Zinc in PDB 5tcd: Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine

All present enzymatic activity of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine:
3.1.4.12;

The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine, PDB code: 5tcd 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)	38.44 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.223, 104.223, 113.893, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.8

The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine also contains other interesting chemical elements:

Iodine	(I)	37 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine (pdb code 5tcd). 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 (ENPP7) in Complex with Phosphocholine, PDB code: 5tcd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine


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 (ENPP7) in Complex with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.9 occ:1.00 OD1 A:ASP39 1.9 23.4 1.0 OD2 A:ASP246 2.1 28.4 1.0 NE2 A:HIS247 2.1 26.4 1.0 OG1 A:THR75 2.2 22.2 1.0 CG A:ASP39 2.6 23.6 1.0 OD2 A:ASP39 2.7 26.0 1.0 HA A:THR75 2.9 27.2 1.0 HG23 A:THR75 2.9 28.7 1.0 CE1 A:HIS247 3.0 25.5 1.0 CD2 A:HIS247 3.0 25.4 1.0 CG A:ASP246 3.0 26.6 1.0 CB A:THR75 3.1 22.4 1.0 HE1 A:HIS247 3.2 30.6 1.0 HD2 A:HIS247 3.2 30.4 1.0 OD1 A:ASP246 3.3 25.6 1.0 CG2 A:THR75 3.4 23.9 1.0 CA A:THR75 3.4 22.6 1.0 O3 A:PC552 3.5 65.1 1.0 HG21 A:THR75 3.7 28.7 1.0 H A:GLY40 3.7 28.9 1.0 HE1 A:HIS79 3.8 29.9 1.0 H11 A:PC552 3.8 80.5 1.0 HB A:THR75 3.9 26.9 1.0 HE1 A:HIS353 3.9 26.7 1.0 N A:THR75 4.0 23.1 1.0 ND1 A:HIS247 4.0 25.7 1.0 OD1 A:ASP199 4.0 27.5 1.0 CB A:ASP39 4.0 22.7 1.0 CG A:HIS247 4.1 26.3 1.0 H A:THR75 4.1 27.7 1.0 CE1 A:HIS353 4.1 22.3 1.0 N A:GLY40 4.2 24.1 1.0 HA A:ASP39 4.2 25.9 1.0 HG22 A:THR75 4.3 28.7 1.0 CG A:ASP199 4.3 27.0 1.0 NE2 A:HIS353 4.3 21.0 1.0 HB2 A:ASP199 4.3 32.8 1.0 CB A:ASP246 4.3 25.6 1.0 ZN A:ZN502 4.4 28.9 1.0 HB2 A:ASP246 4.4 30.7 1.0 H21 A:PC552 4.5 82.8 1.0 CA A:ASP39 4.5 21.6 1.0 HB3 A:ASP39 4.5 27.2 1.0 HB2 A:ASP39 4.6 27.2 1.0 HH A:TYR194 4.6 28.6 1.0 HA2 A:GLY40 4.6 26.5 1.0 OD2 A:ASP199 4.6 29.0 1.0 CE1 A:HIS79 4.6 24.9 1.0 C A:ASP39 4.7 18.9 1.0 H22 A:PC552 4.7 82.8 1.0 C1 A:PC552 4.7 67.1 1.0 HA3 A:GLY40 4.7 26.5 1.0 HD1 A:HIS79 4.7 31.5 1.0 HB3 A:ASP246 4.7 30.7 1.0 C A:MET74 4.7 27.6 1.0 C A:THR75 4.8 24.3 1.0 HD1 A:HIS247 4.8 30.9 1.0 CA A:GLY40 4.8 22.1 1.0 CB A:ASP199 4.8 27.3 1.0 ND1 A:HIS353 4.8 23.0 1.0 C2 A:PC552 4.9 69.0 1.0 P1 A:PC552 4.9 65.5 1.0

Zinc binding site 2 out of 2 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine


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 (ENPP7) in Complex with Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.9 occ:1.00 O1 A:PC552 2.0 65.3 1.0 NE2 A:HIS353 2.1 21.0 1.0 NE2 A:HIS203 2.1 20.8 1.0 OD2 A:ASP199 2.3 29.0 1.0 OD1 A:ASP199 2.6 27.5 1.0 O3 A:PC552 2.7 65.1 1.0 CG A:ASP199 2.8 27.0 1.0 P1 A:PC552 2.9 65.5 1.0 CD2 A:HIS203 3.0 20.8 1.0 CE1 A:HIS353 3.0 22.3 1.0 HD2 A:HIS203 3.1 25.0 1.0 CD2 A:HIS353 3.1 21.8 1.0 HE1 A:HIS353 3.2 26.7 1.0 CE1 A:HIS203 3.2 22.7 1.0 HD2 A:HIS353 3.3 26.1 1.0 HE1 A:HIS203 3.4 27.2 1.0 H21 A:PC552 3.7 82.8 1.0 HE1 A:HIS247 3.7 30.6 1.0 O2 A:PC552 3.9 65.5 1.0 HE1 A:MET249 3.9 32.9 1.0 O4 A:PC552 4.1 65.5 1.0 ND1 A:HIS353 4.1 23.0 1.0 CG A:HIS203 4.2 21.0 1.0 OG1 A:THR75 4.2 22.2 1.0 CG A:HIS353 4.2 23.0 1.0 ND1 A:HIS203 4.2 21.3 1.0 H11 A:PC552 4.2 80.5 1.0 CB A:ASP199 4.3 27.3 1.0 H43 A:PC552 4.3 83.4 1.0 CE1 A:HIS247 4.3 25.5 1.0 ZN A:ZN501 4.4 26.9 1.0 NE2 A:HIS247 4.4 26.4 1.0 C1 A:PC552 4.4 67.1 1.0 C2 A:PC552 4.5 69.0 1.0 HB3 A:ASP199 4.6 32.8 1.0 HB2 A:ASP199 4.7 32.8 1.0 H42 A:PC552 4.7 83.4 1.0 OD1 A:ASP39 4.8 23.4 1.0 CE A:MET249 4.9 27.4 1.0 HD1 A:HIS353 4.9 27.6 1.0 C4 A:PC552 4.9 69.5 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