Calcium in PDB 4o6n: Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound)

The structure of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound), PDB code: 4o6n 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)	46.30 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.329, 90.670, 106.444, 90.00, 92.07, 90.00
R / Rfree (%)	22.6 / 26.2

The binding sites of Calcium atom in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound) (pdb code 4o6n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound), PDB code: 4o6n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-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 (Cdp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:47.5 occ:1.00 O A:ASP214 2.3 47.6 1.0 OD2 A:ASP235 2.4 40.1 1.0 OD1 A:ASP217 2.4 43.9 1.0 OD2 A:ASP217 2.4 45.8 1.0 OD1 A:ASP235 2.4 42.4 1.0 O2A A:CDP403 2.6 47.7 1.0 O3B A:CDP403 2.6 64.0 1.0 CG A:ASP217 2.7 41.9 1.0 CG A:ASP235 2.7 40.1 1.0 OD2 A:ASP214 3.2 55.8 1.0 C A:ASP214 3.5 41.6 1.0 CG A:ASP214 3.6 52.3 1.0 H5'1 A:CDP403 3.7 63.3 1.0 OD1 A:ASP214 3.8 50.7 1.0 H A:GLY218 3.9 45.9 1.0 CA A:CA402 4.0 40.0 0.3 HA A:ASP214 4.0 48.8 1.0 PA A:CDP403 4.0 55.5 1.0 PB A:CDP403 4.0 89.4 1.0 H5 A:CDP403 4.1 46.7 1.0 HA2 A:GLY215 4.1 48.0 1.0 CA A:ASP214 4.2 40.7 1.0 H6 A:CDP403 4.2 50.4 1.0 CB A:ASP235 4.2 36.8 1.0 CB A:ASP217 4.2 38.5 1.0 HG1 A:THR178 4.3 46.9 1.0 O3A A:CDP403 4.4 71.1 1.0 H A:ASP217 4.4 47.2 1.0 CB A:ASP214 4.5 44.9 1.0 HB2 A:ASP235 4.5 44.2 1.0 N A:GLY215 4.5 41.2 1.0 C5' A:CDP403 4.5 52.8 1.0 N A:GLY218 4.5 38.3 1.0 HB2 A:ASP217 4.6 46.2 1.0 HB3 A:ASP217 4.7 46.2 1.0 H5'2 A:CDP403 4.7 63.3 1.0 CA A:GLY215 4.7 40.0 1.0 HB3 A:ASP235 4.7 44.2 1.0 O5' A:CDP403 4.8 54.9 1.0 OD2 A:ASP239 4.8 38.1 1.0 C5 A:CDP403 4.8 38.9 1.0 HB3 A:ASP214 4.8 53.9 1.0 HA A:ASP235 4.8 41.3 1.0 O1B A:CDP403 4.9 80.4 1.0 C6 A:CDP403 4.9 42.0 1.0 HA3 A:GLY218 4.9 48.9 1.0 O2B A:CDP403 4.9 73.1 1.0 HG23 A:THR178 4.9 39.6 1.0 O1A A:CDP403 5.0 51.1 1.0 N A:ASP217 5.0 39.3 1.0

Calcium binding site 2 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-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 (Cdp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:40.0 occ:0.33 OD1 A:ASP239 2.3 36.6 1.0 OD1 A:ASP235 2.3 42.4 1.0 O A:ASP235 2.4 37.8 1.0 OD1 A:ASP214 2.4 50.7 1.0 O A:HOH503 2.4 35.5 1.0 OD2 A:ASP239 2.4 38.1 1.0 CG A:ASP239 2.5 35.8 1.0 HA A:ASP235 3.1 41.3 1.0 C A:ASP235 3.3 36.3 1.0 CG A:ASP214 3.3 52.3 1.0 HG23 A:THR178 3.3 39.6 1.0 CG A:ASP235 3.4 40.1 1.0 OD2 A:ASP214 3.5 55.8 1.0 CA A:ASP235 3.6 34.4 1.0 O A:HOH505 3.8 34.4 1.0 CB A:ASP239 3.8 35.0 1.0 H A:ASP239 3.9 37.6 1.0 CA A:CA401 4.0 47.5 1.0 HB2 A:ASP239 4.0 42.0 1.0 CB A:ASP235 4.1 36.8 1.0 HB2 A:LEU238 4.2 41.4 1.0 N A:ASP239 4.3 31.4 1.0 CG2 A:THR178 4.3 33.0 1.0 OD2 A:ASP217 4.3 45.8 1.0 OD2 A:ASP235 4.4 40.1 1.0 HA A:ASP239 4.4 44.2 1.0 CA A:ASP239 4.4 36.9 1.0 HG22 A:THR178 4.5 39.6 1.0 N A:GLY236 4.5 36.0 1.0 HB3 A:ASP239 4.6 42.0 1.0 HG21 A:THR178 4.6 39.6 1.0 HA2 A:GLY236 4.7 42.9 1.0 HB3 A:ASP235 4.7 44.2 1.0 CB A:ASP214 4.7 44.9 1.0 HB2 A:ASP235 4.8 44.2 1.0 HA A:THR178 4.8 39.8 1.0 HG A:SER181 4.8 49.7 1.0 HB2 A:ASP214 4.9 53.9 1.0 HG1 A:THR178 4.9 46.9 1.0 O A:LEU234 4.9 33.4 1.0 HE1 A:HIS210 5.0 42.4 1.0 N A:ASP235 5.0 35.1 1.0 HA A:ASP214 5.0 48.8 1.0

Calcium binding site 3 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-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 (Cdp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:36.0 occ:1.00 O B:ASP214 2.2 39.9 1.0 OD2 B:ASP217 2.3 37.3 1.0 OD2 B:ASP235 2.4 40.7 1.0 OD1 B:ASP235 2.4 38.9 1.0 OD1 B:ASP217 2.4 37.9 1.0 O2A B:CDP403 2.5 39.3 0.5 O2A B:CDP403 2.5 39.6 0.5 OD1 B:ASP214 2.5 40.7 1.0 CG B:ASP217 2.7 36.6 1.0 CG B:ASP235 2.8 35.8 1.0 O3B B:CDP403 2.9 43.5 0.5 C B:ASP214 3.4 39.0 1.0 CG B:ASP214 3.4 44.0 1.0 CA B:CA402 3.8 37.6 0.5 PA B:CDP403 3.8 41.3 0.5 PB B:CDP403 3.8 51.8 0.5 H5'2 B:CDP403 3.8 46.4 0.5 PA B:CDP403 3.8 40.4 0.5 HA B:ASP214 3.8 45.7 1.0 H5'2 B:CDP403 3.9 46.3 0.5 H B:GLY218 3.9 43.2 1.0 O1B B:CDP403 3.9 45.8 0.5 OD2 B:ASP214 4.0 48.1 1.0 CA B:ASP214 4.1 38.1 1.0 HA2 B:GLY215 4.1 44.8 1.0 O3A B:CDP403 4.1 43.3 0.5 H5 B:CDP403 4.1 44.0 0.5 H5 B:CDP403 4.1 44.0 0.5 O3A B:CDP403 4.1 43.2 0.5 H6 B:CDP403 4.2 43.4 0.5 CB B:ASP217 4.2 35.1 1.0 H6 B:CDP403 4.2 43.4 0.5 CB B:ASP235 4.3 33.6 1.0 CB B:ASP214 4.3 40.0 1.0 H B:ASP217 4.4 42.8 1.0 N B:GLY215 4.4 37.4 1.0 N B:GLY218 4.5 36.0 1.0 HB2 B:ASP217 4.5 42.2 1.0 HB2 B:ASP235 4.6 40.4 1.0 C5' B:CDP403 4.6 38.7 0.5 HB3 B:ASP214 4.7 48.0 1.0 HB3 B:ASP217 4.7 42.2 1.0 C5' B:CDP403 4.7 38.6 0.5 CA B:GLY215 4.7 37.4 1.0 HB3 B:ASP235 4.7 40.4 1.0 O5' B:CDP403 4.7 39.8 0.5 O5' B:CDP403 4.7 39.8 0.5 O1A B:CDP403 4.8 39.7 0.5 O1A B:CDP403 4.8 39.7 0.5 OD2 B:ASP239 4.8 41.3 1.0 HG23 B:THR178 4.8 40.1 1.0 C5 B:CDP403 4.9 36.7 0.5 HA B:ASP235 4.9 37.9 1.0 C5 B:CDP403 4.9 36.7 0.5 HA3 B:GLY218 4.9 43.9 1.0 C6 B:CDP403 4.9 36.2 0.5 C6 B:CDP403 4.9 36.2 0.5 H5'1 B:CDP403 4.9 46.4 0.5 N B:ASP217 5.0 35.7 1.0 H5'1 B:CDP403 5.0 46.3 0.5

Calcium binding site 4 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of AF2299, A Cdp-Alcohol Phosphotransferase (Cdp-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:37.6 occ:0.46 OD1 B:ASP235 2.2 38.9 1.0 OD1 B:ASP239 2.3 33.2 1.0 O B:HOH527 2.4 33.9 1.0 O B:ASP235 2.5 34.3 1.0 OD1 B:ASP214 2.5 40.7 1.0 CG B:ASP239 2.9 35.1 1.0 OD2 B:ASP239 3.0 41.3 1.0 HA B:ASP235 3.1 37.9 1.0 CG B:ASP214 3.2 44.0 1.0 HG23 B:THR178 3.2 40.1 1.0 OD2 B:ASP214 3.2 48.1 1.0 CG B:ASP235 3.4 35.8 1.0 C B:ASP235 3.4 32.5 1.0 CA B:ASP235 3.6 31.6 1.0 O B:HOH504 3.7 34.7 1.0 CA B:CA401 3.8 36.0 1.0 H B:ASP239 4.1 36.6 1.0 HB2 B:LEU238 4.1 37.5 1.0 CB B:ASP235 4.1 33.6 1.0 CG2 B:THR178 4.1 33.5 1.0 OD2 B:ASP217 4.2 37.3 1.0 CB B:ASP239 4.2 34.7 1.0 OD2 B:ASP235 4.3 40.7 1.0 HG22 B:THR178 4.4 40.1 1.0 N B:ASP239 4.4 30.5 1.0 HB2 B:ASP239 4.4 41.7 1.0 HG B:SER181 4.5 53.0 1.0 HA B:ASP239 4.5 42.2 1.0 HG21 B:THR178 4.5 40.1 1.0 HA B:THR178 4.6 36.5 1.0 CA B:ASP239 4.6 35.1 1.0 CB B:ASP214 4.6 40.0 1.0 N B:GLY236 4.6 32.4 1.0 HB3 B:ASP235 4.7 40.4 1.0 HB3 B:SER181 4.7 44.4 1.0 HB2 B:ASP235 4.7 40.4 1.0 HE1 B:HIS210 4.7 40.8 1.0 HB2 B:ASP214 4.8 48.0 1.0 HA B:ASP214 4.8 45.7 1.0 HA2 B:GLY236 4.9 39.4 1.0 O3B B:CDP403 4.9 43.5 0.5 HB3 B:ASP239 4.9 41.7 1.0 CB B:LEU238 5.0 31.2 1.0 O B:LEU234 5.0 29.3 1.0 N B:ASP235 5.0 30.4 1.0 OG B:SER181 5.0 44.2 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