Zinc in PDB 5fib: Open Form of Murine Acid Sphingomyelinase

All present enzymatic activity of Open Form of Murine Acid Sphingomyelinase:
3.1.4.12;

The structure of Open Form of Murine Acid Sphingomyelinase, PDB code: 5fib 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)	45.70 / 2.80
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.173, 181.173, 109.891, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.8

The binding sites of Zinc atom in the Open Form of Murine Acid Sphingomyelinase (pdb code 5fib). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Open Form of Murine Acid Sphingomyelinase, PDB code: 5fib:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:29.0 occ:1.00 O A:HOH802 2.0 17.1 1.0 NE2 A:HIS206 2.0 22.4 1.0 OD1 A:ASP204 2.0 39.5 1.0 NE2 A:HIS457 2.1 26.0 1.0 OD1 A:ASP276 2.2 15.0 1.0 HB3 A:ASP204 2.9 36.3 1.0 CD2 A:HIS206 2.9 25.3 1.0 CD2 A:HIS457 2.9 29.6 1.0 CG A:ASP204 3.0 35.2 1.0 CE1 A:HIS206 3.0 30.5 1.0 HD2 A:HIS457 3.1 35.5 1.0 HB3 A:ASP276 3.1 34.4 1.0 HD2 A:HIS206 3.1 30.4 1.0 CE1 A:HIS457 3.1 34.7 1.0 CG A:ASP276 3.2 23.1 1.0 HE1 A:HIS206 3.3 36.6 1.0 CB A:ASP204 3.4 30.2 1.0 HE1 A:HIS457 3.4 41.7 1.0 ZN A:ZN702 3.5 30.5 1.0 CB A:ASP276 3.5 28.7 1.0 HB2 A:ASP276 3.7 34.4 1.0 HA A:ASP204 3.7 32.2 1.0 HA A:HIS455 3.8 34.1 1.0 HE1 A:HIS423 3.8 51.5 1.0 OD2 A:ASP204 4.1 28.9 1.0 CG A:HIS206 4.1 36.4 1.0 ND1 A:HIS206 4.1 32.1 1.0 HE1 A:HIS280 4.1 50.2 1.0 CA A:ASP204 4.1 26.8 1.0 O A:HIS455 4.1 33.0 1.0 CG A:HIS457 4.1 24.6 1.0 HB2 A:ASP204 4.2 36.3 1.0 ND1 A:HIS457 4.2 29.0 1.0 NE2 A:HIS423 4.3 36.5 1.0 OD2 A:ASP276 4.4 22.6 1.0 CE1 A:HIS423 4.4 43.0 1.0 NE2 A:HIS280 4.6 35.4 1.0 HD2 A:HIS317 4.6 38.5 1.0 CE1 A:HIS280 4.6 41.8 1.0 CA A:HIS455 4.6 28.4 1.0 HG21 A:THR484 4.8 37.3 1.0 C A:HIS455 4.8 22.0 1.0 ND1 A:HIS455 4.8 23.6 1.0 H A:HIS455 4.8 37.6 1.0 HD1 A:HIS206 4.9 38.6 1.0 CD2 A:HIS317 4.9 32.0 1.0 CA A:ASP276 5.0 34.9 1.0 HD1 A:HIS457 5.0 34.8 1.0

Zinc binding site 2 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:30.5 occ:1.00 NE2 A:HIS423 2.1 36.5 1.0 OD1 A:ASN316 2.1 45.6 1.0 ND1 A:HIS455 2.1 23.6 1.0 OD1 A:ASP276 2.1 15.0 1.0 O A:HOH802 2.3 17.1 1.0 HA A:HIS455 2.8 34.1 1.0 CE1 A:HIS455 2.9 34.9 1.0 CD2 A:HIS423 2.9 29.0 1.0 CG A:ASP276 2.9 23.1 1.0 HE1 A:HIS455 3.0 41.9 1.0 HD2 A:HIS423 3.0 34.8 1.0 OD2 A:ASP276 3.2 22.6 1.0 CE1 A:HIS423 3.2 43.0 1.0 CG A:ASN316 3.2 31.6 1.0 CG A:HIS455 3.2 43.4 1.0 HE1 A:HIS423 3.4 51.5 1.0 ZN A:ZN701 3.5 29.0 1.0 HD2 A:HIS317 3.5 38.5 1.0 HD21 A:ASN316 3.6 35.1 1.0 HB2 A:HIS455 3.6 54.8 1.0 CA A:HIS455 3.6 28.4 1.0 H A:ASN316 3.7 42.4 1.0 CB A:HIS455 3.7 45.7 1.0 OD1 A:ASP204 3.8 39.5 1.0 ND2 A:ASN316 3.8 29.2 1.0 NE2 A:HIS455 4.1 45.6 1.0 CG A:HIS423 4.1 19.9 1.0 O A:HIS455 4.2 33.0 1.0 ND1 A:HIS423 4.2 28.4 1.0 CB A:ASP276 4.2 28.7 1.0 CD2 A:HIS455 4.3 31.0 1.0 HB2 A:ASP276 4.3 34.4 1.0 CD2 A:HIS317 4.3 32.0 1.0 CB A:ASN316 4.4 30.6 1.0 HB3 A:ASN316 4.4 36.7 1.0 C A:HIS455 4.4 22.0 1.0 N A:ASN316 4.5 35.3 1.0 HG12 A:ILE424 4.5 38.3 1.0 HB3 A:ASP276 4.6 34.4 1.0 HD22 A:ASN316 4.6 35.1 1.0 H A:HIS455 4.6 37.6 1.0 HB3 A:HIS455 4.7 54.8 1.0 N A:HIS455 4.7 31.3 1.0 HE2 A:HIS317 4.7 43.3 1.0 HE1 A:HIS206 4.7 36.6 1.0 H A:HIS317 4.8 32.3 1.0 CG A:ASP204 4.8 35.2 1.0 HE2 A:HIS455 4.8 54.7 1.0 NE2 A:HIS317 4.9 36.1 1.0 NE2 A:HIS206 4.9 22.4 1.0 HD2 A:HIS457 4.9 35.5 1.0

Zinc binding site 3 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:47.8 occ:1.00 NE2 A:HIS78 2.0 49.0 1.0 NE2 A:HIS80 2.0 44.5 1.0 HE1 A:HIS80 2.7 62.4 1.0 CE1 A:HIS80 2.7 52.0 1.0 O A:HOH814 2.8 26.8 1.0 CE1 A:HIS78 3.0 49.3 1.0 CD2 A:HIS78 3.1 66.8 1.0 HE1 A:HIS78 3.1 59.1 1.0 CD2 A:HIS80 3.3 48.5 1.0 HD2 A:HIS78 3.3 80.2 1.0 HD2 A:HIS80 3.6 58.3 1.0 ND1 A:HIS80 3.9 36.0 1.0 ND1 A:HIS78 4.1 50.4 1.0 CG A:HIS78 4.2 65.9 1.0 CG A:HIS80 4.2 41.1 1.0 HD1 A:HIS80 4.6 43.2 1.0 HD1 A:HIS78 4.9 60.5 1.0

Zinc binding site 4 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:24.6 occ:1.00 OD1 B:ASP204 2.0 26.1 1.0 NE2 B:HIS457 2.1 14.3 1.0 NE2 B:HIS206 2.1 26.5 1.0 O B:HOH806 2.2 29.9 1.0 OD1 B:ASP276 2.3 22.0 1.0 HB3 B:ASP204 2.9 32.4 1.0 CD2 B:HIS206 3.0 27.2 1.0 CD2 B:HIS457 3.0 18.3 1.0 CE1 B:HIS457 3.1 24.9 1.0 CE1 B:HIS206 3.1 22.2 1.0 CG B:ASP204 3.1 23.6 1.0 HD2 B:HIS206 3.2 32.6 1.0 HD2 B:HIS457 3.2 21.9 1.0 HE1 B:HIS457 3.3 29.9 1.0 CG B:ASP276 3.3 30.4 1.0 HE1 B:HIS206 3.3 26.7 1.0 HB3 B:ASP276 3.3 36.0 1.0 ZN B:ZN702 3.4 32.0 1.0 CB B:ASP204 3.5 27.0 1.0 CB B:ASP276 3.7 30.0 1.0 HA B:HIS455 3.8 32.5 1.0 HB2 B:ASP276 3.8 36.0 1.0 HA B:ASP204 3.8 29.8 1.0 HE1 B:HIS423 3.9 41.1 1.0 HE1 B:HIS280 4.1 38.5 1.0 O B:HIS455 4.1 26.7 1.0 ND1 B:HIS457 4.2 26.4 1.0 ND1 B:HIS206 4.2 26.8 1.0 CG B:HIS206 4.2 30.9 1.0 CG B:HIS457 4.2 19.4 1.0 OD2 B:ASP204 4.2 21.5 1.0 NE2 B:HIS423 4.2 19.8 1.0 CA B:ASP204 4.2 24.8 1.0 HB2 B:ASP204 4.3 32.4 1.0 HD2 B:HIS317 4.3 33.2 1.0 OD2 B:ASP276 4.4 31.8 1.0 CE1 B:HIS423 4.4 34.3 1.0 NE2 B:HIS280 4.5 29.2 1.0 CE1 B:HIS280 4.6 32.1 1.0 CA B:HIS455 4.7 27.1 1.0 CD2 B:HIS317 4.8 27.7 1.0 C B:HIS455 4.8 25.1 1.0 HE2 B:HIS317 4.8 36.7 1.0 ND1 B:HIS455 4.8 32.9 1.0 HG21 B:THR484 4.8 29.5 1.0 H B:HIS455 4.9 23.8 1.0 HD1 B:HIS457 4.9 31.7 1.0 HD1 B:HIS206 4.9 32.2 1.0

Zinc binding site 5 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:32.0 occ:1.00 NE2 B:HIS423 2.0 19.8 1.0 ND1 B:HIS455 2.1 32.9 1.0 OD1 B:ASN316 2.1 37.2 1.0 OD1 B:ASP276 2.1 22.0 1.0 O B:HOH806 2.3 29.9 1.0 CD2 B:HIS423 2.8 16.3 1.0 CE1 B:HIS455 2.8 40.9 1.0 HE1 B:HIS455 2.8 49.1 1.0 HD2 B:HIS423 2.8 19.5 1.0 HA B:HIS455 2.9 32.5 1.0 CG B:ASP276 3.0 30.4 1.0 CE1 B:HIS423 3.2 34.3 1.0 CG B:ASN316 3.2 28.2 1.0 CG B:HIS455 3.3 30.6 1.0 OD2 B:ASP276 3.3 31.8 1.0 ZN B:ZN701 3.4 24.6 1.0 HD21 B:ASN316 3.5 29.7 1.0 HD2 B:HIS317 3.5 33.2 1.0 HE1 B:HIS423 3.5 41.1 1.0 OD1 B:ASP204 3.6 26.1 1.0 CA B:HIS455 3.7 27.1 1.0 H B:ASN316 3.8 31.7 1.0 ND2 B:ASN316 3.8 24.7 1.0 HB2 B:HIS455 3.8 35.4 1.0 CB B:HIS455 3.8 29.5 1.0 CG B:HIS423 4.0 20.3 1.0 NE2 B:HIS455 4.0 40.6 1.0 ND1 B:HIS423 4.2 32.4 1.0 O B:HIS455 4.2 26.7 1.0 CD2 B:HIS455 4.3 33.8 1.0 CB B:ASP276 4.3 30.0 1.0 HB2 B:ASP276 4.3 36.0 1.0 CD2 B:HIS317 4.4 27.7 1.0 C B:HIS455 4.5 25.1 1.0 CB B:ASN316 4.5 26.5 1.0 HB3 B:ASN316 4.6 31.9 1.0 N B:ASN316 4.6 26.4 1.0 HD22 B:ASN316 4.6 29.7 1.0 HE1 B:HIS206 4.6 26.7 1.0 HE2 B:HIS317 4.7 36.7 1.0 HB3 B:ASP276 4.7 36.0 1.0 H B:HIS455 4.7 23.8 1.0 HE2 B:HIS455 4.8 48.7 1.0 N B:HIS455 4.8 19.8 1.0 HB3 B:HIS455 4.8 35.4 1.0 CG B:ASP204 4.8 23.6 1.0 HG12 B:ILE424 4.8 35.1 1.0 NE2 B:HIS206 4.8 26.5 1.0 NE2 B:HIS317 4.9 30.6 1.0 NE2 B:HIS457 5.0 14.3 1.0 HD1 B:HIS423 5.0 38.9 1.0

Zinc binding site 6 out of 6 in the Open Form of Murine Acid Sphingomyelinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Open Form of Murine Acid Sphingomyelinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:54.5 occ:1.00 NE2 B:HIS78 2.0 57.8 1.0 NE2 B:HIS80 2.0 58.2 1.0 CD2 B:HIS78 2.8 67.3 1.0 HD2 B:HIS78 2.9 80.7 1.0 CE1 B:HIS80 2.9 52.2 1.0 HE1 B:HIS80 3.0 62.7 1.0 CD2 B:HIS80 3.1 59.5 1.0 CE1 B:HIS78 3.2 71.0 1.0 O B:HOH816 3.4 46.3 1.0 HD2 B:HIS80 3.4 71.4 1.0 HE1 B:HIS78 3.5 85.2 1.0 CG B:HIS78 4.0 70.9 1.0 ND1 B:HIS80 4.1 41.9 1.0 ND1 B:HIS78 4.2 72.7 1.0 CG B:HIS80 4.2 47.9 1.0 HD1 B:HIS80 4.8 50.3 1.0 HD1 B:HIS78 5.0 87.2 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