Magnesium in PDB 5u0t: Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside

The structure of Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside, PDB code: 5u0t was solved by P.Bury, F.Huang, P.Leadlay, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.58 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.815, 69.886, 84.700, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 22

The binding sites of Magnesium atom in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside (pdb code 5u0t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside, PDB code: 5u0t:

Magnesium binding site 1 out of 1 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside


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 A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with (1R,2S,3S,4R,6S)-4,6-Diamino-3-{[3- Deoxy-3-(Methylamino)-Alpha-D-Glucopyranosyl]Oxy}-2-Hydroxycyclohexyl 2,6-Diamino-2,6-Dideoxy-Alpha-D-Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.2 occ:1.00 O A:HOH556 2.0 20.5 1.0 OD2 A:ASP206 2.0 23.6 1.0 OE1 A:GLU98 2.1 28.2 1.0 O A:HOH609 2.2 19.2 1.0 O A:HOH512 2.2 20.1 1.0 O A:HOH573 2.2 23.6 1.0 CG A:ASP206 2.9 21.5 1.0 OD1 A:ASP206 3.2 15.0 1.0 CD A:GLU98 3.3 27.8 1.0 OE1 A:GLN101 3.9 29.1 1.0 O A:HOH531 3.9 29.4 1.0 O A:HOH656 4.1 23.9 1.0 OE2 A:GLU98 4.1 26.0 1.0 O A:HOH645 4.1 29.4 1.0 CG A:GLU98 4.3 30.5 1.0 CB A:ASP206 4.3 16.6 1.0 OE1 A:GLU209 4.4 26.1 1.0 CB A:GLU98 4.5 28.5 1.0 O A:HOH597 4.7 46.0 1.0 CD A:GLN101 4.8 27.1 1.0 O A:GLU98 4.8 27.1 1.0 CG1 A:VAL205 4.8 16.0 1.0 CA A:GLU98 5.0 28.1 1.0 CB A:LEU208 5.0 15.3 1.0

P.D.S.Bury, F.Huang, S.Li, Y.Sun, P.F.Leadlay, M.V.B.Dias. Structural Basis of the Selectivity of Genn, An Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis. Acs Chem. Biol. V. 12 2779 2017.
ISSN: ESSN 1554-8937
PubMed: 28876898
DOI: 10.1021/ACSCHEMBIO.7B00466