Magnesium in PDB 9m1g: Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Open-Closed State

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

The structure of Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Open-Closed State, PDB code: 9m1g 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)	24.09 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.01, 94.61, 67.34, 90, 111.46, 90
R / Rfree (%)	18 / 19

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Tryptophanyl-Trna Synthetase Complexed with Chuangxinmycin and Atp in Open-Closed State (pdb code 9m1g). 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 Open-Closed State, PDB code: 9m1g:
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 Open-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 Open-Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:71.3 occ:1.00 O2A A:ATP402 2.5 82.0 1.0 O3A A:ATP402 2.8 79.3 1.0 PA A:ATP402 3.0 84.9 1.0 O5' A:ATP402 3.3 71.3 1.0 O2B A:ATP402 3.4 77.1 1.0 PB A:ATP402 3.6 82.5 1.0 C2' A:ATP402 3.8 71.4 1.0 CA A:GLY147 3.8 51.9 1.0 O3B A:ATP402 3.8 85.8 1.0 N A:GLU148 4.2 49.6 1.0 O2' A:ATP402 4.3 67.3 1.0 C A:GLY147 4.4 50.2 1.0 O3G A:ATP402 4.4 80.6 1.0 C3' A:ATP402 4.4 67.7 1.0 C8 A:ATP402 4.5 60.8 1.0 O1A A:ATP402 4.5 72.0 1.0 C5' A:ATP402 4.6 66.3 1.0 N A:ASP149 4.7 46.3 1.0 N A:GLY147 4.8 52.0 1.0 CB A:ASP149 4.8 50.1 1.0 PG A:ATP402 4.8 89.7 1.0 N9 A:ATP402 4.9 63.7 1.0 C1' A:ATP402 4.9 65.9 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 Open-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 Open-Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:30.6 occ:1.00 O B:HOH640 1.8 33.3 1.0 O B:HOH577 1.9 29.3 1.0 O B:HOH579 1.9 30.8 1.0 O3G B:ATP402 2.1 28.6 1.0 O2B B:ATP402 2.1 28.1 1.0 O2A B:ATP402 2.4 29.9 1.0 PB B:ATP402 3.3 28.4 1.0 PG B:ATP402 3.3 35.8 1.0 O3B B:ATP402 3.4 34.4 1.0 PA B:ATP402 3.6 29.5 1.0 O3A B:ATP402 3.7 31.0 1.0 O B:HOH501 3.8 34.6 1.0 NZ B:LYS113 3.9 39.9 1.0 O B:HOH611 3.9 34.8 1.0 O2G B:ATP402 3.9 33.5 1.0 NE2 B:GLN11 3.9 30.3 1.0 NZ B:LYS195 4.0 30.6 1.0 O02 B:9E0401 4.1 27.1 1.0 O5' B:ATP402 4.2 31.2 1.0 O01 B:9E0401 4.2 27.2 1.0 OD2 B:ASP149 4.2 30.8 1.0 CE B:LYS195 4.2 31.5 1.0 OE1 B:GLN109 4.3 28.8 1.0 O1G B:ATP402 4.5 34.7 1.0 C11 B:9E0401 4.6 29.8 1.0 O1B B:ATP402 4.6 29.4 1.0 CE B:LYS113 4.6 39.5 1.0 NE2 B:GLN150 4.7 26.1 1.0 C8 B:ATP402 4.9 31.4 1.0 O1A B:ATP402 4.9 29.9 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