Chlorine in PDB 7odn: Crystal Structure of TD1-Mebendazole Complex

The structure of Crystal Structure of TD1-Mebendazole Complex, PDB code: 7odn was solved by M.A.Oliva, F.Bonato, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.441, 91.39, 82.671, 90, 97.23, 90
R / Rfree (%)	19 / 22.8

The structure of Crystal Structure of TD1-Mebendazole Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of TD1-Mebendazole Complex (pdb code 7odn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of TD1-Mebendazole Complex, PDB code: 7odn:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of TD1-Mebendazole Complex


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 TD1-Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:86.2 occ:1.00 HZ1 A:LYS336 2.4 82.9 1.0 O A:HOH648 2.7 53.1 1.0 H A:PHE351 2.9 65.3 1.0 NZ A:LYS336 3.2 77.7 1.0 HZ2 A:LYS336 3.3 82.9 1.0 HA2 A:GLY350 3.4 82.2 1.0 HE3 A:LYS336 3.5 77.2 1.0 HA3 A:GLY350 3.7 82.2 1.0 N A:PHE351 3.7 64.7 1.0 HZ3 A:LYS336 3.8 82.9 1.0 CE A:LYS336 3.9 71.4 1.0 CA A:GLY350 3.9 86.4 1.0 HE2 A:LYS336 4.1 77.2 1.0 HD1 A:PHE351 4.1 62.5 1.0 HB2 A:PHE351 4.2 59.8 1.0 O A:PHE351 4.2 58.4 1.0 C A:GLY350 4.4 77.1 1.0 HG21 A:ILE332 4.4 54.6 1.0 CA A:PHE351 4.7 56.8 1.0 HG22 A:ILE332 4.8 54.6 1.0 C A:PHE351 4.9 53.0 1.0 CB A:PHE351 4.9 58.2 1.0 CD1 A:PHE351 5.0 61.6 1.0 O A:THR349 5.0 112.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of TD1-Mebendazole Complex


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 TD1-Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:71.7 occ:1.00 H B:VAL353 2.6 56.0 1.0 HB B:VAL353 3.2 57.8 1.0 HA B:LYS352 3.3 44.9 1.0 HD2 B:LYS352 3.3 47.4 1.0 N B:VAL353 3.4 56.9 1.0 HD3 B:LYS352 3.6 47.4 1.0 O B:VAL353 3.7 66.0 1.0 HG22 A:THR179 3.8 56.9 1.0 CB B:VAL353 3.9 59.8 1.0 CD B:LYS352 3.9 46.3 1.0 HG23 B:VAL353 4.0 58.8 1.0 CA B:VAL353 4.1 57.8 1.0 CA B:LYS352 4.1 44.0 1.0 O A:SER178 4.2 46.4 1.0 HB3 B:LYS352 4.2 46.8 1.0 C B:LYS352 4.2 49.1 1.0 HZ2 B:LYS352 4.3 47.9 1.0 C B:VAL353 4.3 59.8 1.0 CG2 B:VAL353 4.4 60.6 1.0 HG21 B:VAL353 4.4 58.8 1.0 HG23 A:THR179 4.5 56.9 1.0 CB B:LYS352 4.6 45.5 1.0 HZ3 B:LYS352 4.6 47.9 1.0 O A:PRO175 4.6 38.2 1.0 CG2 A:THR179 4.6 57.1 1.0 HA A:THR179 4.7 61.1 1.0 NZ B:LYS352 4.8 47.0 1.0 O B:VAL351 4.8 44.5 1.0 CG B:LYS352 4.9 46.0 1.0 CE B:LYS352 5.0 48.0 1.0 HA B:VAL353 5.0 56.5 1.0

M.A.Oliva, C.Tosat-Bitrian, L.Barrado-Gil, F.Bonato, I.Galindo, U.Garaigorta, B.Alvarez-Bernad, R.Paris-Ogayar, D.Lucena-Agell, J.F.Gimenez-Abian, I.Garcia-Dorival, J.Urquiza, P.Gastaminza, J.F.Diaz, V.Palomo, C.Alonso. Effect of Clinically Used Microtubule Targeting Drugs on Viral Infection and Transport Function. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35408808
DOI: 10.3390/IJMS23073448