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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 7ap3

Go back to Sodium Binding Sites List in 7ap3
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 7ap3

Go back to Sodium Binding Sites List in 7ap3
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

Reference:

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
Page generated: Tue Dec 15 17:25:43 2020

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