Calcium in PDB 4o6m: Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound)

The structure of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound), PDB code: 4o6m was solved by O.B.Clarke, G.Sciara, D.Tomasek, S.Banerjee, K.R.Rajashankar, L.Shapiro, F.Mancia, New York Consortium On Membrane Protein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.33 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.363, 91.148, 107.023, 90.00, 92.05, 90.00
R / Rfree (%)	19.8 / 22.4

The binding sites of Calcium atom in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound) (pdb code 4o6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound), PDB code: 4o6m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:40.5 occ:0.46 CA A:CA401 0.0 40.5 0.5 O A:ASP214 2.3 44.9 1.0 OD2 A:ASP217 2.3 52.4 1.0 O A:HOH580 2.4 53.9 1.0 O A:HOH576 2.4 40.3 1.0 OD2 A:ASP235 2.5 46.2 1.0 OD1 A:ASP235 2.5 41.2 1.0 OD2 A:ASP214 2.6 38.6 1.0 OD1 A:ASP217 2.7 50.0 1.0 CG A:ASP235 2.7 41.0 1.0 CG A:ASP217 2.8 47.2 1.0 CG A:ASP214 3.0 42.7 1.0 CA A:CA401 3.0 58.6 0.5 OD1 A:ASP214 3.3 37.9 1.0 C A:ASP214 3.4 43.0 1.0 HA A:ASP214 3.9 45.4 1.0 HG1 A:THR178 3.9 46.4 1.0 CA A:ASP214 4.0 37.9 1.0 CB A:ASP214 4.0 38.5 1.0 CB A:ASP235 4.0 36.1 1.0 HB2 A:ASP235 4.1 43.4 1.0 HA2 A:GLY215 4.1 45.8 1.0 HB3 A:ASP214 4.2 46.2 1.0 CB A:ASP217 4.3 39.4 1.0 HB3 A:ASP235 4.4 43.4 1.0 N A:GLY215 4.4 38.1 1.0 H A:ASP217 4.4 47.0 1.0 H A:GLY218 4.5 47.8 1.0 HB3 A:ASP217 4.6 47.3 1.0 OD2 A:ASP239 4.6 33.4 1.0 O A:HOH574 4.6 76.0 1.0 OG1 A:THR178 4.7 38.7 1.0 CA A:GLY215 4.7 38.2 1.0 HB2 A:ASP217 4.8 47.3 1.0 HB2 A:ASP214 4.8 46.2 1.0 HA A:THR178 4.9 40.2 1.0 HG23 A:THR178 5.0 44.5 1.0

Calcium binding site 2 out of 3 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:58.6 occ:0.54 CA A:CA401 0.0 58.6 0.5 O A:HOH574 2.3 76.0 1.0 OD2 A:ASP214 2.3 38.6 1.0 OD2 A:ASP235 2.5 46.2 1.0 OD2 A:ASP239 2.6 33.4 1.0 CA A:CA401 3.0 40.5 0.5 O A:HOH538 3.2 43.2 1.0 O A:HOH524 3.4 34.2 1.0 O A:HOH539 3.5 43.0 1.0 CG A:ASP235 3.5 41.0 1.0 CG A:ASP214 3.6 42.7 1.0 OD2 A:ASP148 3.7 64.7 1.0 CG A:ASP239 3.7 30.9 1.0 OD1 A:ASP235 3.8 41.2 1.0 O A:HOH580 4.0 53.9 1.0 OD1 A:ASP148 4.2 76.1 1.0 OD1 A:ASP214 4.2 37.9 1.0 OD1 A:ASP239 4.3 30.2 1.0 HD3 A:ARG301 4.3 39.7 1.0 CG A:ASP148 4.4 71.0 1.0 HH11 A:ARG301 4.4 36.5 1.0 HB3 A:ASP214 4.4 46.2 1.0 O A:ASP214 4.5 44.9 1.0 CB A:ASP214 4.6 38.5 1.0 HB3 A:ASP235 4.8 43.4 1.0 CB A:ASP235 4.8 36.1 1.0 CB A:ASP239 4.9 28.0 1.0 NH1 A:ARG301 5.0 30.4 1.0

Calcium binding site 3 out of 3 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cmp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:29.7 occ:0.64 O B:ASP214 2.3 41.3 1.0 OD2 B:ASP235 2.3 41.4 1.0 OD1 B:ASP217 2.4 42.2 1.0 O B:HOH578 2.4 44.9 1.0 O1P B:C5P422 2.5 33.4 0.7 OD2 B:ASP217 2.5 39.5 1.0 OD1 B:ASP235 2.7 35.4 1.0 CG B:ASP217 2.8 38.0 1.0 CG B:ASP235 2.8 38.3 1.0 OD1 B:ASP214 3.1 36.6 1.0 OD2 B:ASP214 3.1 39.4 1.0 CG B:ASP214 3.2 40.8 1.0 C B:ASP214 3.4 34.3 1.0 P B:C5P422 3.7 32.8 0.7 HA B:ASP214 3.9 41.3 1.0 H B:GLY218 4.0 38.3 1.0 H5'1 B:C5P422 4.0 50.6 0.7 O2P B:C5P422 4.0 42.7 0.7 CA B:ASP214 4.1 34.4 1.0 HA2 B:GLY215 4.1 36.8 1.0 H5 B:C5P422 4.1 44.2 0.7 CB B:ASP214 4.2 32.2 1.0 H6 B:C5P422 4.2 45.0 0.7 HG1 B:THR178 4.3 42.2 1.0 CB B:ASP235 4.3 28.7 1.0 CB B:ASP217 4.3 34.9 1.0 H B:ASP217 4.4 37.9 1.0 N B:GLY215 4.5 32.0 1.0 HB2 B:ASP235 4.5 34.5 1.0 HB3 B:ASP214 4.5 38.6 1.0 N B:GLY218 4.6 31.9 1.0 OD2 B:ASP239 4.7 34.5 1.0 HB2 B:ASP217 4.7 41.9 1.0 HB3 B:ASP235 4.7 34.5 1.0 O B:HOH568 4.7 46.7 1.0 CA B:GLY215 4.7 30.7 1.0 O3P B:C5P422 4.7 34.7 0.7 O5' B:C5P422 4.7 37.3 0.7 HB3 B:ASP217 4.8 41.9 1.0 C5' B:C5P422 4.8 42.2 0.7 C5 B:C5P422 4.9 36.9 0.7 C6 B:C5P422 4.9 37.5 0.7 HB2 B:ASP214 4.9 38.6 1.0 N B:ASP217 5.0 31.6 1.0

G.Sciara, O.B.Clarke, D.Tomasek, B.Kloss, S.Tabuso, R.Byfield, R.Cohn, S.Banerjee, K.R.Rajashankar, V.Slavkovic, J.H.Graziano, L.Shapiro, F.Mancia. Structural Basis For Catalysis in A Cdp-Alcohol Phosphotransferase. Nat Commun V. 5 4068 2014.
ISSN: ESSN 2041-1723
PubMed: 24923293
DOI: 10.1038/NCOMMS5068