Cadmium in PDB 3wtn: Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid

The structure of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid, PDB code: 3wtn 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)	47.84 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.006, 118.401, 243.591, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.2

The structure of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid also contains other interesting chemical elements:

Chlorine	(Cl)	15 atoms
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid (pdb code 3wtn). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 54 binding sites of Cadmium where determined in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid, PDB code: 3wtn:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:30.9 occ:0.97 OD1 A:ASP2 2.2 35.0 1.0 OD2 G:ASP2 2.3 34.2 1.0 OD1 A:ASP5 2.4 34.1 1.0 OD1 G:ASP5 2.5 28.8 1.0 OD2 G:ASP5 2.6 28.6 1.0 OD2 A:ASP2 2.6 31.0 1.0 OD2 A:ASP5 2.7 35.7 1.0 CG A:ASP2 2.7 32.7 1.0 OD1 G:ASP2 2.7 32.3 1.0 CG G:ASP5 2.8 28.2 1.0 CG A:ASP5 2.8 33.3 1.0 CG G:ASP2 2.9 32.3 1.0 O G:HOH520 3.8 43.0 1.0 CB A:ASP2 4.1 32.5 1.0 CB G:ASP5 4.3 25.9 1.0 CB A:ASP5 4.3 30.9 1.0 CB G:ASP2 4.3 32.3 1.0 N A:ASP5 4.4 27.3 1.0 CB A:ALA4 4.5 27.6 1.0 N G:ASP5 4.5 25.4 1.0 O E:HOH416 4.5 41.3 1.0 N A:ASP2 4.5 35.0 1.0 N G:ASP2 4.6 34.7 1.0 CB G:ALA4 4.7 25.4 1.0 CA A:ASP5 4.8 28.0 1.0 CA G:ASP5 4.9 27.1 1.0 O F:HOH466 4.9 32.2 1.0 CA A:ASP2 4.9 32.3 1.0

Cadmium binding site 2 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:74.7 occ:0.74 OE1 A:GLU-1 2.5 60.6 1.0 ND1 A:HIS69 2.6 48.3 1.0 O F:HOH490 3.1 49.2 1.0 OE2 A:GLU-1 3.2 60.9 1.0 CD A:GLU-1 3.2 59.7 1.0 CE1 A:HIS69 3.4 49.5 1.0 CG A:HIS69 3.6 48.6 1.0 CB A:HIS69 3.9 46.3 1.0 NH1 F:ARG23 4.0 71.3 1.0 CA A:HIS69 4.2 44.5 1.0 O A:HOH535 4.3 39.8 1.0 NE2 A:HIS69 4.6 49.5 1.0 O A:SER68 4.7 45.9 1.0 CG A:GLU-1 4.7 57.6 1.0 CD2 A:HIS69 4.7 48.7 1.0

Cadmium binding site 3 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:83.1 occ:0.65 OD2 A:ASP72 2.6 44.8 1.0 OD1 A:ASP72 3.1 45.5 1.0 CG A:ASP72 3.2 43.2 1.0 O A:HOH446 3.4 53.0 1.0 O A:HOH497 3.4 38.1 1.0 CB A:ASP72 4.6 40.1 1.0 O A:HOH519 4.9 45.8 1.0

Cadmium binding site 4 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:91.7 occ:0.91 OE2 A:GLU43 2.5 42.8 1.0 OE1 A:GLU43 3.0 42.9 1.0 CD A:GLU43 3.1 43.0 1.0 OD2 A:ASP129 3.6 58.2 1.0 CB A:ASP129 3.7 52.1 1.0 CG A:ASP129 4.1 56.0 1.0 N A:ASP129 4.4 44.9 1.0 CG A:GLU43 4.5 41.2 1.0 CA A:ASP129 4.6 48.4 1.0 N A:GLY127 4.7 39.1 1.0 CA A:GLY127 5.0 40.2 1.0

Cadmium binding site 5 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:68.8 occ:0.65 OE2 G:GLU-1 2.4 68.0 1.0 O A:HOH535 2.7 39.8 1.0 N A:ALA-2 2.8 54.2 1.0 CD G:GLU-1 3.5 66.6 1.0 CA A:ALA-2 4.0 55.6 1.0 CG G:GLU-1 4.2 65.2 1.0 OE1 G:GLU-1 4.5 67.8 1.0 N G:ALA-2 4.5 62.8 1.0 O G:HOH420 4.7 54.1 1.0 C A:ALA-2 4.7 55.4 1.0 CD G:CD302 4.9 79.8 0.8 C G:ALA-2 4.9 63.3 1.0

Cadmium binding site 6 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:92.2 occ:0.64 NE2 A:HIS69 2.4 49.5 1.0 O A:HOH490 2.9 55.9 1.0 CD2 A:HIS69 3.1 48.7 1.0 CE1 A:HIS69 3.6 49.5 1.0 NH2 F:ARG23 4.3 71.2 1.0 CG A:HIS69 4.3 48.6 1.0 CZ F:ARG23 4.5 71.1 1.0 ND1 A:HIS69 4.6 48.3 1.0 OG A:SER68 4.6 48.6 1.0 NE F:ARG23 4.8 70.5 1.0 NH1 F:ARG23 4.8 71.3 1.0

Cadmium binding site 7 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:55.5 occ:0.19 OD2 A:ASP129 2.5 58.2 1.0 OD1 A:ASP129 2.7 59.1 1.0 CG A:ASP129 2.9 56.0 1.0 CD A:LYS203 4.2 48.5 1.0 O A:HOH455 4.3 59.3 1.0 CB A:ASP129 4.4 52.1 1.0 CE A:LYS203 4.7 52.6 1.0

Cadmium binding site 8 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:46.4 occ:0.29 O A:HOH554 2.2 43.0 1.0 OE2 A:GLU172 2.5 38.5 1.0 OE1 A:GLU172 2.9 40.4 1.0 CD A:GLU172 3.0 38.3 1.0 NH2 A:ARG202 4.1 45.3 1.0 CG A:GLU172 4.5 35.7 1.0 O A:HOH552 4.6 41.4 1.0 N A:GLY205 4.6 48.6 1.0 NE A:ARG202 4.6 47.0 1.0 O A:HOH436 4.7 47.1 1.0 CA A:LYS204 4.7 44.4 1.0 CG A:LYS204 4.7 41.6 1.0 CZ A:ARG202 4.8 46.2 1.0 CB A:LYS204 4.8 42.7 1.0

Cadmium binding site 9 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:34.5 occ:0.97 OD2 F:ASP2 2.2 39.0 1.0 OD1 B:ASP2 2.2 37.0 1.0 OD1 F:ASP5 2.3 38.1 1.0 OD2 B:ASP5 2.4 27.9 1.0 OD2 F:ASP5 2.6 38.3 1.0 OD1 B:ASP5 2.6 33.3 1.0 CG F:ASP5 2.7 38.3 1.0 OD2 B:ASP2 2.8 32.3 1.0 CG B:ASP2 2.8 33.1 1.0 CG B:ASP5 2.8 28.2 1.0 OD1 F:ASP2 2.8 34.3 1.0 CG F:ASP2 2.8 37.8 1.0 O B:HOH559 4.1 37.7 1.0 CB F:ASP5 4.2 34.9 1.0 CB B:ASP5 4.2 26.8 1.0 CB B:ASP2 4.2 33.6 1.0 CB F:ASP2 4.3 37.4 1.0 N F:ASP5 4.3 30.9 1.0 N B:ASP5 4.4 23.0 1.0 CB F:ALA4 4.5 32.4 1.0 N B:ASP2 4.6 35.2 1.0 N F:ASP2 4.6 39.2 1.0 O B:HOH402 4.6 38.2 1.0 CB B:ALA4 4.7 23.1 1.0 O F:HOH459 4.7 43.4 1.0 CA F:ASP5 4.7 32.1 1.0 CA B:ASP5 4.8 24.6 1.0 CA B:ASP2 5.0 32.2 1.0 CA F:ASP2 5.0 37.3 1.0

Cadmium binding site 10 out of 54 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:83.1 occ:0.97 ND1 B:HIS69 2.4 51.6 1.0 OE2 B:GLU-1 2.4 63.5 1.0 OE1 B:GLU-1 3.1 63.7 1.0 CD B:GLU-1 3.1 62.4 1.0 CE1 B:HIS69 3.2 51.3 1.0 CG B:HIS69 3.4 51.5 1.0 CB B:HIS69 3.8 49.5 1.0 CA B:HIS69 4.2 47.5 1.0 NE2 B:HIS69 4.3 51.4 1.0 CD2 B:HIS69 4.5 50.7 1.0 CG B:GLU-1 4.6 60.3 1.0 O B:SER68 4.7 51.1 1.0 O B:HOH514 4.9 42.8 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