Zinc in PDB 5jg8: Crystal Structure of Human Acid Sphingomyelinase

All present enzymatic activity of Crystal Structure of Human Acid Sphingomyelinase:
3.1.4.12;

The structure of Crystal Structure of Human Acid Sphingomyelinase, PDB code: 5jg8 was solved by Z.J.Xiong, G.G.Prive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.76 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.531, 143.658, 193.620, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.9

The binding sites of Zinc atom in the Crystal Structure of Human Acid Sphingomyelinase (pdb code 5jg8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Acid Sphingomyelinase, PDB code: 5jg8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:55.2 occ:1.00 OD2 A:ASP206 1.8 45.7 1.0 NE2 A:HIS459 1.9 46.0 1.0 OD2 A:ASP278 2.0 72.1 1.0 NE2 A:HIS208 2.0 56.7 1.0 O A:ACT703 2.1 62.6 1.0 CE1 A:HIS459 2.8 46.9 1.0 CG A:ASP206 2.9 49.3 1.0 CE1 A:HIS208 3.0 65.5 1.0 ZN A:ZN702 3.0 90.5 1.0 CD2 A:HIS459 3.0 42.0 1.0 CG A:ASP278 3.0 69.2 1.0 CD2 A:HIS208 3.1 63.0 1.0 C A:ACT703 3.2 81.4 1.0 CB A:ASP278 3.5 50.1 1.0 CB A:ASP206 3.5 48.1 1.0 OD1 A:ASP206 4.0 55.6 1.0 ND1 A:HIS459 4.0 31.1 1.0 OXT A:ACT703 4.0 80.6 1.0 CG A:HIS459 4.1 28.0 1.0 ND1 A:HIS208 4.1 58.6 1.0 OD1 A:ASP278 4.2 75.1 1.0 CG A:HIS208 4.2 53.9 1.0 CH3 A:ACT703 4.2 53.9 1.0 CE1 A:HIS425 4.2 64.6 1.0 CA A:ASP206 4.3 47.0 1.0 NE2 A:HIS425 4.3 57.7 1.0 CE1 A:HIS282 4.4 65.9 1.0 OD1 A:ASN318 4.5 71.7 1.0 O A:HIS457 4.5 31.9 1.0 ND1 A:HIS457 4.6 70.7 1.0 CA A:HIS457 4.8 47.8 1.0 NE2 A:HIS282 4.8 64.2 1.0 CA A:ASP278 5.0 67.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:90.5 occ:1.00 OD1 A:ASN318 1.8 71.7 1.0 NE2 A:HIS425 1.8 57.7 1.0 OD2 A:ASP278 1.9 72.1 1.0 CG A:ASP278 2.4 69.2 1.0 ND1 A:HIS457 2.5 70.7 1.0 O A:ACT703 2.5 62.6 1.0 OD1 A:ASP278 2.6 75.1 1.0 CE1 A:HIS425 2.6 64.6 1.0 CD2 A:HIS425 3.0 52.9 1.0 CG A:ASN318 3.0 62.0 1.0 ZN A:ZN701 3.0 55.2 1.0 CE1 A:HIS457 3.1 65.2 1.0 CH3 A:ACT703 3.2 53.9 1.0 C A:ACT703 3.3 81.4 1.0 OD2 A:ASP206 3.3 45.7 1.0 CB A:ASP278 3.7 50.1 1.0 CG A:HIS457 3.7 73.5 1.0 ND1 A:HIS425 3.8 50.3 1.0 ND2 A:ASN318 3.8 52.2 1.0 CG A:HIS425 4.0 37.9 1.0 CB A:ASN318 4.1 41.3 1.0 CA A:HIS457 4.1 47.8 1.0 N A:ASN318 4.1 45.3 1.0 CB A:HIS457 4.2 52.0 1.0 CD2 A:HIS319 4.3 45.5 1.0 CG A:ASP206 4.4 49.3 1.0 NE2 A:HIS457 4.4 43.4 1.0 OXT A:ACT703 4.5 80.6 1.0 NE2 A:HIS208 4.5 56.7 1.0 NE2 A:HIS459 4.6 46.0 1.0 O A:HIS457 4.6 31.9 1.0 CA A:ASN318 4.7 44.7 1.0 CD2 A:HIS457 4.7 56.1 1.0 OD1 A:ASP206 4.7 55.6 1.0 CA A:ASP278 4.8 67.3 1.0 CE1 A:HIS208 4.9 65.5 1.0 NE2 A:HIS319 4.9 48.9 1.0 C A:HIS457 4.9 48.9 1.0 N A:HIS457 4.9 46.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:45.5 occ:1.00 OD2 B:ASP206 1.7 53.9 1.0 NE2 B:HIS459 1.8 41.4 1.0 OXT B:ACT703 1.9 79.2 1.0 NE2 B:HIS208 2.1 62.8 1.0 OD2 B:ASP278 2.2 69.7 1.0 CD2 B:HIS459 2.7 59.5 1.0 C B:ACT703 2.8 72.4 1.0 CG B:ASP206 2.8 54.0 1.0 CE1 B:HIS459 2.9 46.3 1.0 ZN B:ZN702 3.0 98.5 1.0 O B:ACT703 3.1 68.3 1.0 CE1 B:HIS208 3.1 53.8 1.0 CD2 B:HIS208 3.1 60.9 1.0 CG B:ASP278 3.3 63.4 1.0 CB B:ASP206 3.4 49.0 1.0 CB B:ASP278 3.7 57.2 1.0 CG B:HIS459 3.9 55.9 1.0 OD1 B:ASP206 3.9 55.2 1.0 ND1 B:HIS459 3.9 34.8 1.0 CH3 B:ACT703 4.1 46.5 1.0 CE1 B:HIS425 4.2 56.6 1.0 ND1 B:HIS208 4.2 49.4 1.0 CA B:ASP206 4.3 54.4 1.0 CG B:HIS208 4.3 53.8 1.0 O B:HIS457 4.3 31.8 1.0 OD1 B:ASP278 4.3 46.8 1.0 NE2 B:HIS425 4.4 50.0 1.0 CE1 B:HIS282 4.5 76.0 1.0 CA B:HIS457 4.6 41.2 1.0 ND1 B:HIS457 4.6 74.0 1.0 OD1 B:ASN318 4.8 57.7 1.0 C B:HIS457 4.8 40.2 1.0 NE2 B:HIS282 4.9 74.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:98.5 occ:1.00 OD2 B:ASP278 1.8 69.7 1.0 NE2 B:HIS425 1.8 50.0 1.0 OXT B:ACT703 2.0 79.2 1.0 OD1 B:ASN318 2.0 57.7 1.0 ND1 B:HIS457 2.4 74.0 1.0 CE1 B:HIS425 2.5 56.6 1.0 CG B:ASP278 2.7 63.4 1.0 C B:ACT703 2.9 72.4 1.0 ZN B:ZN701 3.0 45.5 1.0 CE1 B:HIS457 3.0 73.4 1.0 OD1 B:ASP278 3.1 46.8 1.0 CD2 B:HIS425 3.1 54.2 1.0 CG B:ASN318 3.2 62.3 1.0 OD2 B:ASP206 3.3 53.9 1.0 CH3 B:ACT703 3.3 46.5 1.0 CG B:HIS457 3.5 57.5 1.0 ND1 B:HIS425 3.7 38.6 1.0 CA B:HIS457 3.9 41.2 1.0 ND2 B:ASN318 3.9 47.6 1.0 CB B:ASP278 3.9 57.2 1.0 CG B:HIS425 4.0 42.2 1.0 CB B:HIS457 4.0 42.4 1.0 O B:ACT703 4.1 68.3 1.0 NE2 B:HIS457 4.3 26.0 1.0 O B:HIS457 4.3 31.8 1.0 N B:ASN318 4.4 52.1 1.0 CD2 B:HIS319 4.4 46.3 1.0 CB B:ASN318 4.4 38.6 1.0 CG B:ASP206 4.4 54.0 1.0 NE2 B:HIS208 4.5 62.8 1.0 NE2 B:HIS459 4.5 41.4 1.0 CD2 B:HIS457 4.5 32.5 1.0 C B:HIS457 4.6 40.2 1.0 N B:HIS457 4.7 49.5 1.0 CE1 B:HIS208 4.7 53.8 1.0 OD1 B:ASP206 4.8 55.2 1.0 CA B:ASN318 4.9 50.1 1.0 CD2 B:HIS459 4.9 59.5 1.0 NE2 B:HIS319 5.0 51.8 1.0

Z.J.Xiong, J.Huang, G.Poda, R.Pomes, G.G.Prive. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. J.Mol.Biol. V. 428 3026 2016.
ISSN: ESSN 1089-8638
PubMed: 27349982
DOI: 10.1016/J.JMB.2016.06.012