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

The structure of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Clarithromycin, PDB code: 5igw 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)	37.45 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.173, 81.103, 97.580, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 22.9

The binding sites of Magnesium atom in the Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Clarithromycin (pdb code 5igw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Clarithromycin, PDB code: 5igw:
Jump to Magnesium binding site number: 1; 2;

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


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 Clarithromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:29.4 occ:1.00 O A:HOH590 2.3 24.5 1.0 O A:HOH563 2.4 30.1 1.0 OD1 A:ASP219 2.6 38.2 1.0 O A:HOH526 2.6 28.6 1.0 OG1 A:THR221 2.7 29.3 1.0 OD2 A:ASP219 2.7 50.5 1.0 CG A:ASP219 3.0 40.7 1.0 CG2 A:THR221 3.7 24.5 1.0 CB A:THR221 3.7 28.2 1.0 O1B A:GDP401 3.8 42.2 1.0 O A:HOH675 3.8 32.4 1.0 MG A:MG403 4.4 40.9 1.0 CB A:ASP219 4.5 29.1 1.0 OE2 A:GLU222 4.5 31.7 1.0 OD2 A:ASP200 4.5 23.4 1.0 O A:HOH657 4.5 44.5 1.0 C28 A:CTY404 4.6 22.2 1.0 N A:THR221 4.7 21.7 1.0 PB A:GDP401 4.8 43.8 0.7 CA A:THR221 4.8 21.5 1.0 C29 A:CTY404 4.9 29.9 1.0 O3B A:GDP401 5.0 37.6 0.8 N1 A:CTY404 5.0 28.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Clarithromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:40.9 occ:1.00 O A:HOH637 2.1 32.6 1.0 O A:HOH675 2.1 32.4 1.0 OD2 A:ASP219 2.2 50.5 1.0 O1A A:GDP401 2.2 33.9 1.0 O3B A:GDP401 2.3 37.6 0.8 NE2 A:HIS205 2.4 19.6 1.0 CE1 A:HIS205 3.2 20.3 1.0 CG A:ASP219 3.3 40.7 1.0 CD2 A:HIS205 3.4 21.4 1.0 PB A:GDP401 3.5 43.8 0.7 PA A:GDP401 3.5 44.7 0.6 O A:HOH590 3.7 24.5 1.0 CB A:ASP219 3.7 29.1 1.0 O3A A:GDP401 3.8 41.8 0.7 O1B A:GDP401 3.9 42.2 1.0 O A:HOH533 4.0 25.7 1.0 O A:HOH700 4.1 46.9 1.0 O A:HOH759 4.1 37.8 1.0 O3' A:GDP401 4.3 48.4 1.0 ND1 A:HIS205 4.4 19.9 1.0 OD1 A:ASP219 4.4 38.2 1.0 MG A:MG402 4.4 29.4 1.0 O5' A:GDP401 4.5 54.5 1.0 C5' A:GDP401 4.5 52.6 1.0 CG A:HIS205 4.5 18.6 1.0 O2A A:GDP401 4.5 45.7 1.0 O A:HOH526 4.7 28.6 1.0 O2B A:GDP401 4.7 42.5 0.6 C3' A:GDP401 4.8 47.7 1.0 O A:HOH563 4.9 30.1 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