Zinc 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:

Iodine	(I)	25 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) (pdb code 5udy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7), PDB code: 5udy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.5 occ:1.00 OD2 A:ASP246 1.9 41.0 1.0 OD1 A:ASP39 1.9 31.1 1.0 NE2 A:HIS247 2.1 27.4 1.0 OG1 A:THR75 2.2 24.5 1.0 CG A:ASP39 2.6 29.6 1.0 HA A:THR75 2.7 29.1 1.0 OD2 A:ASP39 2.7 29.4 1.0 CG A:ASP246 2.9 38.5 1.0 HG23 A:THR75 2.9 29.6 1.0 CD2 A:HIS247 2.9 28.0 1.0 CE1 A:HIS247 3.0 27.6 1.0 CB A:THR75 3.1 24.2 1.0 HD2 A:HIS247 3.1 33.6 1.0 HE1 A:HIS247 3.2 33.1 1.0 OD1 A:ASP246 3.3 38.5 1.0 CA A:THR75 3.3 24.3 1.0 CG2 A:THR75 3.4 24.7 1.0 H A:GLY40 3.7 35.5 1.0 HG21 A:THR75 3.8 29.6 1.0 N A:THR75 3.9 24.4 1.0 HE1 A:HIS353 3.9 25.4 1.0 HE1 A:HIS79 3.9 36.5 1.0 HB A:THR75 3.9 29.0 1.0 ND1 A:HIS247 4.0 28.5 1.0 CG A:HIS247 4.0 28.8 1.0 H A:THR75 4.0 29.2 1.0 CB A:ASP39 4.0 28.2 1.0 OD1 A:ASP199 4.0 31.7 1.0 HA A:ASP39 4.1 32.4 1.0 N A:GLY40 4.1 29.6 1.0 CE1 A:HIS353 4.1 21.2 1.0 HB2 A:ASP199 4.2 35.8 1.0 CB A:ASP246 4.2 34.0 1.0 HG22 A:THR75 4.3 29.6 1.0 CG A:ASP199 4.3 32.7 1.0 HB2 A:ASP246 4.3 40.8 1.0 NE2 A:HIS353 4.4 19.5 1.0 CA A:ASP39 4.5 27.0 1.0 ZN A:ZN502 4.5 29.5 1.0 HB2 A:ASP39 4.5 33.9 1.0 HB3 A:ASP39 4.6 33.9 1.0 HD1 A:HIS79 4.6 35.9 1.0 HB3 A:ASP246 4.6 40.8 1.0 C A:THR75 4.6 26.5 1.0 HA2 A:GLY40 4.6 32.4 1.0 O A:HOH696 4.6 30.9 1.0 CE1 A:HIS79 4.6 30.4 1.0 C A:ASP39 4.6 29.1 1.0 OD2 A:ASP199 4.6 36.6 1.0 C A:MET74 4.7 23.3 1.0 HA3 A:GLY40 4.7 32.4 1.0 CB A:ASP199 4.7 29.9 1.0 HH A:TYR194 4.7 36.2 1.0 HD1 A:HIS247 4.7 34.2 1.0 CA A:GLY40 4.8 27.0 1.0 ND1 A:HIS353 4.8 22.2 1.0 HB3 A:ASP199 4.9 35.8 1.0 ND1 A:HIS79 4.9 29.9 1.0 O A:THR75 5.0 27.5 1.0 HE1 A:TYR194 5.0 34.9 1.0

Zinc binding site 2 out of 2 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:29.5 occ:1.00 NE2 A:HIS353 2.1 19.5 1.0 NE2 A:HIS203 2.2 28.7 1.0 OD2 A:ASP199 2.4 36.6 1.0 O A:HOH752 2.5 35.5 1.0 OD1 A:ASP199 2.7 31.7 1.0 CG A:ASP199 2.9 32.7 1.0 CE1 A:HIS353 2.9 21.2 1.0 CD2 A:HIS203 3.0 28.6 1.0 HE1 A:HIS353 3.0 25.4 1.0 O A:HOH696 3.1 30.9 1.0 HD2 A:HIS203 3.1 34.4 1.0 CD2 A:HIS353 3.2 21.4 1.0 CE1 A:HIS203 3.2 29.6 1.0 HD2 A:HIS353 3.5 25.6 1.0 HE1 A:HIS203 3.5 35.5 1.0 OG1 A:THR75 3.9 24.5 1.0 HE1 A:HIS247 4.0 33.1 1.0 ND1 A:HIS353 4.1 22.2 1.0 HE1 A:MET249 4.2 27.3 1.0 CG A:HIS203 4.2 28.3 1.0 CG A:HIS353 4.3 22.9 1.0 ND1 A:HIS203 4.3 28.7 1.0 CB A:ASP199 4.4 29.9 1.0 O A:HOH601 4.5 30.1 1.0 NE2 A:HIS247 4.5 27.4 1.0 ZN A:ZN501 4.5 27.5 1.0 CE1 A:HIS247 4.5 27.6 1.0 HB3 A:ASP199 4.7 35.8 1.0 OD1 A:ASP39 4.8 31.1 1.0 HB2 A:ASP199 4.8 35.8 1.0 HD21 A:ASN96 4.8 41.5 1.0 HD1 A:HIS353 4.9 26.7 1.0 O A:HOH708 5.0 44.8 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