Calcium in PDB 6c01: Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)

All present enzymatic activity of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C):
3.1.4.1; 3.6.1.9;

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), PDB code: 6c01 was solved by A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.184, 133.640, 167.430, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.4

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) (pdb code 6c01). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), PDB code: 6c01:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:28.1 occ:1.00 OD1 A:ASP760 2.3 26.4 1.0 OD1 A:ASN754 2.3 31.8 1.0 OD1 A:ASP752 2.4 31.1 1.0 OD1 A:ASP756 2.4 29.8 1.0 O A:HIS758 2.4 23.3 1.0 O A:HOH1390 2.5 34.4 1.0 HA A:ASP752 3.0 32.8 1.0 HD21 A:ASN754 3.2 43.4 1.0 CG A:ASN754 3.3 33.1 1.0 CG A:ASP756 3.3 31.7 1.0 H A:HIS758 3.4 23.7 1.0 H A:ASP756 3.5 31.3 1.0 CG A:ASP752 3.5 28.1 1.0 C A:HIS758 3.5 23.4 1.0 CG A:ASP760 3.5 28.4 1.0 HA A:ASP760 3.5 32.0 1.0 ND2 A:ASN754 3.6 36.1 1.0 HB2 A:HIS758 3.8 32.1 1.0 H A:ASN754 3.8 31.9 1.0 OD2 A:ASP756 3.8 32.8 1.0 CA A:ASP752 3.9 27.3 1.0 N A:ASP760 4.0 27.3 1.0 N A:HIS758 4.0 19.7 1.0 C A:PHE759 4.1 29.4 1.0 CA A:ASP760 4.1 26.7 1.0 CB A:ASP752 4.2 27.4 1.0 H A:ASP760 4.2 32.8 1.0 CA A:HIS758 4.2 24.2 1.0 O A:PHE759 4.2 30.5 1.0 N A:ASP756 4.3 26.1 1.0 HB2 A:ASP752 4.3 32.9 1.0 OD2 A:ASP760 4.3 28.2 1.0 O A:PHE751 4.4 21.1 1.0 CB A:ASP760 4.4 26.4 1.0 OD2 A:ASP752 4.4 26.6 1.0 C A:ASP752 4.4 27.1 1.0 HD22 A:ASN754 4.5 43.4 1.0 CB A:ASP756 4.5 29.2 1.0 H A:GLY757 4.5 31.7 1.0 CB A:HIS758 4.5 26.8 1.0 N A:PHE759 4.5 32.1 1.0 H A:TYR753 4.5 31.8 1.0 H A:TYR755 4.6 29.7 1.0 HB3 A:ASP756 4.6 35.1 1.0 N A:ASN754 4.6 26.6 1.0 CB A:ASN754 4.6 28.8 1.0 HA A:PHE759 4.6 39.2 1.0 CA A:PHE759 4.7 32.7 1.0 OE1 A:GLU764 4.7 47.6 1.0 N A:TYR753 4.7 26.5 1.0 N A:TYR755 4.7 24.7 1.0 N A:GLY757 4.8 26.4 1.0 CA A:ASP756 4.8 26.9 1.0 C A:ASN754 4.9 25.1 1.0 HB3 A:HIS758 4.9 32.1 1.0 CA A:ASN754 5.0 25.9 1.0 C A:ASP756 5.0 27.0 1.0 O A:HOH1274 5.0 30.9 1.0 HB3 A:ASP760 5.0 31.7 1.0 N A:ASP752 5.0 27.3 1.0

Calcium binding site 2 out of 2 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:27.9 occ:1.00 OD1 B:ASP760 2.3 27.9 1.0 OD1 B:ASN754 2.3 35.1 1.0 OD1 B:ASP756 2.3 33.0 1.0 O B:HIS758 2.3 29.5 1.0 OD1 B:ASP752 2.3 22.5 1.0 O B:HOH1215 2.5 30.7 1.0 HA B:ASP752 3.1 31.1 1.0 HD21 B:ASN754 3.3 39.2 1.0 CG B:ASP756 3.3 31.3 1.0 CG B:ASN754 3.3 31.6 1.0 H B:HIS758 3.4 34.4 1.0 C B:HIS758 3.5 30.6 1.0 H B:ASP756 3.5 29.5 1.0 CG B:ASP752 3.5 24.4 1.0 HA B:ASP760 3.5 32.9 1.0 CG B:ASP760 3.5 30.8 1.0 ND2 B:ASN754 3.7 32.6 1.0 HB2 B:HIS758 3.8 36.4 1.0 OD2 B:ASP756 3.8 30.6 1.0 H B:ASN754 3.9 30.8 1.0 CA B:ASP752 4.0 25.9 1.0 N B:ASP760 4.0 22.3 1.0 N B:HIS758 4.0 28.7 1.0 C B:PHE759 4.1 28.4 1.0 CA B:ASP760 4.1 27.4 1.0 CA B:HIS758 4.2 31.8 1.0 H B:ASP760 4.2 26.8 1.0 CB B:ASP752 4.2 21.8 1.0 O B:PHE759 4.2 30.3 1.0 N B:ASP756 4.3 24.6 1.0 OE1 B:GLU764 4.4 48.4 1.0 OD2 B:ASP760 4.4 30.1 1.0 OD2 B:ASP752 4.4 24.0 1.0 CB B:ASP760 4.4 28.7 1.0 HB2 B:ASP752 4.4 26.1 1.0 CB B:HIS758 4.4 30.3 1.0 O B:PHE751 4.4 24.7 1.0 N B:PHE759 4.5 30.0 1.0 CB B:ASP756 4.5 29.4 1.0 C B:ASP752 4.5 25.0 1.0 HD22 B:ASN754 4.5 39.2 1.0 H B:TYR755 4.6 34.6 1.0 H B:GLY757 4.6 26.9 1.0 HB3 B:ASP756 4.6 35.2 1.0 N B:ASN754 4.6 25.6 1.0 H B:TYR753 4.6 29.1 1.0 HA B:PHE759 4.7 36.1 1.0 O B:HOH1311 4.7 43.0 1.0 CA B:PHE759 4.7 30.1 1.0 CB B:ASN754 4.7 27.8 1.0 N B:TYR755 4.8 28.8 1.0 N B:TYR753 4.8 24.2 1.0 HB3 B:HIS758 4.8 36.4 1.0 CA B:ASP756 4.8 25.9 1.0 N B:GLY757 4.9 22.4 1.0 C B:ASN754 4.9 27.8 1.0 CA B:ASN754 5.0 25.1 1.0

A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar. Structural Basis For Nucleotide Recognition By the Ectoenzyme CD203C. Febs J. V. 285 2481 2018.
ISSN: ISSN 1742-4658
PubMed: 29717535
DOI: 10.1111/FEBS.14489