Sodium in PDB 5udy: Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)

All present enzymatic activity of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7):
3.1.4.12;

The structure of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7), PDB code: 5udy was solved by A.Gorelik, F.Liu, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.20 / 2.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.246, 103.246, 113.554, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 20.7

The structure of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	25 atoms

The binding sites of Sodium atom in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) (pdb code 5udy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7), PDB code: 5udy:

Sodium binding site 1 out of 1 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:44.5 occ:1.00 O A:HOH649 2.2 44.4 1.0 O A:ASP46 2.3 38.0 1.0 O A:VAL49 2.5 40.1 1.0 OG1 A:THR51 2.5 43.4 1.0 O A:HOH709 2.6 30.8 1.0 HG1 A:THR51 2.7 52.1 1.0 O A:HOH725 2.7 28.7 1.0 H A:THR51 2.9 53.0 1.0 HB2 A:ASP46 3.5 48.7 1.0 C A:ASP46 3.5 36.7 1.0 N A:THR51 3.6 44.2 1.0 C A:VAL49 3.7 41.8 1.0 HA A:ASP50 3.7 64.0 1.0 CB A:THR51 3.8 41.2 1.0 HG23 A:THR51 3.8 46.9 1.0 H A:VAL49 3.9 44.2 1.0 HA A:GLN47 4.0 44.8 1.0 OD2 A:ASP55 4.0 50.3 1.0 HA A:ASP46 4.2 44.0 1.0 OD1 A:ASP55 4.2 49.6 1.0 CA A:THR51 4.2 41.0 1.0 CG2 A:THR51 4.2 39.1 1.0 CB A:ASP46 4.2 40.6 1.0 CA A:ASP46 4.2 36.7 1.0 HG21 A:THR51 4.3 46.9 1.0 CA A:ASP50 4.4 53.4 1.0 C A:ASP50 4.4 47.8 1.0 N A:GLN47 4.5 36.2 1.0 HB A:THR51 4.5 49.5 1.0 N A:ASP50 4.5 47.2 1.0 CG A:ASP55 4.5 49.2 1.0 CA A:GLN47 4.6 37.3 1.0 N A:VAL49 4.6 36.9 1.0 O A:GLN47 4.7 41.7 1.0 C A:GLN47 4.7 38.7 1.0 CA A:VAL49 4.7 38.5 1.0 O A:THR51 4.7 39.0 1.0 HB A:VAL49 4.8 44.0 1.0 C A:THR51 4.8 39.2 1.0 CG A:ASP46 4.9 44.2 1.0 HB3 A:ASP46 5.0 48.7 1.0

A.Gorelik, F.Liu, K.Illes, B.Nagar. Crystal Structure of the Human Alkaline Sphingomyelinase Provides Insights Into Substrate Recognition. J. Biol. Chem. V. 292 7087 2017.
ISSN: ESSN 1083-351X
PubMed: 28292932
DOI: 10.1074/JBC.M116.769273