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

The structure of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Spiramycin, PDB code: 5igz 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)	44.90 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.240, 72.430, 77.080, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

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


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 Spiramycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:24.8 occ:1.00 O3B A:GDP401 2.3 16.1 1.0 O A:HOH555 2.3 22.8 1.0 OD1 A:ASP219 2.3 15.1 1.0 O A:HOH723 2.6 20.3 1.0 OD2 A:ASP219 2.7 17.6 1.0 CG A:ASP219 2.8 13.1 1.0 OG1 A:THR221 3.0 24.2 1.0 HG21 A:THR221 3.3 28.3 1.0 HG23 A:THR221 3.3 28.3 1.0 OD2 A:ASP32 3.5 22.7 1.0 HG1 A:THR221 3.6 29.0 1.0 CG2 A:THR221 3.7 23.6 1.0 PB A:GDP401 3.7 16.8 1.0 HH21 A:ARG49 3.9 20.4 1.0 HB2 A:ASP32 3.9 18.5 1.0 HH22 A:ARG49 3.9 20.4 1.0 O1B A:GDP401 4.0 18.7 1.0 CB A:THR221 4.0 23.1 1.0 H A:THR221 4.1 20.1 1.0 O A:HOH525 4.2 39.4 1.0 NH2 A:ARG49 4.2 17.0 1.0 OD2 A:ASP200 4.2 21.5 1.0 HE2 A:PHE33 4.3 22.0 1.0 CB A:ASP219 4.4 14.9 1.0 HD2 A:PHE33 4.4 19.1 1.0 MG A:MG403 4.4 15.8 1.0 CG A:ASP32 4.4 25.1 1.0 H7A1 A:SPR404 4.5 20.3 1.0 HG22 A:THR221 4.6 28.3 1.0 O A:HOH679 4.6 14.0 1.0 O3A A:GDP401 4.6 14.9 1.0 CB A:ASP32 4.6 15.4 1.0 HB A:THR221 4.6 27.7 1.0 HH22 A:ARG59 4.6 35.8 1.0 H7A3 A:SPR404 4.6 20.3 1.0 H8A2 A:SPR404 4.6 24.3 1.0 HH21 A:ARG59 4.7 35.8 1.0 O2B A:GDP401 4.7 17.9 1.0 H8A1 A:SPR404 4.8 24.3 1.0 HB3 A:ASP219 4.8 17.9 1.0 HB2 A:ASP219 4.8 17.9 1.0 C7A A:SPR404 4.8 17.0 1.0 HA A:ASP219 4.8 16.3 1.0 OE2 A:GLU222 4.8 31.4 1.0 HB3 A:ASP32 4.9 18.5 1.0 N A:THR221 4.9 16.7 1.0 HE1 A:HIS205 4.9 16.7 1.0 NH2 A:ARG59 4.9 29.9 1.0 HG2 A:GLU222 4.9 29.2 1.0 H7A2 A:SPR404 4.9 20.3 1.0 CE2 A:PHE33 5.0 18.4 1.0 N3A A:SPR404 5.0 16.3 1.0

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


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 Spiramycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:15.8 occ:1.00 O1A A:GDP401 2.0 15.2 1.0 O1B A:GDP401 2.0 18.7 1.0 NE2 A:HIS205 2.1 15.0 1.0 OD2 A:ASP219 2.1 17.6 1.0 O A:HOH647 2.2 15.0 1.0 O A:HOH679 2.2 14.0 1.0 CE1 A:HIS205 3.0 13.9 1.0 HE1 A:HIS205 3.1 16.7 1.0 CG A:ASP219 3.1 13.1 1.0 PB A:GDP401 3.2 16.8 1.0 HE2 A:HIS202 3.2 19.2 1.0 CD2 A:HIS205 3.2 15.2 1.0 PA A:GDP401 3.2 16.3 1.0 HB2 A:ASP219 3.3 17.9 1.0 HD2 A:HIS205 3.4 18.2 1.0 O3A A:GDP401 3.5 14.9 1.0 HB3 A:ASP219 3.5 17.9 1.0 CB A:ASP219 3.5 14.9 1.0 O3B A:GDP401 3.8 16.1 1.0 O A:HOH541 3.9 16.7 1.0 H5' A:GDP401 4.0 19.1 1.0 NE2 A:HIS202 4.0 16.0 1.0 H3' A:GDP401 4.2 20.0 1.0 ND1 A:HIS205 4.2 15.2 1.0 O2A A:GDP401 4.2 17.3 1.0 O A:HOH723 4.2 20.3 1.0 OD1 A:ASP219 4.2 15.1 1.0 HO3' A:GDP401 4.3 21.0 1.0 O3' A:GDP401 4.3 17.6 1.0 CG A:HIS205 4.3 13.7 1.0 OD2 A:ASP200 4.3 21.5 1.0 HA2 A:GLY30 4.4 21.2 1.0 HO2A A:SPR404 4.4 18.4 1.0 O5' A:GDP401 4.4 15.7 1.0 MG A:MG402 4.4 24.8 1.0 O2B A:GDP401 4.5 17.9 1.0 O A:HOH609 4.6 16.1 1.0 O A:HOH704 4.6 17.5 1.0 C5' A:GDP401 4.7 16.0 1.0 HE1 A:HIS202 4.7 20.8 1.0 C3' A:GDP401 4.7 16.7 1.0 CE1 A:HIS202 4.8 17.4 1.0 HA3 A:GLY30 4.8 21.2 1.0 HD12 A:ILE218 4.9 20.9 1.0 HD1 A:HIS205 4.9 18.1 1.0 O A:HOH555 5.0 22.8 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