Magnesium in PDB 5igv: Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Azithromycin

The structure of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Azithromycin, PDB code: 5igv 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)	41.36 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.230, 80.450, 96.430, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.9

The structure of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Azithromycin also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

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

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


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 - Complex with Gdp and Azithromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:17.0 occ:1.00 OD2 A:ASP219 1.6 35.3 0.2 HE2 A:HIS205 1.6 19.8 1.0 O3B A:GDP403 2.1 20.4 0.8 O A:HOH770 2.1 22.4 1.0 O1A A:GDP403 2.2 18.3 0.9 O A:HOH578 2.2 28.8 1.0 OD2 A:ASP219 2.3 17.7 0.8 NE2 A:HIS205 2.4 16.5 1.0 CG A:ASP219 2.7 28.4 0.2 CE1 A:HIS205 3.2 13.4 1.0 OD1 A:ASP219 3.2 13.1 0.2 HB2 A:ASP219 3.3 12.6 0.8 HE1 A:HIS205 3.3 16.1 1.0 CG A:ASP219 3.3 20.6 0.8 PA A:GDP403 3.4 24.1 0.9 PB A:GDP403 3.4 23.8 0.8 CD2 A:HIS205 3.4 11.7 1.0 H5' A:GDP403 3.6 47.4 1.0 CB A:ASP219 3.6 10.5 0.8 HD2 A:HIS205 3.6 14.1 1.0 HB3 A:ASP219 3.7 12.6 0.8 O A:HOH711 3.7 21.7 1.0 O3A A:GDP403 3.7 24.8 0.9 CB A:ASP219 3.9 23.4 0.2 HB3 A:ASP219 4.0 28.0 0.2 H3' A:GDP403 4.0 40.2 1.0 O A:HOH812 4.0 43.9 1.0 O A:HOH625 4.1 24.8 1.0 HB2 A:ASP219 4.1 28.0 0.2 O A:HOH799 4.1 55.7 1.0 O1B A:GDP403 4.1 25.4 0.8 HO3' A:GDP403 4.2 44.0 1.0 O3' A:GDP403 4.2 36.6 1.0 O A:HOH854 4.3 36.4 1.0 ND1 A:HIS205 4.4 11.8 1.0 O2A A:GDP403 4.4 23.3 0.9 OD1 A:ASP219 4.5 20.2 0.8 O5' A:GDP403 4.5 37.3 1.0 C5' A:GDP403 4.5 39.5 1.0 CA A:CA402 4.5 22.6 1.0 CG A:HIS205 4.5 9.9 1.0 O2B A:GDP403 4.5 29.4 0.8 C3' A:GDP403 4.6 33.5 1.0 HE2 A:HIS202 4.6 17.6 1.0 O A:HOH610 4.8 18.9 1.0 O A:HOH592 4.9 19.7 1.0 HA A:ASP219 5.0 12.4 0.2

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