Calcium in PDB 6f2y: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A

All present enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A:
3.1.4.1; 3.6.1.9;

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A, PDB code: 6f2y was solved by C.Dohler, M.Zebisch, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.940, 126.850, 114.480, 90.00, 97.54, 90.00
R / Rfree (%)	20.4 / 21.7

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A (pdb code 6f2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A, PDB code: 6f2y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:51.6 occ:1.00 OD1 A:ASN754 2.2 46.8 1.0 OD1 A:ASP756 2.2 52.0 1.0 OD1 A:ASP752 2.4 45.7 1.0 O A:HIS758 2.5 44.5 1.0 OD1 A:ASP760 2.6 56.0 1.0 CG A:ASN754 3.2 55.5 1.0 CG A:ASP756 3.3 51.8 1.0 C A:HIS758 3.5 44.7 1.0 ND2 A:ASN754 3.6 47.9 1.0 CG A:ASP752 3.6 45.5 1.0 CG A:ASP760 3.8 56.2 1.0 OD2 A:ASP756 3.8 58.2 1.0 C A:PHE759 4.0 47.6 1.0 O A:PHE759 4.0 47.7 1.0 N A:ASP760 4.0 45.3 1.0 CA A:ASP760 4.1 46.2 1.0 CA A:ASP752 4.1 37.0 1.0 N A:HIS758 4.2 40.8 1.0 CA A:HIS758 4.2 40.7 1.0 CB A:ASP752 4.3 37.6 1.0 N A:ASP756 4.4 40.6 1.0 CB A:HIS758 4.4 41.9 1.0 N A:PHE759 4.4 41.6 1.0 CB A:ASP756 4.4 42.3 1.0 OD2 A:ASP752 4.5 49.9 1.0 O A:PHE751 4.5 40.3 1.0 OE2 A:GLU764 4.5 59.9 1.0 CB A:ASP760 4.5 48.2 1.0 CB A:ASN754 4.6 40.9 1.0 CA A:PHE759 4.7 41.8 1.0 OD2 A:ASP760 4.7 62.0 1.0 N A:ASN754 4.7 41.2 1.0 C A:ASP752 4.7 42.0 1.0 CA A:ASP756 4.8 40.1 1.0 N A:TYR755 4.9 40.9 1.0 CD A:GLU764 4.9 69.1 1.0 OE1 A:GLU764 4.9 62.5 1.0 N A:GLY757 5.0 39.8 1.0 N A:TYR753 5.0 39.3 1.0 CA A:ASN754 5.0 41.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:38.5 occ:1.00 OD1 B:ASN754 2.2 57.3 1.0 OD1 B:ASP756 2.2 53.7 1.0 OD1 B:ASP752 2.2 47.5 1.0 O B:HOH1163 2.3 34.8 1.0 O B:HIS758 2.4 40.6 1.0 OD1 B:ASP760 2.6 49.9 1.0 CG B:ASN754 3.2 64.3 1.0 CG B:ASP756 3.3 54.4 1.0 CG B:ASP752 3.4 46.3 1.0 C B:HIS758 3.5 40.8 1.0 ND2 B:ASN754 3.6 56.8 1.0 CG B:ASP760 3.8 49.4 1.0 OD2 B:ASP756 3.9 61.6 1.0 CA B:ASP752 4.0 35.9 1.0 C B:PHE759 4.1 42.8 1.0 N B:ASP760 4.1 39.8 1.0 N B:HIS758 4.1 37.5 1.0 O B:PHE759 4.1 43.7 1.0 CB B:ASP752 4.1 36.9 1.0 CA B:ASP760 4.2 40.8 1.0 CA B:HIS758 4.2 37.0 1.0 N B:ASP756 4.2 42.0 1.0 OD2 B:ASP752 4.3 50.6 1.0 CB B:ASP756 4.4 45.2 1.0 O B:PHE751 4.4 38.4 1.0 N B:PHE759 4.5 37.3 1.0 CB B:HIS758 4.5 38.5 1.0 CB B:ASN754 4.6 43.6 1.0 CB B:ASP760 4.6 42.3 1.0 C B:ASP752 4.6 40.9 1.0 N B:ASN754 4.6 41.3 1.0 OD2 B:ASP760 4.6 54.3 1.0 OE2 B:GLU764 4.7 58.1 1.0 N B:TYR755 4.7 42.0 1.0 CA B:PHE759 4.7 37.4 1.0 CA B:ASP756 4.7 42.2 1.0 N B:GLY757 4.8 40.1 1.0 N B:TYR753 4.9 38.1 1.0 CA B:ASN754 4.9 42.4 1.0 C B:ASN754 4.9 46.4 1.0

C.Dohler, M.Zebisch, N.Strater. Crystal Structure and Substrate Binding Mode of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3). Sci Rep V. 8 10874 2018.
ISSN: ESSN 2045-2322
PubMed: 30022031
DOI: 10.1038/S41598-018-28814-Y