Sodium 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:

Cadmium	(Cd)	54 atoms
Chlorine	(Cl)	15 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid, PDB code: 3wtn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Lymnaea Stagnalis Acetylcholine Binding Protein Complexed with Desnitro-Imidacloprid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 B:Na309 b:52.4 occ:0.97 O B:SER70 2.7 40.1 1.0 OD1 B:ASP72 2.7 43.7 1.0 O B:HOH514 2.8 42.8 1.0 O B:SER67 2.8 41.5 1.0 O B:HOH517 2.9 49.4 1.0 CD B:CD304 3.3 92.2 0.8 CG B:ASP72 3.3 43.9 1.0 OD2 B:ASP72 3.4 46.4 1.0 C B:SER70 3.8 41.1 1.0 C B:SER67 4.0 43.7 1.0 N B:SER70 4.2 44.4 1.0 CB B:SER67 4.4 41.0 1.0 N B:ASP72 4.4 35.2 1.0 C B:PRO71 4.5 36.1 1.0 CA B:PRO71 4.6 37.7 1.0 CB B:ASP72 4.7 39.6 1.0 N B:PRO71 4.7 39.7 1.0 CA B:SER70 4.7 42.8 1.0 CA B:SER67 4.7 41.9 1.0 OG B:SER67 4.7 43.8 1.0 C B:SER68 4.8 48.8 1.0 O B:SER68 4.8 51.1 1.0 CA B:ASP72 4.9 35.8 1.0 O B:PRO71 4.9 35.4 1.0 N B:HIS69 5.0 47.4 1.0 O B:HOH565 5.0 48.8 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 C:Na309 b:28.2 occ:0.97 O C:ASN158 2.4 28.2 1.0 OD1 C:ASP161 2.4 22.7 1.0 O C:HOH424 2.8 33.1 1.0 CG C:ASP161 3.3 21.1 1.0 C C:ASN158 3.5 30.6 1.0 CA C:SER159 3.7 25.9 1.0 ND2 C:ASN158 3.9 40.5 1.0 OD2 C:ASP161 3.9 18.6 1.0 CB C:ASP161 4.1 22.8 1.0 C C:SER159 4.1 24.2 1.0 N C:SER159 4.1 28.8 1.0 O C:SER159 4.2 21.9 1.0 CG C:ASN158 4.4 40.0 1.0 N C:ASP161 4.6 19.1 1.0 O C:VAL176 4.6 31.2 1.0 CB C:ASN158 4.7 35.7 1.0 CA C:ASN158 4.7 33.6 1.0 O C:HOH450 4.7 21.3 1.0 N C:ASP160 4.8 22.3 1.0 CB C:SER159 4.9 27.0 1.0 CA C:ASP161 5.0 21.0 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