Atomistry » Calcium » PDB 5i77-5ik8 » 5igv
Atomistry »
  Calcium »
    PDB 5i77-5ik8 »
      5igv »

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

Protein crystallography data

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

Other elements in 5igv:

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

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Macrolide 2'-Phosphotransferase Type II - Complex with Gdp and Azithromycin, PDB code: 5igv:

Calcium binding site 1 out of 1 in 5igv

Go back to Calcium Binding Sites List in 5igv
Calcium 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 Calcium with other atoms in the Ca 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:Ca402

b:22.6
occ:1.00
O A:HOH711 2.4 21.7 1.0
O A:HOH774 2.4 33.8 1.0
O A:HOH592 2.4 19.7 1.0
O A:HOH780 2.4 24.9 1.0
OG1 A:THR221 2.4 15.8 1.0
OD1 A:ASP219 2.5 20.2 0.8
O A:HOH610 2.5 18.9 1.0
OD2 A:ASP219 2.5 17.7 0.8
CG A:ASP219 2.8 20.6 0.8
HG21 A:THR221 3.1 21.6 1.0
HG23 A:THR221 3.4 21.6 1.0
CB A:THR221 3.5 15.3 1.0
CG2 A:THR221 3.5 18.0 1.0
OD2 A:ASP219 3.8 35.3 0.2
H A:THR221 3.9 16.1 1.0
HB A:THR221 4.0 18.4 1.0
O1B A:GDP403 4.0 25.4 0.8
HB3 A:ASP219 4.0 28.0 0.2
CG A:ASP219 4.2 28.4 0.2
O A:HOH770 4.2 22.4 1.0
OE2 A:GLU222 4.3 20.6 1.0
CB A:ASP219 4.4 10.5 0.8
HG2 A:GLU222 4.4 14.2 1.0
HG22 A:THR221 4.5 21.6 1.0
MG A:MG401 4.5 17.0 1.0
OD2 A:ASP200 4.6 12.6 1.0
N A:THR221 4.6 13.4 1.0
CB A:ASP219 4.6 23.4 0.2
CA A:THR221 4.6 12.7 1.0
HA A:ASP219 4.7 12.4 0.2
O A:HOH675 4.7 33.3 1.0
O3B A:GDP403 4.7 20.4 0.8
C7A A:ZIT404 4.7 20.4 1.0
HE1 A:HIS205 4.7 16.1 1.0
HB3 A:ASP219 4.7 12.6 0.8
O A:HOH910 4.7 51.8 1.0
C8A A:ZIT404 4.8 23.7 1.0
HB2 A:ASP219 4.8 12.6 0.8
OD1 A:ASP219 4.8 13.1 0.2
O A:ASP219 4.9 14.1 0.8
O A:HOH891 4.9 43.4 1.0
PB A:GDP403 4.9 23.8 0.8
HA A:ASP219 5.0 13.4 0.8

Reference:

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
Page generated: Sun Jul 14 20:31:48 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy