Sodium 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
Calcium	(Ca)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), PDB code: 6c01:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na931 b:58.5 occ:1.00 O A:TYR682 2.2 40.1 1.0 O A:ASP685 2.5 43.9 1.0 O A:HOH1392 2.5 45.2 1.0 O A:HOH1370 2.5 44.0 1.0 O A:ILE688 2.5 41.6 1.0 O A:HOH1355 2.6 44.3 1.0 C A:TYR682 3.3 38.0 1.0 HA A:THR689 3.5 44.0 1.0 C A:ILE688 3.7 38.7 1.0 HA A:LEU683 3.7 60.3 1.0 C A:ASP685 3.7 46.4 1.0 HA A:LYS686 3.7 63.4 1.0 HB3 A:TYR682 3.8 44.0 1.0 H A:ILE688 3.9 51.7 1.0 HB A:THR689 4.0 46.5 1.0 HA A:TYR682 4.1 41.9 1.0 CA A:TYR682 4.2 34.9 1.0 N A:LEU683 4.2 45.3 1.0 CA A:THR689 4.2 36.6 1.0 HB3 A:ASP685 4.3 49.9 1.0 CA A:LEU683 4.3 50.3 1.0 CA A:LYS686 4.4 52.8 1.0 N A:THR689 4.4 34.8 1.0 O A:LYS686 4.4 52.1 1.0 C A:LYS686 4.5 51.2 1.0 N A:LYS686 4.5 52.7 1.0 O A:HOH1444 4.5 61.6 1.0 CB A:TYR682 4.5 36.6 1.0 O A:LEU683 4.5 52.0 1.0 N A:ILE688 4.5 43.1 1.0 H A:ASP685 4.5 48.8 1.0 C A:LEU683 4.5 50.7 1.0 CB A:THR689 4.5 38.8 1.0 CA A:ASP685 4.7 42.9 1.0 CA A:ILE688 4.7 40.9 1.0 N A:ASP685 4.8 40.7 1.0 HD23 A:LEU683 4.8 71.3 1.0 HD1 A:TYR682 4.8 40.5 1.0 HD3 A:LYS686 4.9 72.1 1.0 OG1 A:THR689 4.9 41.9 1.0 HG23 A:ILE688 4.9 45.3 1.0 CB A:ASP685 5.0 41.6 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na930 b:56.6 occ:1.00 O B:TYR682 2.3 39.5 1.0 O B:HOH1338 2.4 41.0 1.0 O B:HOH1358 2.5 53.4 1.0 O B:ASP685 2.5 43.0 1.0 O B:ILE688 2.6 48.5 1.0 O B:HOH1228 2.6 51.0 1.0 C B:TYR682 3.5 38.6 1.0 HA B:THR689 3.5 48.8 1.0 HA B:LYS686 3.6 66.8 1.0 C B:ILE688 3.7 47.1 1.0 C B:ASP685 3.7 46.8 1.0 HA B:LEU683 3.7 62.1 1.0 H B:ILE688 3.9 62.1 1.0 HB3 B:TYR682 4.0 46.3 1.0 HB B:THR689 4.1 45.9 1.0 O B:HOH1364 4.1 58.9 1.0 CA B:THR689 4.2 40.7 1.0 HA B:TYR682 4.2 45.5 1.0 CA B:LYS686 4.3 55.7 1.0 HG1 B:THR689 4.3 52.7 1.0 N B:THR689 4.3 41.7 1.0 N B:LEU683 4.4 44.5 1.0 O B:LYS686 4.4 56.6 1.0 CA B:LEU683 4.4 51.8 1.0 HB3 B:ASP685 4.4 53.1 1.0 CA B:TYR682 4.4 38.0 1.0 C B:LYS686 4.4 55.0 1.0 N B:LYS686 4.4 53.5 1.0 O B:LEU683 4.5 50.8 1.0 N B:ILE688 4.5 51.8 1.0 H B:ASP685 4.5 55.3 1.0 CB B:THR689 4.6 38.2 1.0 C B:LEU683 4.6 52.1 1.0 CB B:TYR682 4.7 38.5 1.0 CA B:ILE688 4.7 50.1 1.0 CA B:ASP685 4.7 45.8 1.0 HD23 B:LEU683 4.8 72.3 1.0 N B:ASP685 4.8 46.1 1.0 HD3 B:LYS686 4.8 69.8 1.0 OG1 B:THR689 4.9 43.9 1.0 HD1 B:TYR682 4.9 44.5 1.0 HG23 B:ILE688 5.0 57.3 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