Magnesium in PDB 3zju: Ternary Complex of E .Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN3016 in the Editing Conformation

All present enzymatic activity of Ternary Complex of E .Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN3016 in the Editing Conformation:
6.1.1.4;

The structure of Ternary Complex of E .Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN3016 in the Editing Conformation, PDB code: 3zju was solved by S.Cusack, A.Palencia, T.Crepin, V.Hernandez, T.Akama, S.J.Baker, W.Bu, L.Feng, Y.R.Freund, L.Liu, M.Meewan, M.Mohan, W.Mao, F.L.Rock, H.Sexton, A.Sheoran, Y.Zhang, Y.Zhang, Y.Zhou, J.A.Nieman, M.R.Anugula, E.M.Keramane, K.Savariraj, D.S.Reddy, R.Sharma, R.Subedi, R.Singh, A.Oleary, N.L.Simon, P.L.Demarsh, S.Mushtaq, M.Warner, D.M.Livermore, M.R.K.Alley, J.J.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.720, 120.030, 142.810, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.1

The binding sites of Magnesium atom in the Ternary Complex of E .Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN3016 in the Editing Conformation (pdb code 3zju). 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 AN3016 in the Editing Conformation, PDB code: 3zju:
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 AN3016 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 AN3016 in the Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1861 b:47.3 occ:1.00 OP1 B:A14 2.7 46.3 1.0 O5' B:A14 3.2 43.5 1.0 P B:A14 3.6 48.3 1.0 ND2 A:ASN723 3.6 22.6 1.0 CG A:PRO651 3.7 20.7 1.0 OD1 A:ASN723 4.0 26.4 1.0 O3' B:A14 4.2 32.7 1.0 CG A:ASN723 4.3 24.9 1.0 CG2 A:THR724 4.3 21.4 1.0 CG2 A:THR721 4.3 23.8 1.0 C5' B:A14 4.4 35.8 1.0 OP2 B:A15 4.4 31.1 1.0 CB A:PRO651 4.4 20.5 1.0 O3' B:G13 4.5 47.7 1.0 C4' B:A14 4.5 33.5 1.0 CB A:THR721 4.6 22.8 1.0 CD A:PRO651 4.6 21.6 1.0 P B:A15 4.6 32.6 1.0 OP1 B:A15 4.7 35.2 1.0 OP2 B:A14 4.8 40.4 1.0 C3' B:A14 4.9 32.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of E .Coli Leucyl-Trna Synthetase, Trna(Leu) and the Benzoxaborole AN3016 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 AN3016 in the Editing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1862 b:55.7 occ:1.00 OP2 B:U16 2.1 54.6 1.0 O2 B:U60 2.5 37.5 1.0 OP1 B:G19 2.6 36.0 1.0 O6 B:G59 2.7 35.9 1.0 OP2 B:G19 3.1 33.0 1.0 P B:G19 3.1 34.5 1.0 C2 B:U60 3.4 37.2 1.0 P B:U16 3.5 55.4 1.0 N3 B:U60 3.6 36.9 1.0 C6 B:G59 3.6 35.3 1.0 O3' B:G18 3.7 34.7 1.0 N1 B:G59 4.0 39.3 1.0 O5' B:U16 4.1 50.2 1.0 O2' B:C17 4.2 74.5 1.0 C3' B:G18 4.3 39.0 1.0 OP1 B:U16 4.3 51.8 1.0 O2' B:A15 4.4 40.2 1.0 C4' B:G18 4.5 43.0 1.0 O3' B:A15 4.6 45.9 1.0 C2' B:A15 4.6 37.4 1.0 O5' B:G19 4.6 37.5 1.0 N1 B:U60 4.7 41.4 1.0 C5 B:G59 4.8 36.1 1.0 C5' B:G18 4.9 49.0 1.0 C4 B:U60 4.9 38.1 1.0

V.Hernandez, T.Crepin, A.Palencia, S.Cusack, T.Akama, S.J.Baker, W.Bu, L.Feng, Y.R.Freund, L.Liu, M.Meewan, M.Mohan, W.Mao, F.L.Rock, H.Sexton, A.Sheoran, Y.Zhang, Y.Zhang, Y.Zhou, J.A.Nieman, M.R.Anugula, E.M.Keramane, K.Savariraj, D.S.Reddy, R.Sharma, R.Subedi, R.Singh, A.O'leary, N.L.Simon, P.L.De Marsh, S.Mushtaq, M.Warner, D.M.Livermore, M.R.K.Alley, J.J.Plattner. Discovery of A Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria. Antimicrob.Agents Chemother. V. 57 1394 2013.
ISSN: ISSN 0066-4804
PubMed: 23295920
DOI: 10.1128/AAC.02058-12