Magnesium in PDB 4ari: Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation

All present enzymatic activity of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation:
6.1.1.4;

The structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation, PDB code: 4ari was solved by A.Palencia, T.Crepin, M.T.Vu, T.L.Lincecum Jr, S.A.Martinis, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.91 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.180, 118.940, 141.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.4

The binding sites of Magnesium atom in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation (pdb code 4ari). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation, PDB code: 4ari:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1865 b:51.8 occ:1.00 O A:TYR239 2.0 43.3 1.0 O A:HOH2108 2.5 40.4 1.0 O A:VAL236 2.6 35.2 1.0 C A:TYR239 3.2 46.9 1.0 C A:VAL236 3.7 37.2 1.0 N A:TYR239 3.8 45.4 1.0 O A:ASN241 3.9 36.5 1.0 CA A:TYR239 4.1 46.6 1.0 N A:ASP240 4.2 48.5 1.0 N A:VAL236 4.3 30.8 1.0 N A:ASN241 4.3 44.9 1.0 CA A:ASP240 4.3 50.1 1.0 CB A:TYR239 4.5 44.9 1.0 CA A:VAL236 4.6 35.2 1.0 N A:ASP238 4.6 46.2 1.0 N A:ASN237 4.7 41.9 1.0 C A:ASN241 4.8 40.3 1.0 C A:ASP240 4.8 49.6 1.0 CA A:ASN237 4.8 41.6 1.0 C A:ASN237 4.9 43.0 1.0 OD1 A:ASP240 5.0 64.1 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN2679 in the Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1076 b:44.1 occ:1.00 O B:HOH2005 1.8 39.0 1.0 OP1 B:U8 2.0 35.8 1.0 OP2 B:G9 2.2 38.2 1.0 O B:HOH2003 2.5 31.0 1.0 P B:U8 3.4 43.3 1.0 P B:G9 3.6 40.8 1.0 O5' B:U8 4.0 41.5 1.0 OP2 B:U8 4.2 41.3 1.0 OP1 B:G9 4.2 42.6 1.0 C5' B:U8 4.4 37.8 1.0 O5' B:G9 4.4 37.4 1.0 O3' B:A7 4.5 45.4 1.0 C5' B:G9 4.5 36.0 1.0 O B:HOH2006 4.6 35.1 1.0 O3' B:U8 4.8 38.4 1.0 OP1 B:U11 5.0 40.6 1.0

A.Palencia, T.Crepin, M.T.Vu, T.L.Lincecum Jr, S.A.Martinis, S.Cusack. Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-Trna Synthetase Nat.Struct.Mol.Biol. V. 19 677 2012.
ISSN: ISSN 1545-9993
PubMed: 22683997
DOI: 10.1038/NSMB.2317