Calcium in PDB 6f2t: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)

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

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3), PDB code: 6f2t 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)	47.35 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.843, 124.063, 110.673, 90.00, 97.03, 90.00
R / Rfree (%)	21.5 / 22.9

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) 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) (pdb code 6f2t). 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), PDB code: 6f2t:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:48.8 occ:1.00 OD1 A:ASN754 2.2 53.5 1.0 OD1 A:ASP752 2.2 51.6 1.0 OD1 A:ASP756 2.3 57.0 1.0 O A:HOH1178 2.4 41.9 1.0 O A:HIS758 2.5 47.5 1.0 OD1 A:ASP760 2.5 60.5 1.0 CG A:ASN754 3.3 62.9 1.0 CG A:ASP752 3.3 51.5 1.0 CG A:ASP756 3.4 56.6 1.0 C A:HIS758 3.6 47.8 1.0 CG A:ASP760 3.7 60.8 1.0 ND2 A:ASN754 3.7 56.2 1.0 CA A:ASP752 3.9 43.7 1.0 OD2 A:ASP756 4.0 63.3 1.0 CB A:ASP752 4.1 44.3 1.0 N A:ASP760 4.1 49.3 1.0 C A:PHE759 4.1 51.7 1.0 N A:HIS758 4.2 43.1 1.0 O A:PHE759 4.2 52.2 1.0 CA A:ASP760 4.2 50.7 1.0 N A:ASP756 4.2 44.3 1.0 OD2 A:ASP752 4.3 55.9 1.0 CA A:HIS758 4.3 43.0 1.0 O A:PHE751 4.4 46.9 1.0 CB A:ASP756 4.4 46.6 1.0 OE2 A:GLU764 4.5 69.0 1.0 C A:ASP752 4.5 48.8 1.0 CB A:ASP760 4.5 52.6 1.0 CB A:HIS758 4.5 44.4 1.0 N A:PHE759 4.5 45.0 1.0 CB A:ASN754 4.6 47.4 1.0 OD2 A:ASP760 4.6 67.0 1.0 N A:ASN754 4.6 46.8 1.0 N A:TYR755 4.7 45.5 1.0 CA A:ASP756 4.7 44.0 1.0 CA A:PHE759 4.8 45.4 1.0 N A:TYR753 4.8 46.2 1.0 N A:GLY757 4.8 41.9 1.0 CA A:ASN754 4.9 46.9 1.0 C A:ASN754 4.9 50.3 1.0 CD A:GLU764 5.0 79.2 1.0 N A:ASP752 5.0 43.8 1.0

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:41.5 occ:1.00 OD1 B:ASP752 2.3 50.6 1.0 OD1 B:ASP756 2.3 56.7 1.0 OD1 B:ASN754 2.3 43.7 1.0 O B:HIS758 2.3 45.0 1.0 OD1 B:ASP760 2.4 51.4 1.0 O B:HOH1234 2.5 34.7 1.0 C B:HIS758 3.4 45.1 1.0 CG B:ASP752 3.4 48.8 1.0 CG B:ASN754 3.4 55.1 1.0 CG B:ASP756 3.4 56.4 1.0 CG B:ASP760 3.6 51.4 1.0 ND2 B:ASN754 3.9 47.9 1.0 N B:ASP760 3.9 41.2 1.0 CA B:ASP752 3.9 36.5 1.0 C B:PHE759 3.9 44.5 1.0 O B:PHE759 4.0 44.7 1.0 CA B:ASP760 4.0 41.6 1.0 OD2 B:ASP756 4.0 63.0 1.0 CB B:ASP752 4.1 38.0 1.0 N B:HIS758 4.1 41.4 1.0 CA B:HIS758 4.2 41.5 1.0 O B:PHE751 4.3 37.8 1.0 CB B:ASP760 4.3 43.0 1.0 OD2 B:ASP752 4.4 53.2 1.0 N B:PHE759 4.4 41.2 1.0 N B:ASP756 4.4 44.6 1.0 CB B:HIS758 4.4 43.3 1.0 OE2 B:GLU764 4.4 54.6 1.0 OD2 B:ASP760 4.5 58.6 1.0 CB B:ASP756 4.5 47.2 1.0 C B:ASP752 4.6 41.9 1.0 CA B:PHE759 4.6 40.3 1.0 CB B:ASN754 4.7 41.9 1.0 N B:ASN754 4.8 42.0 1.0 CD B:GLU764 4.8 67.4 1.0 CA B:ASP756 4.8 44.7 1.0 OE1 B:GLU764 4.8 70.0 1.0 N B:TYR755 4.9 43.6 1.0 N B:GLY757 4.9 42.0 1.0 N B:TYR753 4.9 39.4 1.0 N B:ASP752 5.0 35.9 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