Calcium in PDB 5u1i: Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B

The structure of Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B, PDB code: 5u1i 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)	43.90 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.045, 70.052, 86.008, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.4

The binding sites of Calcium atom in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B (pdb code 5u1i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B, PDB code: 5u1i:

Calcium binding site 1 out of 1 in the Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Methyltransferase Involved in the Biosynthesis of Gentamicin in Complex with the Methylated Kanamycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.4 occ:1.00 OE1 A:GLU98 2.3 25.3 1.0 O A:HOH632 2.3 28.9 1.0 OD2 A:ASP206 2.4 14.0 1.0 O A:HOH556 2.4 13.9 1.0 O A:HOH626 2.4 26.5 1.0 O A:HOH569 2.4 17.0 1.0 CG A:ASP206 3.4 20.3 1.0 CD A:GLU98 3.5 26.2 1.0 OD1 A:ASP206 3.7 12.2 1.0 OE1 A:GLN101 4.0 19.9 1.0 OE2 A:GLU98 4.3 23.2 1.0 CB A:GLU98 4.5 14.7 1.0 CG A:GLU98 4.5 18.3 1.0 OE1 A:GLU209 4.5 17.4 1.0 O A:HOH593 4.6 18.6 1.0 O A:HOH647 4.6 13.8 1.0 CB A:ASP206 4.7 15.3 1.0 O A:GLU98 4.8 14.5 1.0 CG1 A:VAL205 4.9 14.4 1.0 CD A:GLN101 4.9 15.4 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