Calcium in PDB 4b56: Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)

All present enzymatic activity of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1):
3.1.4.1; 3.6.1.9;

The structure of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1), PDB code: 4b56 was solved by S.Jansen, A.Perrakis, C.Ulens, C.Winkler, M.Andries, R.P.Joosten, M.Van Acker, F.P.Luyten, W.H.Moolenaar, M.Bollen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.470 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.385, 105.412, 245.258, 90.00, 90.00, 90.00
R / Rfree (%)	20.02 / 23.35

The structure of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) (pdb code 4b56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1), PDB code: 4b56:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:89.1 occ:1.00 OD1 A:ASP783 2.2 82.5 1.0 O A:ARG787 2.2 86.3 1.0 OD1 A:ASP789 2.4 0.5 1.0 OD1 A:ASP781 2.4 90.8 1.0 OD1 A:ASP785 2.5 91.1 1.0 CG A:ASP783 3.1 85.0 1.0 OD2 A:ASP783 3.2 84.6 1.0 CG A:ASP785 3.3 90.5 1.0 C A:ARG787 3.4 89.0 1.0 CG A:ASP781 3.5 88.6 1.0 CG A:ASP789 3.6 98.7 1.0 OD2 A:ASP785 3.6 91.9 1.0 N A:ARG787 3.9 87.3 1.0 N A:ASP789 4.0 95.3 1.0 C A:TYR788 4.0 92.7 1.0 CA A:ASP781 4.0 85.7 1.0 CA A:ASP789 4.0 98.7 1.0 O A:TYR788 4.1 92.1 1.0 CA A:ARG787 4.1 88.2 1.0 CB A:ASP781 4.2 85.7 1.0 N A:ASP785 4.2 87.8 1.0 OD2 A:ASP781 4.3 88.4 1.0 N A:TYR788 4.4 89.3 1.0 CB A:ASP789 4.4 99.4 1.0 OD2 A:ASP789 4.4 0.4 1.0 CB A:ASP785 4.5 88.7 1.0 C A:ASP781 4.5 85.4 1.0 CB A:ASP783 4.5 85.6 1.0 CB A:ARG787 4.6 90.8 1.0 O A:PHE780 4.6 87.1 1.0 CA A:TYR788 4.6 90.2 1.0 N A:GLY786 4.7 81.4 1.0 N A:ASP783 4.7 85.9 1.0 CA A:ASP785 4.7 86.4 1.0 C A:ASP785 4.8 85.1 1.0 N A:TYR784 4.8 84.4 1.0 N A:PHE782 4.8 86.5 1.0 CA A:ASP783 4.9 86.0 1.0 C A:ASP783 5.0 85.1 1.0

Calcium binding site 2 out of 2 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:0.2 occ:1.00 OD1 B:ASP783 2.3 0.4 1.0 O B:ARG787 2.3 0.8 1.0 OD1 B:ASP789 2.3 0.5 1.0 OD1 B:ASP781 2.5 0.2 1.0 OD1 B:ASP785 2.5 1.0 1.0 CG B:ASP783 3.1 0.1 1.0 OD2 B:ASP783 3.2 0.0 1.0 CG B:ASP785 3.3 0.1 1.0 C B:ARG787 3.4 0.6 1.0 CG B:ASP789 3.5 0.6 1.0 CG B:ASP781 3.5 0.6 1.0 OD2 B:ASP785 3.6 0.5 1.0 N B:ASP789 3.9 0.5 1.0 C B:TYR788 3.9 0.7 1.0 CA B:ASP789 3.9 1.0 1.0 N B:ARG787 4.0 0.7 1.0 CA B:ASP781 4.0 0.1 1.0 O B:TYR788 4.0 0.3 1.0 CA B:ARG787 4.2 0.1 1.0 CB B:ASP781 4.2 0.5 1.0 N B:ASP785 4.3 0.3 1.0 CB B:ASP789 4.3 1.0 1.0 OD2 B:ASP789 4.4 0.3 1.0 N B:TYR788 4.4 0.4 1.0 OD2 B:ASP781 4.4 0.5 1.0 CB B:ASP785 4.5 0.4 1.0 C B:ASP781 4.5 0.3 1.0 O B:PHE780 4.5 0.5 1.0 CB B:ASP783 4.5 0.6 1.0 CA B:TYR788 4.6 0.1 1.0 CB B:ARG787 4.6 0.1 1.0 N B:ASP783 4.7 0.9 1.0 CA B:ASP785 4.8 0.1 1.0 N B:GLY786 4.8 0.9 1.0 N B:PHE782 4.8 0.5 1.0 N B:TYR784 4.8 0.4 1.0 C B:ASP785 4.9 0.5 1.0 CA B:ASP783 5.0 0.4 1.0

S.Jansen, A.Perrakis, C.Ulens, C.Winkler, M.Andries, R.P.Joosten, M.Van Acker, F.P.Luyten, W.H.Moolenaar, M.Bollen. Structure of NPP1, An Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification. Structure V. 20 1948 2012.
ISSN: ISSN 0969-2126
PubMed: 23041369
DOI: 10.1016/J.STR.2012.09.001