA E:LEU112 4.7 32.4 1.0
C E:LEU102 4.7 29.1 1.0
CB E:MET114 4.7 35.4 1.0
CB D:THR144 4.8 30.6 1.0
N E:ALA103 4.8 28.9 1.0
CD1 E:LEU112 4.8 33.7 1.0
O E:ALA103 4.9 33.1 1.0
CG E:ARG104 4.9 36.3 1.0
CA E:MET114 4.9 34.4 1.0

Chlorine binding site 5 out of 6 in 3wto

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Chlorine binding site 5 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-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 Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:2.6
occ:0.50
 CL1 E:N2Y301 0.0 2.6 0.5
CL1 E:N2Y301 0.6 27.1 0.5
C4 E:N2Y301 1.8 14.8 0.5
C4 E:N2Y301 1.8 31.0 0.5
N6 E:N2Y301 2.5 32.4 0.5
N6 E:N2Y301 2.7 17.6 0.5
C8 E:N2Y301 2.7 16.8 0.5
O A:LEU112 3.0 33.2 1.0
C8 E:N2Y301 3.0 31.2 0.5
O E:HOH402 3.2 29.8 1.0
N A:ARG104 3.5 33.9 1.0
CB A:ARG104 3.7 35.8 1.0
O A:LEU102 3.7 28.6 1.0
C A:LEU112 3.8 32.9 1.0
C5 E:N2Y301 3.8 31.3 0.5
C5 E:N2Y301 4.0 18.4 0.5
CG A:LEU112 4.0 33.7 1.0
C A:ALA103 4.0 33.5 1.0
CA A:ALA103 4.0 30.3 1.0
C7 E:N2Y301 4.0 19.9 0.5
N A:MET114 4.1 31.2 1.0
CA A:TYR113 4.1 32.0 1.0
CG2 E:THR144 4.1 30.1 1.0
CA A:ARG104 4.2 35.4 1.0
C7 E:N2Y301 4.2 31.1 0.5
N A:TYR113 4.3 30.2 1.0
CD2 A:LEU112 4.3 37.8 1.0
CB A:LEU112 4.5 30.6 1.0
C6 E:N2Y301 4.6 32.1 0.5
C6 E:N2Y301 4.6 20.7 0.5
C A:TYR113 4.6 31.4 1.0
C A:LEU102 4.6 29.8 1.0
CB E:THR144 4.7 30.4 1.0
N A:ALA103 4.8 29.7 1.0
CA A:LEU112 4.8 31.5 1.0
CG A:ARG104 4.8 39.4 1.0
CB A:MET114 4.9 35.3 1.0
O A:ALA103 4.9 34.7 1.0

Chlorine binding site 6 out of 6 in 3wto

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Chlorine binding site 6 out of 6 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Lymnaea Stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Desnitro-Imidacloprid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:27.1
occ:0.50
 CL1 E:N2Y301 0.0 27.1 0.5
CL1 E:N2Y301 0.6 2.6 0.5
C4 E:N2Y301 1.6 14.8 0.5
C4 E:N2Y301 1.7 31.0 0.5
C8 E:N2Y301 2.3 16.8 0.5
N6 E:N2Y301 2.7 32.4 0.5
N6 E:N2Y301 2.7 17.6 0.5
C8 E:N2Y301 2.8 31.2 0.5
O A:LEU112 3.0 33.2 1.0
CB A:ARG104 3.3 35.8 1.0
N A:ARG104 3.6 33.9 1.0
C7 E:N2Y301 3.6 19.9 0.5
CG A:LEU112 3.6 33.7 1.0
C A:LEU112 3.8 32.9 1.0
O E:HOH402 3.8 29.8 1.0
CD2 A:LEU112 3.8 37.8 1.0
C5 E:N2Y301 3.9 18.4 0.5
C5 E:N2Y301 3.9 31.3 0.5
C7 E:N2Y301 4.1 31.1 0.5
CA A:ARG104 4.1 35.4 1.0
CB A:LEU112 4.1 30.6 1.0
C A:ALA103 4.2 33.5 1.0
O A:LEU102 4.3 28.6 1.0
C6 E:N2Y301 4.3 20.7 0.5
N A:MET114 4.4 31.2 1.0
CG2 E:THR144 4.4 30.1 1.0
N A:TYR113 4.4 30.2 1.0
CA A:TYR113 4.4 32.0 1.0
CA A:ALA103 4.4 30.3 1.0
CG A:ARG104 4.4 39.4 1.0
C6 E:N2Y301 4.5 32.1 0.5
CA A:LEU112 4.6 31.5 1.0
CB E:THR144 4.8 30.4 1.0
C A:TYR113 4.8 31.4 1.0
CD1 A:LEU112 4.9 34.5 1.0
CB A:MET114 5.0 35.3 1.0
CD A:ARG104 5.0 37.2 1.0

Reference:

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
Page generated: Sun Jul 21 07:45:01 2024

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