Zinc in PDB 4p3n: Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1

All present enzymatic activity of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1:
6.1.1.3;

The structure of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1, PDB code: 4p3n was solved by P.Fang, X.Yu, K.Chen, X.Chen, M.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.870, 78.000, 118.050, 86.99, 83.32, 84.39
R / Rfree (%)	22.8 / 25.5

The binding sites of Zinc atom in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 (pdb code 4p3n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1, PDB code: 4p3n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:44.2 occ:1.00 NE2 A:HIS464 2.1 39.9 1.0 SG A:CYS413 2.4 36.5 1.0 ND1 A:HIS590 2.4 47.6 1.0 CE1 A:HIS464 2.9 40.0 1.0 O A:HOH907 3.0 31.5 1.0 CD2 A:HIS464 3.2 39.9 1.0 CG A:HIS590 3.3 47.2 1.0 CE1 A:HIS590 3.3 48.5 1.0 CB A:HIS590 3.5 45.5 1.0 CB A:CYS413 3.8 49.2 1.0 OD1 A:ASP462 3.9 44.1 1.0 C9 A:2CR800 4.0 42.6 1.0 ND1 A:HIS464 4.1 39.5 1.0 CG A:HIS464 4.2 39.5 1.0 CA A:HIS590 4.2 44.4 1.0 OD2 A:ASP462 4.3 43.1 1.0 C7 A:2CR800 4.3 41.5 1.0 NE2 A:HIS590 4.4 49.2 1.0 CD2 A:HIS590 4.4 48.7 1.0 C5 A:2CR800 4.5 42.0 1.0 CG A:ASP462 4.5 43.5 1.0 C8 A:2CR800 4.5 42.2 1.0 CA A:CYS413 4.5 48.0 1.0 N A:CYS413 4.7 47.2 1.0

Zinc binding site 2 out of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:50.5 occ:1.00 NE2 B:HIS464 2.1 39.2 1.0 ND1 B:HIS590 2.3 50.8 1.0 SG B:CYS413 2.4 34.1 1.0 CE1 B:HIS464 2.9 39.4 1.0 CG B:HIS590 3.1 50.2 1.0 CD2 B:HIS464 3.2 40.0 1.0 CE1 B:HIS590 3.3 51.5 1.0 O B:HOH917 3.3 53.5 1.0 CB B:HIS590 3.3 48.7 1.0 CB B:CYS413 3.8 47.2 1.0 OD1 B:ASP462 3.8 51.2 1.0 ND1 B:HIS464 4.0 39.3 1.0 CA B:HIS590 4.1 47.5 1.0 C9 B:2CR800 4.2 46.1 1.0 CG B:HIS464 4.2 39.9 1.0 OD2 B:ASP462 4.3 51.2 1.0 C7 B:2CR800 4.3 46.4 1.0 CD2 B:HIS590 4.3 51.5 1.0 NE2 B:HIS590 4.4 51.9 1.0 C5 B:2CR800 4.5 46.8 1.0 CG B:ASP462 4.5 50.5 1.0 CE B:MET411 4.6 54.0 1.0 CA B:CYS413 4.6 46.5 1.0 C8 B:2CR800 4.6 46.3 1.0 N B:CYS413 4.7 47.0 1.0

Zinc binding site 3 out of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:58.1 occ:1.00 ND1 C:HIS590 2.1 46.8 1.0 NE2 C:HIS464 2.1 51.3 1.0 SG C:CYS413 2.3 46.5 1.0 CG C:HIS590 3.0 47.1 1.0 CD2 C:HIS464 3.1 51.1 1.0 CE1 C:HIS464 3.1 51.0 1.0 CE1 C:HIS590 3.2 47.6 1.0 O C:HOH906 3.2 39.1 1.0 CB C:HIS590 3.2 46.9 1.0 CB C:CYS413 3.7 57.1 1.0 OD1 C:ASP462 4.0 56.5 1.0 CA C:HIS590 4.0 47.3 1.0 OD2 C:ASP462 4.1 55.5 1.0 C7 C:2CR800 4.1 52.5 1.0 ND1 C:HIS464 4.2 50.5 1.0 C9 C:2CR800 4.2 53.2 1.0 CG C:HIS464 4.2 50.3 1.0 CD2 C:HIS590 4.2 47.6 1.0 NE2 C:HIS590 4.2 47.9 1.0 CG C:ASP462 4.5 55.7 1.0 CA C:CYS413 4.6 56.0 1.0 C8 C:2CR800 4.6 53.0 1.0 C5 C:2CR800 4.7 52.5 1.0 N C:CYS413 4.7 55.2 1.0 C1 C:2CR800 5.0 52.7 1.0

Zinc binding site 4 out of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:52.8 occ:1.00 NE2 D:HIS464 2.2 41.9 1.0 ND1 D:HIS590 2.2 49.4 1.0 SG D:CYS413 2.3 42.8 1.0 CE1 D:HIS464 3.1 42.1 1.0 CD2 D:HIS464 3.1 42.0 1.0 CG D:HIS590 3.1 48.6 1.0 CE1 D:HIS590 3.2 50.2 1.0 O D:HOH925 3.3 51.1 1.0 CB D:HIS590 3.4 47.9 1.0 CB D:CYS413 3.8 54.8 1.0 OD1 D:ASP462 4.0 45.4 1.0 OD2 D:ASP462 4.0 46.4 1.0 C9 D:2CR800 4.0 52.9 1.0 CA D:HIS590 4.1 47.4 1.0 C7 D:2CR800 4.1 52.1 1.0 ND1 D:HIS464 4.1 41.5 1.0 CG D:HIS464 4.2 41.8 1.0 NE2 D:HIS590 4.3 50.1 1.0 CD2 D:HIS590 4.3 49.2 1.0 C5 D:2CR800 4.3 52.3 1.0 CG D:ASP462 4.4 46.0 1.0 C8 D:2CR800 4.5 52.8 1.0 CA D:CYS413 4.6 54.1 1.0 N D:CYS413 4.7 53.9 1.0 CE D:MET411 4.9 32.4 1.0 C1 D:2CR800 4.9 52.6 1.0

P.Fang, X.Yu, S.Jeong, A.Mirando, K.Chen, X.Chen, S.Kim, C.S.Francklyn, M.Guo. Structural Basis For Full-Spectrum Inhibition of Translational and Nontranslational Functions on A Human Trna Synthetase To Be Published.