Zinc in PDB 5hqn: Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1)

All present enzymatic activity of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1):
3.1.4.12;

The structure of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1), PDB code: 5hqn was solved by A.Gorelik, K.Illes, L.X.Heinz, G.Superti-Furga, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.86 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.844, 127.297, 102.523, 90.00, 121.67, 90.00
R / Rfree (%)	21.3 / 25.8

The binding sites of Zinc atom in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1) (pdb code 5hqn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1), PDB code: 5hqn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:24.1 occ:1.00 O A:HOH801 2.0 38.4 1.0 OD1 A:ASP204 2.0 39.0 1.0 NE2 A:HIS457 2.0 36.8 1.0 OD2 A:ASP276 2.0 36.4 1.0 O1 A:PO4710 2.0 45.8 1.0 NE2 A:HIS206 2.1 44.7 1.0 CE1 A:HIS457 2.8 43.5 1.0 CG A:ASP276 2.9 39.0 1.0 HE1 A:HIS457 3.0 52.1 1.0 CE1 A:HIS206 3.0 39.7 1.0 HB3 A:ASP276 3.1 47.0 1.0 CD2 A:HIS457 3.1 38.9 1.0 HE1 A:HIS206 3.1 47.6 1.0 CD2 A:HIS206 3.1 42.0 1.0 CG A:ASP204 3.1 39.0 1.0 P A:PO4710 3.2 46.7 1.0 HB3 A:ASP204 3.3 41.4 1.0 HD2 A:HIS206 3.4 50.4 1.0 HD2 A:HIS457 3.4 46.6 1.0 O3 A:PO4710 3.4 37.0 1.0 CB A:ASP276 3.4 39.2 1.0 ZN A:ZN702 3.6 23.6 1.0 HB2 A:ASP276 3.6 47.0 1.0 CB A:ASP204 3.8 34.5 1.0 HE1 A:HIS423 3.8 47.5 1.0 HE2 A:HIS280 3.9 58.0 1.0 O4 A:PO4710 3.9 42.7 1.0 HA A:HIS455 3.9 47.9 1.0 ND1 A:HIS457 4.0 42.9 1.0 OD1 A:ASP276 4.0 40.6 1.0 O A:HIS455 4.1 42.7 1.0 CG A:HIS457 4.1 40.4 1.0 ND1 A:HIS206 4.1 42.2 1.0 HD2 A:HIS317 4.1 54.2 1.0 OD2 A:ASP204 4.2 42.6 1.0 HA A:ASP204 4.2 49.1 1.0 HE1 A:HIS280 4.2 60.0 1.0 CG A:HIS206 4.2 40.6 1.0 O2 A:PO4710 4.4 31.3 1.0 NE2 A:HIS280 4.5 48.4 1.0 CE1 A:HIS423 4.5 39.6 1.0 HB2 A:ASP204 4.5 41.4 1.0 NE2 A:HIS423 4.6 31.1 1.0 CA A:ASP204 4.6 41.0 1.0 CE1 A:HIS280 4.7 50.0 1.0 CA A:HIS455 4.8 39.9 1.0 CD2 A:HIS317 4.8 45.1 1.0 C A:HIS455 4.8 37.5 1.0 HD1 A:HIS206 4.9 50.6 1.0 CA A:ASP276 4.9 43.1 1.0 ND1 A:HIS455 5.0 43.6 1.0

Zinc binding site 2 out of 4 in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:23.6 occ:1.00 O3 A:PO4710 1.9 37.0 1.0 NE2 A:HIS423 2.0 31.1 1.0 OD1 A:ASN316 2.0 42.1 1.0 ND1 A:HIS455 2.1 43.6 1.0 OD2 A:ASP276 2.1 36.4 1.0 O A:HOH801 2.2 38.4 1.0 HE1 A:HIS455 2.7 45.9 1.0 CE1 A:HIS455 2.7 38.2 1.0 CG A:ASP276 2.9 39.0 1.0 CE1 A:HIS423 3.0 39.6 1.0 OD1 A:ASP276 3.0 40.6 1.0 CD2 A:HIS423 3.1 29.5 1.0 HA A:HIS455 3.1 47.9 1.0 HE1 A:HIS423 3.1 47.5 1.0 CG A:ASN316 3.1 41.9 1.0 HD2 A:HIS423 3.3 35.4 1.0 P A:PO4710 3.3 46.7 1.0 CG A:HIS455 3.3 42.8 1.0 HD21 A:ASN316 3.3 55.3 1.0 ZN A:ZN701 3.6 24.1 1.0 HD2 A:HIS317 3.6 54.2 1.0 ND2 A:ASN316 3.6 46.1 1.0 O1 A:PO4710 3.6 45.8 1.0 H A:ASN316 3.8 57.5 1.0 CA A:HIS455 3.9 39.9 1.0 HB2 A:HIS455 3.9 47.4 1.0 CB A:HIS455 3.9 39.5 1.0 OD1 A:ASP204 3.9 39.0 1.0 NE2 A:HIS455 3.9 40.7 1.0 ND1 A:HIS423 4.1 40.3 1.0 O4 A:PO4710 4.1 42.7 1.0 CG A:HIS423 4.2 32.3 1.0 CD2 A:HIS455 4.2 38.8 1.0 O A:HIS455 4.3 42.7 1.0 CB A:ASP276 4.3 39.2 1.0 O2 A:PO4710 4.3 31.3 1.0 HB2 A:ASP276 4.3 47.0 1.0 CB A:ASN316 4.5 39.0 1.0 HD22 A:ASN316 4.5 55.3 1.0 CD2 A:HIS317 4.5 45.1 1.0 HB3 A:ASN316 4.5 46.8 1.0 C A:HIS455 4.6 37.5 1.0 HG12 A:ILE424 4.6 46.7 1.0 HE2 A:HIS455 4.6 48.9 1.0 N A:ASN316 4.6 48.0 1.0 HB3 A:ASP276 4.7 47.0 1.0 HB3 A:HIS455 4.8 47.4 1.0 HD1 A:HIS423 4.9 48.3 1.0 HE1 A:HIS206 4.9 47.6 1.0 H A:HIS455 5.0 46.3 1.0 N A:HIS455 5.0 38.6 1.0 H A:HIS317 5.0 56.4 1.0 HG13 A:ILE424 5.0 46.7 1.0

Zinc binding site 3 out of 4 in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:28.1 occ:1.00 OD1 B:ASP204 2.0 45.4 1.0 NE2 B:HIS457 2.0 41.9 1.0 OD2 B:ASP276 2.1 41.7 1.0 NE2 B:HIS206 2.1 44.8 1.0 O3 B:PO4712 2.1 43.8 1.0 O B:HOH801 2.1 35.3 1.0 CE1 B:HIS457 2.9 47.8 1.0 CG B:ASP276 3.0 45.3 1.0 CE1 B:HIS206 3.0 46.5 1.0 CD2 B:HIS457 3.0 38.7 1.0 HE1 B:HIS457 3.0 57.3 1.0 HB3 B:ASP276 3.1 53.6 1.0 CG B:ASP204 3.1 47.7 1.0 CD2 B:HIS206 3.1 43.1 1.0 HE1 B:HIS206 3.2 55.8 1.0 HB3 B:ASP204 3.2 49.4 1.0 HD2 B:HIS457 3.3 46.5 1.0 HD2 B:HIS206 3.3 51.7 1.0 P B:PO4712 3.4 47.8 1.0 CB B:ASP276 3.5 44.7 1.0 ZN B:ZN702 3.6 27.6 1.0 O2 B:PO4712 3.6 31.9 1.0 HE2 B:HIS280 3.6 53.2 1.0 CB B:ASP204 3.7 41.2 1.0 HB2 B:ASP276 3.7 53.6 1.0 HE1 B:HIS423 3.9 47.7 1.0 HA B:HIS455 3.9 47.0 1.0 ND1 B:HIS457 4.0 41.0 1.0 OD1 B:ASP276 4.1 43.8 1.0 CG B:HIS457 4.1 45.0 1.0 O B:HIS455 4.1 39.1 1.0 OD2 B:ASP204 4.1 46.2 1.0 ND1 B:HIS206 4.1 45.4 1.0 HA B:ASP204 4.2 52.3 1.0 HE1 B:HIS280 4.2 59.0 1.0 CG B:HIS206 4.2 46.6 1.0 O4 B:PO4712 4.3 40.3 1.0 NE2 B:HIS280 4.3 44.3 1.0 HD2 B:HIS317 4.4 51.1 1.0 HB2 B:ASP204 4.4 49.4 1.0 O1 B:PO4712 4.5 40.8 1.0 CE1 B:HIS423 4.5 39.8 1.0 NE2 B:HIS423 4.5 38.4 1.0 CA B:ASP204 4.5 43.5 1.0 CE1 B:HIS280 4.6 49.2 1.0 HD1 B:HIS457 4.7 49.2 1.0 CA B:HIS455 4.8 39.2 1.0 HG21 B:THR484 4.8 51.9 1.0 C B:HIS455 4.8 33.5 1.0 CA B:ASP276 4.9 49.6 1.0 HD1 B:HIS206 4.9 54.5 1.0 CD2 B:HIS317 5.0 42.6 1.0

Zinc binding site 4 out of 4 in the Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of Murine Acid Sphingomyelinase (Asmase, Asm, SMPD1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:27.6 occ:1.00 O B:HOH801 2.0 35.3 1.0 OD1 B:ASN316 2.0 44.0 1.0 O2 B:PO4712 2.0 31.9 1.0 NE2 B:HIS423 2.0 38.4 1.0 ND1 B:HIS455 2.1 40.3 1.0 OD2 B:ASP276 2.1 41.7 1.0 CE1 B:HIS455 2.8 40.7 1.0 HE1 B:HIS455 2.8 48.8 1.0 CG B:ASP276 2.8 45.3 1.0 OD1 B:ASP276 3.0 43.8 1.0 HA B:HIS455 3.0 47.0 1.0 CD2 B:HIS423 3.0 37.3 1.0 CE1 B:HIS423 3.0 39.8 1.0 CG B:ASN316 3.1 47.7 1.0 HD2 B:HIS423 3.1 44.8 1.0 CG B:HIS455 3.2 42.0 1.0 HE1 B:HIS423 3.3 47.7 1.0 HD21 B:ASN316 3.3 63.8 1.0 P B:PO4712 3.4 47.8 1.0 ZN B:ZN701 3.6 28.1 1.0 ND2 B:ASN316 3.6 53.2 1.0 O3 B:PO4712 3.6 43.8 1.0 HB2 B:HIS455 3.7 49.8 1.0 H B:ASN316 3.8 56.9 1.0 CA B:HIS455 3.8 39.2 1.0 CB B:HIS455 3.8 41.5 1.0 OD1 B:ASP204 3.8 45.4 1.0 HD2 B:HIS317 3.8 51.1 1.0 NE2 B:HIS455 4.0 40.2 1.0 ND1 B:HIS423 4.1 39.3 1.0 CG B:HIS423 4.1 40.0 1.0 O B:HIS455 4.2 39.1 1.0 CD2 B:HIS455 4.2 39.9 1.0 O4 B:PO4712 4.2 40.3 1.0 CB B:ASP276 4.3 44.7 1.0 HB2 B:ASP276 4.4 53.6 1.0 CB B:ASN316 4.4 48.9 1.0 O1 B:PO4712 4.4 40.8 1.0 HG12 B:ILE424 4.4 54.1 1.0 HB3 B:ASN316 4.5 58.7 1.0 C B:HIS455 4.5 33.5 1.0 HD22 B:ASN316 4.5 63.8 1.0 N B:ASN316 4.6 47.4 1.0 HB3 B:ASP276 4.7 53.6 1.0 HE2 B:HIS455 4.7 48.3 1.0 HB3 B:HIS455 4.7 49.8 1.0 CD2 B:HIS317 4.8 42.6 1.0 H B:HIS455 4.8 49.7 1.0 H B:HIS317 4.9 58.9 1.0 N B:HIS455 4.9 41.4 1.0 CG B:ASP204 4.9 47.7 1.0 HE1 B:HIS206 4.9 55.8 1.0 HG13 B:ILE424 4.9 54.1 1.0 HD1 B:HIS423 4.9 47.1 1.0

A.Gorelik, K.Illes, L.X.Heinz, G.Superti-Furga, B.Nagar. Crystal Structure of Mammalian Acid Sphingomyelinase. Nat Commun V. 7 12196 2016.
ISSN: ESSN 2041-1723
PubMed: 27435900
DOI: 10.1038/NCOMMS12196