Calcium in PDB 6f30: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac

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

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac, PDB code: 6f30 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)	37.51 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.270, 127.682, 113.414, 90.00, 97.14, 90.00
R / Rfree (%)	19.6 / 21.3

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac 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 Udpglcnac (pdb code 6f30). 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 Udpglcnac, PDB code: 6f30:
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 Udpglcnac


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 Udpglcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:51.6 occ:1.00 OD1 A:ASN754 2.2 52.6 1.0 OD1 A:ASP756 2.3 53.6 1.0 OD1 A:ASP752 2.3 45.9 1.0 O A:HOH1210 2.4 45.2 1.0 OD1 A:ASP760 2.4 57.0 1.0 O A:HIS758 2.5 45.9 1.0 CG A:ASN754 3.3 60.4 1.0 CG A:ASP756 3.4 53.8 1.0 CG A:ASP752 3.5 46.3 1.0 C A:HIS758 3.5 45.9 1.0 CG A:ASP760 3.6 57.7 1.0 ND2 A:ASN754 3.8 49.4 1.0 CA A:ASP752 3.9 42.0 1.0 OD2 A:ASP756 4.0 58.8 1.0 N A:ASP760 4.0 46.7 1.0 C A:PHE759 4.1 48.7 1.0 CB A:ASP752 4.1 42.3 1.0 CA A:ASP760 4.1 47.8 1.0 O A:PHE759 4.2 48.4 1.0 N A:HIS758 4.2 41.6 1.0 CA A:HIS758 4.3 41.3 1.0 N A:ASP756 4.3 45.0 1.0 O A:PHE751 4.4 45.5 1.0 OD2 A:ASP752 4.4 48.6 1.0 CB A:ASP760 4.5 50.1 1.0 OE2 A:GLU764 4.5 57.7 1.0 CB A:HIS758 4.5 42.4 1.0 C A:ASP752 4.5 47.0 1.0 OD2 A:ASP760 4.5 64.0 1.0 CB A:ASP756 4.5 46.2 1.0 N A:PHE759 4.5 42.8 1.0 N A:ASN754 4.6 47.8 1.0 CB A:ASN754 4.6 47.0 1.0 N A:TYR755 4.7 45.7 1.0 CA A:PHE759 4.7 43.5 1.0 N A:TYR753 4.7 45.1 1.0 CA A:ASP756 4.8 44.0 1.0 C A:ASN754 4.9 50.6 1.0 CA A:ASN754 4.9 47.7 1.0 N A:ASP752 5.0 42.8 1.0 N A:GLY757 5.0 43.0 1.0 CD A:GLU764 5.0 72.2 1.0

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


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 Udpglcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:43.0 occ:1.00 OD1 B:ASN754 2.2 55.6 1.0 OD1 B:ASP756 2.3 56.9 1.0 OD1 B:ASP752 2.3 47.1 1.0 O B:HOH1165 2.4 37.1 1.0 OD1 B:ASP760 2.4 48.0 1.0 O B:HIS758 2.5 40.7 1.0 CG B:ASN754 3.3 65.3 1.0 CG B:ASP756 3.4 57.1 1.0 CG B:ASP752 3.5 46.3 1.0 C B:HIS758 3.5 39.6 1.0 CG B:ASP760 3.6 47.8 1.0 ND2 B:ASN754 3.8 58.0 1.0 CA B:ASP752 3.9 38.2 1.0 OD2 B:ASP756 4.0 63.4 1.0 N B:ASP760 4.0 37.5 1.0 C B:PHE759 4.1 40.1 1.0 CB B:ASP752 4.1 39.0 1.0 CA B:ASP760 4.1 39.2 1.0 O B:PHE759 4.2 41.2 1.0 N B:HIS758 4.2 37.2 1.0 CA B:HIS758 4.3 36.4 1.0 N B:ASP756 4.3 44.2 1.0 O B:PHE751 4.4 40.4 1.0 OD2 B:ASP752 4.4 52.2 1.0 CB B:ASP760 4.4 40.7 1.0 OE2 B:GLU764 4.5 58.5 1.0 C B:ASP752 4.5 43.6 1.0 CB B:HIS758 4.5 38.5 1.0 OD2 B:ASP760 4.5 53.3 1.0 CB B:ASP756 4.5 47.7 1.0 N B:PHE759 4.5 34.1 1.0 N B:ASN754 4.6 45.1 1.0 CB B:ASN754 4.6 48.2 1.0 N B:TYR755 4.7 44.7 1.0 CA B:PHE759 4.7 33.5 1.0 N B:TYR753 4.7 41.6 1.0 CA B:ASP756 4.8 44.5 1.0 C B:ASN754 4.9 49.9 1.0 CA B:ASN754 4.9 46.8 1.0 N B:ASP752 5.0 37.7 1.0 N B:GLY757 5.0 41.5 1.0 CD B:GLU764 5.0 73.9 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