Sodium in PDB 7ap3: Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA

All present enzymatic activity of Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA:
6.1.1.1;

The structure of Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA, PDB code: 7ap3 was solved by S.De Graef, L.Pang, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.68 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.166, 65.124, 90.978, 90.00, 101.33, 90.00
R / Rfree (%)	20.3 / 25.3

The binding sites of Sodium atom in the Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA (pdb code 7ap3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA, PDB code: 7ap3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:35.1 occ:1.00 O3' A:RRB501 2.7 26.4 1.0 O A:HOH684 2.8 25.9 1.0 O A:GLY39 2.9 22.4 1.0 C3' A:RRB501 3.1 22.7 1.0 C05 A:RRB501 3.6 21.6 1.0 C4' A:RRB501 3.6 22.6 1.0 CG A:GLN201 3.7 27.4 1.0 SG A:CYS38 3.8 30.9 1.0 CA A:RRB501 3.9 27.5 1.0 C A:GLY39 3.9 26.5 1.0 C5' A:RRB501 3.9 28.2 1.0 N A:GLY39 3.9 26.0 1.0 CB A:RRB501 3.9 25.6 1.0 N3S A:RRB501 4.0 33.3 1.0 C04 A:RRB501 4.3 28.2 1.0 CD A:GLN201 4.3 34.3 1.0 CA A:GLY39 4.3 28.8 1.0 CA A:GLY197 4.3 21.8 1.0 NE2 A:GLN201 4.4 26.0 1.0 O A:ILE196 4.4 22.7 1.0 CB A:GLN201 4.5 20.8 1.0 C2' A:RRB501 4.5 33.2 1.0 C A:RRB501 4.6 28.6 1.0 C06 A:RRB501 4.7 24.8 1.0 O5' A:RRB501 4.8 28.8 1.0 NE2 A:GLN179 4.8 28.5 1.0 O2' A:RRB501 4.9 30.7 1.0 C A:CYS38 5.0 24.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of E. Coli Tyrosyl-Trna Synthetase in Complex with TYRS7HMDDA within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:31.3 occ:1.00 O3' B:RRB501 2.8 24.5 1.0 O B:HOH614 2.8 25.5 1.0 O B:GLY39 2.8 21.1 1.0 C3' B:RRB501 3.1 23.5 1.0 C05 B:RRB501 3.6 32.1 1.0 C4' B:RRB501 3.7 21.7 1.0 CG B:GLN201 3.7 23.6 1.0 SG B:CYS38 3.7 27.7 1.0 C B:GLY39 3.9 24.4 1.0 N B:GLY39 3.9 17.4 1.0 CB B:RRB501 4.0 25.3 1.0 CA B:RRB501 4.0 20.9 1.0 C5' B:RRB501 4.1 17.2 1.0 CA B:GLY197 4.1 24.1 1.0 N3S B:RRB501 4.2 26.2 1.0 C04 B:RRB501 4.3 30.3 1.0 O B:ILE196 4.3 21.3 1.0 CA B:GLY39 4.3 25.1 1.0 CD B:GLN201 4.3 29.2 1.0 CB B:GLN201 4.5 26.8 1.0 C2' B:RRB501 4.5 22.8 1.0 OE1 B:GLN201 4.6 30.1 1.0 C06 B:RRB501 4.6 24.6 1.0 C B:RRB501 4.7 22.1 1.0 NE2 B:GLN179 4.8 26.7 1.0 O5' B:RRB501 4.9 24.9 1.0 N B:GLY198 4.9 23.8 1.0 C B:CYS38 5.0 26.2 1.0

B.Zhang, L.Pang, M.Nautiyal, S.De Graef, B.Gadakh, E.Lescrinier, J.Rozenski, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues As Aminoacyl-Trna Synthetase Inhibitors. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33081246
DOI: 10.3390/MOLECULES25204751