Magnesium in PDB 5ih0: Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin

The structure of Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin, PDB code: 5ih0 was solved by A.M.Berghuis, D.H.Fong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.40 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.920, 80.090, 96.710, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21

The binding sites of Magnesium atom in the Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin (pdb code 5ih0). 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 Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin, PDB code: 5ih0:

Magnesium binding site 1 out of 1 in the Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Macrolide 2'-Phosphotransferase Type II Y92M Mutant - Complex with Gdp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.7 occ:1.00 HE2 A:HIS205 1.6 10.7 1.0 O A:HOH645 2.0 21.4 1.0 O1A A:GDP403 2.1 32.0 0.9 O A:HOH705 2.2 19.3 1.0 O2B A:GDP403 2.2 44.0 0.9 OD2 A:ASP219 2.2 19.9 1.0 NE2 A:HIS205 2.4 8.9 1.0 PB A:GDP403 3.1 54.5 0.9 CE1 A:HIS205 3.1 8.0 1.0 HE1 A:HIS205 3.2 9.5 1.0 CG A:ASP219 3.3 17.2 1.0 O1B A:GDP403 3.3 59.7 0.9 HB2 A:ASP219 3.4 15.9 1.0 PA A:GDP403 3.4 39.4 0.9 CD2 A:HIS205 3.5 8.4 1.0 O3A A:GDP403 3.7 47.1 0.9 CB A:ASP219 3.7 13.3 1.0 HD2 A:HIS205 3.7 10.1 1.0 H5' A:GDP403 3.8 53.3 1.0 HB3 A:ASP219 3.8 15.9 1.0 O A:HOH560 3.8 26.8 1.0 H3' A:GDP403 4.0 47.7 1.0 HO3' A:GDP403 4.1 46.2 1.0 O3' A:GDP403 4.1 38.5 1.0 O A:HOH661 4.2 18.4 1.0 ND1 A:HIS205 4.3 7.2 1.0 O2A A:GDP403 4.3 46.7 0.9 O5' A:GDP403 4.4 46.5 1.0 OD1 A:ASP219 4.4 18.4 1.0 O3B A:GDP403 4.5 58.4 0.9 CG A:HIS205 4.5 7.3 1.0 C5' A:GDP403 4.6 44.4 1.0 C3' A:GDP403 4.6 39.8 1.0 O A:HOH524 4.6 3.7 1.0 HE2 A:HIS202 4.7 12.2 1.0 O A:HOH869 4.8 33.8 1.0 O A:HOH550 4.9 17.2 1.0

D.H.Fong, D.L.Burk, J.Blanchet, A.Y.Yan, A.M.Berghuis. Structural Basis For Kinase-Mediated Macrolide Antibiotic Resistance. Structure V. 25 750 2017.
ISSN: ISSN 1878-4186
PubMed: 28416110
DOI: 10.1016/J.STR.2017.03.007