Zinc in PDB 2v0c: Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site

The structure of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site, PDB code: 2v0c was solved by F.Rock, W.Mao, A.Yaremchuk, M.Tukalo, T.Crepin, H.Zhou, Y.Zhang, V.Hernandez, T.Akama, S.Baker, J.Plattner, L.Shapiro, S.A.Martinis, S.J.Benkovic, S.Cusack, M.R.K.Alley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.37 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.830, 154.230, 174.950, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.2

The structure of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site (pdb code 2v0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site, PDB code: 2v0c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1815 b:35.0 occ:1.00 SG A:CYS439 2.2 31.5 1.0 SG A:CYS442 2.4 34.7 1.0 SG A:CYS487 2.4 36.9 1.0 SG A:CYS484 2.4 33.0 1.0 CB A:CYS484 3.1 34.7 1.0 CB A:CYS439 3.2 31.7 1.0 CB A:CYS442 3.3 32.4 1.0 CB A:CYS487 3.3 37.8 1.0 N A:CYS487 3.7 38.4 1.0 N A:CYS442 3.9 32.6 1.0 CA A:CYS487 4.1 38.2 1.0 CA A:CYS442 4.2 31.8 1.0 O A:HOH2439 4.3 33.9 1.0 CB A:LYS486 4.4 37.9 1.0 CA A:CYS484 4.5 34.7 1.0 CB A:ALA441 4.6 31.9 1.0 CA A:CYS439 4.7 31.5 1.0 C A:LYS486 4.7 38.0 1.0 C A:CYS487 4.8 38.8 1.0 N A:GLY488 4.9 38.6 1.0 CG2 A:VAL445 4.9 27.3 1.0 C A:ALA441 4.9 32.6 1.0 CA A:LYS486 5.0 37.9 1.0 N A:LYS486 5.0 37.0 1.0

Zinc binding site 2 out of 2 in the Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Leucyl-Trna Synthetase From Thermus Thermophilus Complexed with A Sulphamoyl Analogue of Leucyl-Adenylate in the Synthetic Site and An Adduct of Amp with 5-Fluoro-1,3- Dihydro-1-Hydroxy-2,1-Benzoxaborole (AN2690) in the Editing Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1816 b:27.7 occ:1.00 ND1 A:HIS179 2.2 29.8 1.0 SG A:CYS176 2.3 28.1 1.0 SG A:CYS162 2.3 28.4 1.0 SG A:CYS159 2.3 29.3 1.0 CE1 A:HIS179 3.0 31.6 1.0 CB A:CYS176 3.3 29.2 1.0 CB A:CYS159 3.3 29.8 1.0 CG A:HIS179 3.4 32.3 1.0 CB A:CYS162 3.4 29.4 1.0 N A:CYS162 3.7 30.1 1.0 CB A:HIS179 3.8 32.7 1.0 CA A:CYS162 4.1 29.5 1.0 N A:HIS179 4.1 32.6 1.0 NE2 A:HIS179 4.2 31.8 1.0 CD2 A:HIS179 4.4 32.5 1.0 CB A:ARG178 4.4 30.6 1.0 CB A:LYS161 4.5 32.1 1.0 C A:LYS161 4.6 30.9 1.0 CA A:HIS179 4.6 33.3 1.0 CA A:CYS176 4.7 30.1 1.0 CA A:CYS159 4.7 29.6 1.0 C A:ARG178 4.9 31.9 1.0 CA A:LYS161 4.9 31.7 1.0 N A:LYS161 5.0 31.1 1.0

F.Rock, W.Mao, A.Yaremchuk, M.Tukalo, T.Crepin, H.Zhou, Y.Zhang, V.Hernandez, T.Akama, S.Baker, J.Plattner, L.Shapiro, S.A.Martinis, S.J.Benkovic, S.Cusack, M.R.K.Alley. An Antifungal Agent Inhibits An Aminoacyl-Trna Synthetase By Trapping Trna in the Editing Site. Science V. 316 1759 2007.
ISSN: ISSN 0036-8075
PubMed: 17588934
DOI: 10.1126/SCIENCE.1142189