Calcium in PDB 4q7c: Structure of AF2299, A Cdp-Alcohol Phosphotransferase

The structure of Structure of AF2299, A Cdp-Alcohol Phosphotransferase, PDB code: 4q7c 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)	69.13 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.417, 90.852, 106.611, 90.00, 92.21, 90.00
R / Rfree (%)	23.8 / 26.9

The binding sites of Calcium atom in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase (pdb code 4q7c). 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, PDB code: 4q7c:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:34.2 occ:1.00 O1B A:C2G408 2.2 32.9 1.0 O A:ASP214 2.3 32.6 1.0 OD1 A:ASP235 2.4 33.7 1.0 OD2 A:ASP217 2.4 33.0 1.0 OD2 A:ASP235 2.5 33.2 1.0 OD1 A:ASP217 2.5 33.2 1.0 OD2 A:ASP214 2.5 34.1 1.0 O2A A:C2G408 2.6 33.0 1.0 CG A:ASP235 2.8 33.1 1.0 CG A:ASP217 2.8 32.6 1.0 CG A:ASP214 3.1 33.7 1.0 C A:ASP214 3.4 32.8 1.0 OD1 A:ASP214 3.6 33.0 1.0 PB A:C2G408 3.6 33.1 1.0 CA A:CA402 3.6 32.3 0.5 PA A:C2G408 3.9 33.2 1.0 CA A:ASP214 4.1 32.4 1.0 CB A:ASP214 4.1 32.4 1.0 O3A A:C2G408 4.2 32.7 1.0 CB A:ASP235 4.3 31.8 1.0 O2B A:C2G408 4.3 34.6 1.0 CB A:ASP217 4.3 31.8 1.0 N A:GLY215 4.5 32.8 1.0 OD2 A:ASP239 4.5 30.9 1.0 C3G A:C2G408 4.7 33.3 1.0 O3B A:C2G408 4.7 33.5 1.0 N A:GLY218 4.7 33.4 1.0 O5' A:C2G408 4.8 33.9 1.0 CA A:GLY215 4.8 32.4 1.0 O1A A:C2G408 4.8 32.1 1.0 C5' A:C2G408 4.9 33.9 1.0 C5 A:C2G408 4.9 33.9 1.0

Calcium binding site 2 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:32.3 occ:0.48 OD1 A:ASP214 2.3 33.0 1.0 OD1 A:ASP235 2.3 33.7 1.0 OD1 A:ASP239 2.3 31.2 1.0 O A:ASP235 2.3 31.2 1.0 OD2 A:ASP239 2.4 30.9 1.0 CG A:ASP239 2.5 30.6 1.0 CG A:ASP214 3.1 33.7 1.0 OD2 A:ASP214 3.1 34.1 1.0 C A:ASP235 3.3 31.4 1.0 CG A:ASP235 3.4 33.1 1.0 CA A:CA401 3.6 34.2 1.0 CB A:ASP239 3.7 29.8 1.0 CA A:ASP235 3.8 31.6 1.0 OD2 A:ASP217 4.1 33.0 1.0 N A:ASP239 4.2 29.6 1.0 CB A:ASP235 4.2 31.8 1.0 OD2 A:ASP235 4.2 33.2 1.0 CA A:ASP239 4.3 29.1 1.0 N A:GLY236 4.5 31.6 1.0 CB A:ASP214 4.5 32.4 1.0 CG2 A:THR178 4.7 31.2 1.0 O1B A:C2G408 4.8 32.9 1.0 CA A:GLY236 4.9 30.6 1.0 C A:LEU238 5.0 29.2 1.0

Calcium binding site 3 out of 4 in the Structure of AF2299, A Cdp-Alcohol Phosphotransferase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:32.7 occ:1.00 O B:ASP214 2.3 33.2 1.0 OD2 B:ASP235 2.4 32.3 1.0 OD1 B:ASP235 2.4 33.3 1.0 OD2 B:ASP217 2.4 31.0 1.0 OD1 B:ASP217 2.4 32.7 1.0 O2A B:C2G408 2.5 33.2 1.0 O1B B:C2G408 2.5 33.4 1.0 OD1 B:ASP214 2.6 33.4 1.0 CG B:ASP235 2.7 32.4 1.0 CG B:ASP217 2.7 31.6 1.0 C B:ASP214 3.4 32.8 1.0 CG B:ASP214 3.4 33.8 1.0 PB B:C2G408 3.8 35.7 1.0 PA B:C2G408 3.8 34.0 1.0 CA B:CA402 3.9 32.5 0.6 OD2 B:ASP214 4.0 34.1 1.0 CA B:ASP214 4.0 32.3 1.0 O3A B:C2G408 4.1 34.9 1.0 CB B:ASP235 4.2 31.8 1.0 O3B B:C2G408 4.2 37.2 1.0 CB B:ASP217 4.2 31.2 1.0 CB B:ASP214 4.3 33.2 1.0 N B:GLY218 4.4 32.2 1.0 N B:GLY215 4.4 32.8 1.0 O5' B:C2G408 4.7 33.7 1.0 CA B:GLY215 4.7 33.2 1.0 O1A B:C2G408 4.8 33.7 1.0 C5' B:C2G408 4.9 32.3 1.0 OD2 B:ASP239 4.9 33.1 1.0 N B:ASP217 5.0 31.9 1.0 CA B:ASP217 5.0 31.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:32.5 occ:0.61 OD1 B:ASP235 2.4 33.3 1.0 OD1 B:ASP239 2.4 32.7 1.0 OD1 B:ASP214 2.5 33.4 1.0 O B:ASP235 2.5 31.2 1.0 CG B:ASP239 2.9 32.0 1.0 OD2 B:ASP239 3.1 33.1 1.0 CG B:ASP214 3.3 33.8 1.0 OD2 B:ASP214 3.5 34.1 1.0 C B:ASP235 3.5 30.8 1.0 CG B:ASP235 3.5 32.4 1.0 CA B:ASP235 3.8 31.2 1.0 CA B:CA401 3.9 32.7 1.0 CB B:ASP239 4.2 30.6 1.0 OD2 B:ASP217 4.2 31.0 1.0 CG2 B:THR178 4.2 29.4 1.0 N B:ASP239 4.2 30.4 1.0 CB B:ASP235 4.3 31.8 1.0 OD2 B:ASP235 4.5 32.3 1.0 CA B:ASP239 4.5 30.4 1.0 CB B:ASP214 4.6 33.2 1.0 N B:GLY236 4.7 30.4 1.0 CB B:LEU238 4.8 30.0 1.0 C B:LEU238 4.8 30.5 1.0 O1B B:C2G408 4.9 33.4 1.0 OG B:SER181 4.9 30.2 1.0 O B:LEU234 5.0 30.4 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