Zinc in PDB 8ou8: Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue

All present enzymatic activity of Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue:
6.1.1.3;

The structure of Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue, PDB code: 8ou8 was solved by J.A.Rodriguez Buitrago, E.Parisini, J.Aigars, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.75 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.33, 108.95, 113.96, 90, 90, 90
R / Rfree (%)	18.9 / 26.6

The binding sites of Zinc atom in the Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue (pdb code 8ou8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue, PDB code: 8ou8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:31.6 occ:1.00 NE2 D:HIS144 2.0 24.5 1.0 N7 D:W0U501 2.1 29.8 1.0 O7 D:W0U501 2.1 38.4 1.0 ND1 D:HIS270 2.2 30.3 1.0 SG D:CYS93 2.3 33.1 1.0 C3 D:W0U501 2.9 34.5 1.0 C2 D:W0U501 3.0 38.1 1.0 CD2 D:HIS144 3.0 26.4 1.0 CE1 D:HIS144 3.1 29.6 1.0 CE1 D:HIS270 3.1 30.6 1.0 CG D:HIS270 3.2 31.2 1.0 CB D:CYS93 3.4 32.4 1.0 CB D:HIS270 3.5 33.2 1.0 O D:HOH626 3.6 21.7 1.0 CG D:HIS144 4.2 29.2 1.0 ND1 D:HIS144 4.2 28.5 1.0 CA D:CYS93 4.2 34.0 1.0 NE2 D:HIS270 4.2 35.5 1.0 CD2 D:HIS270 4.3 31.5 1.0 OD2 D:ASP142 4.3 23.5 1.0 C4 D:W0U501 4.3 31.9 1.0 N D:CYS93 4.3 35.2 1.0 C1 D:W0U501 4.4 34.1 1.0 OD1 D:ASP142 4.4 29.3 1.0 CE2 D:TYR221 4.5 32.5 1.0 OH D:TYR221 4.5 37.0 1.0 CA D:HIS270 4.6 33.3 1.0 O6 D:W0U501 4.7 31.3 1.0 CG D:MET91 4.8 44.1 1.0 CG D:ASP142 4.8 27.9 1.0 CZ D:TYR221 4.8 33.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E. Coli Threonyl Trna Synthetase in Complex with A TM84 Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:31.1 occ:1.00 N7 A:W0U502 2.1 29.3 1.0 O7 A:W0U502 2.1 34.1 1.0 NE2 A:HIS144 2.1 26.9 1.0 ND1 A:HIS270 2.2 31.2 1.0 SG A:CYS93 2.4 25.8 1.0 C3 A:W0U502 2.9 35.9 1.0 C2 A:W0U502 3.0 37.2 1.0 CD2 A:HIS144 3.1 28.9 1.0 CE1 A:HIS270 3.1 31.6 1.0 CE1 A:HIS144 3.1 27.1 1.0 CG A:HIS270 3.2 27.4 1.0 CB A:CYS93 3.4 28.0 1.0 CB A:HIS270 3.6 27.3 1.0 O A:HOH612 3.7 27.0 1.0 OD2 A:ASP142 4.1 25.1 1.0 CA A:CYS93 4.1 27.2 1.0 N A:CYS93 4.2 28.8 1.0 CG A:HIS144 4.2 26.6 1.0 NE2 A:HIS270 4.2 31.9 1.0 ND1 A:HIS144 4.2 27.2 1.0 CD2 A:HIS270 4.3 30.5 1.0 C4 A:W0U502 4.3 34.3 1.0 OD1 A:ASP142 4.4 31.1 1.0 C1 A:W0U502 4.4 35.7 1.0 CE2 A:TYR221 4.5 29.5 1.0 CA A:HIS270 4.6 27.6 1.0 OH A:TYR221 4.7 37.7 1.0 CG A:ASP142 4.7 29.5 1.0 O6 A:W0U502 4.7 31.8 1.0 CZ A:TYR221 4.9 31.5 1.0 CE A:MET91 4.9 45.1 0.5

J.A.R.Buitrago, G.Leitis, I.Kanepe-Lapsa, A.Rudnickiha, E.Parisini, A.Jirgensons. Synthesis and Evaluation of An Agrocin 84 Toxic Moiety (TM84) Analogue As A Malarial Threonyl Trna Synthetase Inhibitor. Org.Biomol.Chem. 2023.
ISSN: ESSN 1477-0539
PubMed: 37335076
DOI: 10.1039/D3OB00670K