Zinc in PDB 8qic: Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors

The structure of Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors, PDB code: 8qic was solved by J.A.Rodriguez, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.33 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.78, 110.5, 113.97, 90, 90, 90
R / Rfree (%)	19.5 / 23.3

The binding sites of Zinc atom in the Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors (pdb code 8qic). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors, PDB code: 8qic:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.3 occ:1.00 O3 A:VL0501 1.6 40.1 1.0 NE2 A:HIS144 2.0 20.8 1.0 ND1 A:HIS270 2.0 19.1 1.0 O2 A:VL0501 2.3 36.4 1.0 SG A:CYS93 2.4 20.6 1.0 C7 A:VL0501 2.8 46.2 1.0 CE1 A:HIS270 3.0 22.3 1.0 CD2 A:HIS144 3.0 20.1 1.0 CE1 A:HIS144 3.1 20.9 1.0 CG A:HIS270 3.1 20.9 1.0 C1 A:VL0501 3.2 40.7 1.0 C2 A:VL0501 3.4 45.7 1.0 CB A:CYS93 3.4 23.0 1.0 CB A:HIS270 3.4 19.6 1.0 O A:HOH605 3.7 13.0 1.0 C6 A:VL0501 3.9 65.9 1.0 CG A:HIS144 4.2 19.5 1.0 NE2 A:HIS270 4.2 26.4 1.0 ND1 A:HIS144 4.2 19.1 1.0 CD2 A:HIS270 4.2 23.3 1.0 CA A:CYS93 4.2 23.1 1.0 N A:CYS93 4.3 23.1 1.0 OD2 A:ASP142 4.3 25.5 1.0 O1 A:VL0501 4.4 46.6 1.0 OD1 A:ASP142 4.5 19.0 1.0 CA A:HIS270 4.5 21.4 1.0 CE2 A:TYR221 4.7 30.6 1.0 OH A:TYR221 4.7 20.2 1.0 C3 A:VL0501 4.7 54.9 1.0 CG A:ASP142 4.8 20.2 1.0

Zinc binding site 2 out of 2 in the Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn505 b:25.4 occ:1.00 O1 D:VL0501 1.2 31.6 1.0 NE2 D:HIS144 2.0 19.0 1.0 ND1 D:HIS270 2.1 17.0 1.0 C1 D:VL0501 2.3 42.4 1.0 SG D:CYS93 2.5 20.3 1.0 O3 D:VL0501 2.6 27.4 1.0 CD2 D:HIS144 2.9 20.4 1.0 CE1 D:HIS144 3.0 19.1 1.0 CG D:HIS270 3.0 17.6 1.0 CE1 D:HIS270 3.0 18.2 1.0 O2 D:VL0501 3.2 84.2 1.0 C2 D:VL0501 3.2 39.8 1.0 C7 D:VL0501 3.3 40.1 1.0 CB D:HIS270 3.4 17.4 1.0 CB D:CYS93 3.5 19.8 1.0 O D:HOH605 3.8 13.0 1.0 CG D:HIS144 4.1 20.9 1.0 ND1 D:HIS144 4.1 19.4 1.0 NE2 D:HIS270 4.2 19.1 1.0 CD2 D:HIS270 4.2 18.9 1.0 OD2 D:ASP142 4.2 25.7 1.0 CA D:CYS93 4.3 19.1 1.0 N D:CYS93 4.3 18.4 1.0 OD1 D:ASP142 4.4 21.5 1.0 CA D:HIS270 4.4 19.1 1.0 C3 D:VL0501 4.5 25.3 1.0 C6 D:VL0501 4.6 45.8 1.0 OH D:TYR221 4.7 22.1 1.0 CE2 D:TYR221 4.7 23.9 1.0 CG D:ASP142 4.7 24.2 1.0

R.Bobrovs, J.Bolsakova, J.A.R.Buitrago, L.Varaceva, M.Skvorcova, I.Kanepe, A.Rudnickiha, E.Parisini, A.Jirgensons. Structure-Based Identification of Salicylic Acid Derivatives As Malarial Threonyl Trna-Synthetase Inhibitors. Plos One V. 19 96995 2024.
ISSN: ESSN 1932-6203
PubMed: 38558084
DOI: 10.1371/JOURNAL.PONE.0296995