Magnesium in PDB 9m1f: Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State

All present enzymatic activity of Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State:
6.1.1.2;

The structure of Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State, PDB code: 9m1f was solved by Y.Ren, S.Wang, W.Liu, P.Fang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.45 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.39, 95.28, 64.543, 90, 109.35, 90
R / Rfree (%)	18.2 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State (pdb code 9m1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State, PDB code: 9m1f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:11.9 occ:1.00 O A:HOH644 2.0 13.4 1.0 O A:HOH576 2.1 13.6 1.0 O2A A:ATP402 2.1 10.4 1.0 O2B A:ATP402 2.1 12.5 1.0 O A:HOH540 2.2 11.8 1.0 O3G A:ATP402 2.2 13.4 1.0 PB A:ATP402 3.2 12.3 1.0 PA A:ATP402 3.3 12.4 1.0 O3B A:ATP402 3.3 13.2 1.0 PG A:ATP402 3.4 13.5 1.0 O3A A:ATP402 3.4 13.2 1.0 NE2 A:GLN11 3.8 13.2 1.0 O5' A:ATP402 3.9 10.5 1.0 O02 A:9E0401 4.0 14.9 1.0 O A:HOH565 4.0 16.4 1.0 NZ A:LYS195 4.0 10.7 1.0 O2G A:ATP402 4.1 17.7 1.0 O A:HOH606 4.1 23.2 1.0 O01 A:9E0401 4.1 13.3 1.0 NZ A:LYS113 4.1 19.8 1.0 OD2 A:ASP149 4.4 15.1 1.0 C11 A:9E0401 4.4 15.6 1.0 OE1 A:GLN109 4.5 15.1 1.0 O1B A:ATP402 4.5 13.8 1.0 CE A:LYS195 4.5 14.8 1.0 O1A A:ATP402 4.5 10.7 1.0 O1G A:ATP402 4.6 13.4 1.0 C8 A:ATP402 4.8 15.8 1.0 NE2 A:GLN150 4.8 13.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Closed-Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:10.3 occ:1.00 O B:HOH554 2.1 8.6 1.0 O3G B:ATP402 2.1 7.4 1.0 O B:HOH709 2.1 10.1 1.0 O2B B:ATP402 2.1 11.1 1.0 O2A B:ATP402 2.1 8.1 1.0 O B:HOH566 2.1 8.3 1.0 PB B:ATP402 3.1 10.0 1.0 PG B:ATP402 3.3 12.0 1.0 O3B B:ATP402 3.3 12.1 1.0 PA B:ATP402 3.3 9.4 1.0 O3A B:ATP402 3.4 11.4 1.0 NE2 B:GLN11 3.7 14.3 1.0 O5' B:ATP402 3.9 10.0 1.0 O02 B:9E0401 4.0 12.4 1.0 O B:HOH599 4.0 11.5 1.0 O2G B:ATP402 4.0 12.7 1.0 NZ B:LYS195 4.1 9.4 1.0 NZ B:LYS113 4.1 15.7 1.0 O01 B:9E0401 4.1 12.3 1.0 O B:HOH638 4.2 16.4 1.0 OD2 B:ASP149 4.3 16.5 1.0 O B:HOH695 4.4 24.4 1.0 O1G B:ATP402 4.4 11.2 1.0 C11 B:9E0401 4.4 8.8 1.0 O1B B:ATP402 4.5 12.4 1.0 CE B:LYS195 4.5 10.6 1.0 OE1 B:GLN109 4.5 13.7 1.0 O1A B:ATP402 4.6 8.8 1.0 C8 B:ATP402 4.8 11.3 1.0 NE2 B:GLN150 4.9 10.4 1.0

Y.Ren, S.Wang, W.Liu, J.Wang, P.Fang. Mechanistic Insights Into the Atp-Mediated and Species-Dependent Inhibition of Trprs By Chuangxinmycin. Rsc Chem Biol V. 6 1079 2025.
ISSN: ESSN 2633-0679
PubMed: 40406164
DOI: 10.1039/D5CB00060B