Calcium in PDB 5igy: Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Erythromycin

The structure of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Erythromycin, PDB code: 5igy 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)	41.82 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.870, 80.520, 97.870, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.6

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Erythromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.0 occ:1.00 O1A A:GDP402 2.3 9.2 1.0 O A:HOH742 2.3 17.1 1.0 O2B A:GDP402 2.4 11.8 1.0 O A:HOH756 2.4 8.0 1.0 OD2 A:ASP219 2.4 11.2 1.0 NE2 A:HIS205 2.5 8.6 1.0 O3' A:GDP402 2.8 15.0 1.0 HO3' A:GDP402 2.8 18.0 1.0 CE1 A:HIS205 3.4 6.4 1.0 HB2 A:ASP219 3.4 8.4 1.0 CG A:ASP219 3.4 9.3 1.0 HE1 A:HIS205 3.4 7.6 1.0 H5' A:GDP402 3.5 14.2 1.0 PB A:GDP402 3.5 10.1 1.0 CD2 A:HIS205 3.6 8.7 1.0 PA A:GDP402 3.6 10.8 1.0 HD2 A:HIS205 3.8 10.4 1.0 CB A:ASP219 3.8 7.0 1.0 H3' A:GDP402 3.8 17.0 1.0 C3' A:GDP402 3.8 14.2 1.0 O3A A:GDP402 3.8 10.7 1.0 HB3 A:ASP219 3.8 8.4 1.0 O1B A:GDP402 4.0 12.5 1.0 O A:HOH605 4.1 14.5 1.0 HA2 A:GLY30 4.2 20.6 1.0 O A:HOH564 4.3 14.5 1.0 C5' A:GDP402 4.3 11.8 1.0 O A:HOH580 4.3 15.2 1.0 O A:HOH690 4.3 9.2 1.0 O A:HOH776 4.4 15.7 1.0 O5' A:GDP402 4.4 9.9 1.0 ND1 A:HIS205 4.5 7.5 1.0 OD1 A:ASP219 4.5 9.8 1.0 C4' A:GDP402 4.6 14.5 1.0 CG A:HIS205 4.6 7.7 1.0 O2A A:GDP402 4.7 12.3 1.0 HA3 A:GLY30 4.8 20.6 1.0 H4' A:GDP402 4.8 17.4 1.0 O3B A:GDP402 4.8 10.2 1.0 HD12 A:ILE218 4.9 11.8 1.0 CA A:GLY30 4.9 17.2 1.0 HE2 A:HIS202 4.9 11.7 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