Zinc in PDB 5fi9: Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa

All present enzymatic activity of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa:
3.1.4.12;

The structure of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa, PDB code: 5fi9 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)	46.65 / 2.54
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.394, 72.018, 74.420, 80.47, 71.52, 83.60
R / Rfree (%)	20.1 / 25.2

The binding sites of Zinc atom in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa (pdb code 5fi9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa, PDB code: 5fi9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:43.6 occ:1.00 OD1 A:ASP204 2.0 34.0 1.0 NE2 A:HIS206 2.0 34.7 1.0 NE2 A:HIS457 2.1 44.0 1.0 OD1 A:ASP276 2.3 33.6 1.0 O15 A:NT8718 2.3 40.2 1.0 O13 A:NT8718 2.7 36.6 1.0 CE1 A:HIS206 2.9 32.7 1.0 HB3 A:ASP204 2.9 40.0 1.0 CE1 A:HIS457 3.0 39.8 1.0 HE1 A:HIS457 3.0 47.7 1.0 P12 A:NT8718 3.0 39.2 1.0 HE1 A:HIS206 3.1 39.3 1.0 CG A:ASP204 3.1 35.2 1.0 HB3 A:ASP276 3.1 39.2 1.0 CD2 A:HIS206 3.1 32.3 1.0 CD2 A:HIS457 3.2 41.7 1.0 CG A:ASP276 3.2 34.0 1.0 HD2 A:HIS206 3.4 38.7 1.0 CB A:ASP204 3.4 33.4 1.0 HD2 A:HIS457 3.5 50.0 1.0 HE1 A:HIS423 3.5 39.9 1.0 CB A:ASP276 3.6 32.6 1.0 ZN A:ZN702 3.6 47.8 1.0 HA A:ASP204 3.6 40.9 1.0 HB2 A:ASP276 3.7 39.2 1.0 H032 A:NT8718 3.8 54.3 1.0 HA A:HIS455 3.8 39.4 1.0 O14 A:NT8718 3.9 42.4 1.0 HE2 A:HIS280 4.0 46.0 1.0 ND1 A:HIS206 4.1 35.6 1.0 ND1 A:HIS457 4.1 37.7 1.0 CA A:ASP204 4.1 34.1 1.0 HD2 A:HIS317 4.2 43.5 1.0 OD2 A:ASP204 4.2 31.9 1.0 CG A:HIS206 4.2 35.0 1.0 CE1 A:HIS423 4.2 33.3 1.0 CG A:HIS457 4.3 38.7 1.0 HB2 A:ASP204 4.3 40.0 1.0 OD2 A:ASP276 4.4 31.9 1.0 NE2 A:HIS423 4.4 36.8 1.0 C02 A:NT8718 4.5 44.8 1.0 O A:HIS455 4.5 42.0 1.0 C03 A:NT8718 4.6 45.2 1.0 HE1 A:HIS280 4.6 49.1 1.0 NE2 A:HIS280 4.7 38.4 1.0 CD2 A:HIS317 4.7 36.2 1.0 CA A:HIS455 4.7 32.8 1.0 HE2 A:HIS317 4.8 48.0 1.0 H A:HIS455 4.8 46.1 1.0 HD1 A:HIS206 4.9 42.7 1.0 HD1 A:HIS457 4.9 45.2 1.0 H011 A:NT8718 4.9 51.7 1.0 C A:HIS455 5.0 35.0 1.0 CE1 A:HIS280 5.0 40.9 1.0 NE2 A:HIS317 5.0 40.0 1.0 ND1 A:HIS455 5.0 40.1 1.0

Zinc binding site 2 out of 4 in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:47.8 occ:1.00 NE2 A:HIS423 2.0 36.8 1.0 OD1 A:ASN316 2.1 42.2 1.0 ND1 A:HIS455 2.1 40.1 1.0 OD1 A:ASP276 2.2 33.6 1.0 O14 A:NT8718 2.2 42.4 1.0 O15 A:NT8718 2.5 40.2 1.0 HE1 A:HIS455 2.6 43.4 1.0 CE1 A:HIS455 2.7 36.1 1.0 P12 A:NT8718 2.8 39.2 1.0 HD21 A:ASN316 3.0 38.3 1.0 CG A:ASP276 3.0 34.0 1.0 CG A:ASN316 3.0 34.7 1.0 CD2 A:HIS423 3.0 33.4 1.0 CE1 A:HIS423 3.0 33.3 1.0 HD2 A:HIS317 3.2 43.5 1.0 HD2 A:HIS423 3.2 40.1 1.0 OD2 A:ASP276 3.2 31.9 1.0 HE1 A:HIS423 3.2 39.9 1.0 HA A:HIS455 3.2 39.4 1.0 ND2 A:ASN316 3.4 31.9 1.0 CG A:HIS455 3.4 35.4 1.0 ZN A:ZN701 3.6 43.6 1.0 H011 A:NT8718 3.7 51.7 1.0 H A:ASN316 3.7 38.2 1.0 O13 A:NT8718 3.7 36.6 1.0 NE2 A:HIS455 4.0 35.9 1.0 HB2 A:HIS455 4.0 39.1 1.0 CB A:HIS455 4.0 32.6 1.0 CA A:HIS455 4.0 32.8 1.0 CD2 A:HIS317 4.1 36.2 1.0 OD1 A:ASP204 4.1 34.0 1.0 ND1 A:HIS423 4.1 32.4 1.0 CG A:HIS423 4.2 31.1 1.0 HD22 A:ASN316 4.2 38.3 1.0 CD2 A:HIS455 4.3 28.9 1.0 C02 A:NT8718 4.3 44.8 1.0 CB A:ASP276 4.3 32.6 1.0 HE2 A:HIS317 4.4 48.0 1.0 CB A:ASN316 4.4 32.3 1.0 N01 A:NT8718 4.4 43.1 1.0 HB2 A:ASP276 4.4 39.2 1.0 O A:HIS455 4.5 42.0 1.0 N A:ASN316 4.6 31.8 1.0 HB3 A:ASN316 4.6 38.8 1.0 HG12 A:ILE424 4.6 35.9 1.0 NE2 A:HIS317 4.6 40.0 1.0 HE1 A:HIS206 4.6 39.3 1.0 HE2 A:HIS455 4.7 43.1 1.0 HB3 A:ASP276 4.7 39.2 1.0 H A:HIS317 4.7 43.5 1.0 C A:HIS455 4.8 35.0 1.0 HD1 A:HIS423 4.9 38.9 1.0 HG13 A:ILE424 5.0 35.9 1.0 H012 A:NT8718 5.0 51.7 1.0 HB3 A:HIS455 5.0 39.1 1.0

Zinc binding site 3 out of 4 in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:36.9 occ:1.00 OD1 B:ASP204 2.1 25.9 1.0 NE2 B:HIS206 2.1 27.4 1.0 NE2 B:HIS457 2.1 23.8 1.0 O15 B:NT8717 2.2 29.8 1.0 OD1 B:ASP276 2.3 27.9 1.0 O13 B:NT8717 2.6 32.3 1.0 HB3 B:ASP204 2.9 27.3 1.0 P12 B:NT8717 2.9 31.8 1.0 CE1 B:HIS206 3.0 26.5 1.0 CG B:ASP204 3.0 23.6 1.0 CE1 B:HIS457 3.1 25.4 1.0 CD2 B:HIS457 3.1 24.9 1.0 CD2 B:HIS206 3.1 24.6 1.0 HE1 B:HIS206 3.2 31.8 1.0 HD2 B:HIS457 3.2 29.9 1.0 HB3 B:ASP276 3.2 29.2 1.0 HE1 B:HIS457 3.2 30.6 1.0 HD2 B:HIS206 3.3 29.6 1.0 CG B:ASP276 3.3 26.0 1.0 CB B:ASP204 3.4 22.7 1.0 ZN B:ZN702 3.5 38.5 1.0 HE1 B:HIS423 3.6 30.5 1.0 CB B:ASP276 3.7 24.4 1.0 O14 B:NT8717 3.7 34.4 1.0 HA B:ASP204 3.7 29.2 1.0 HB2 B:ASP276 3.8 29.2 1.0 HA B:HIS455 3.9 32.9 1.0 HE2 B:HIS280 4.1 37.0 1.0 H032 B:NT8717 4.1 36.0 1.0 OD2 B:ASP204 4.1 26.5 1.0 ND1 B:HIS206 4.1 26.5 1.0 CA B:ASP204 4.2 24.4 1.0 ND1 B:HIS457 4.2 27.3 1.0 HB2 B:ASP204 4.2 27.3 1.0 CG B:HIS457 4.2 23.9 1.0 CG B:HIS206 4.2 26.8 1.0 HD2 B:HIS317 4.2 38.4 1.0 CE1 B:HIS423 4.3 25.4 1.0 HE1 B:HIS280 4.3 36.5 1.0 NE2 B:HIS423 4.3 28.2 1.0 O B:HIS455 4.4 34.6 1.0 H041 B:NT8717 4.4 37.0 1.0 OD2 B:ASP276 4.4 28.4 1.0 C02 B:NT8717 4.5 38.6 1.0 NE2 B:HIS280 4.6 30.8 1.0 C03 B:NT8717 4.7 30.0 1.0 H011 B:NT8717 4.7 43.3 1.0 CA B:HIS455 4.7 27.4 1.0 CE1 B:HIS280 4.8 30.4 1.0 CD2 B:HIS317 4.8 32.0 1.0 HG21 B:THR484 4.9 25.7 1.0 H B:HIS455 4.9 29.6 1.0 C B:HIS455 4.9 27.9 1.0 HD1 B:HIS206 4.9 31.9 1.0 HD1 B:HIS457 4.9 32.8 1.0 ND1 B:HIS455 5.0 32.4 1.0

Zinc binding site 4 out of 4 in the Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Closed Form of Murine Acid Sphingomyelinase in Complex with Bisphosphonate Inhibitor Abpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:38.5 occ:1.00 NE2 B:HIS423 2.1 28.2 1.0 O14 B:NT8717 2.1 34.4 1.0 OD1 B:ASN316 2.1 30.2 1.0 ND1 B:HIS455 2.1 32.4 1.0 OD1 B:ASP276 2.2 27.9 1.0 O15 B:NT8717 2.6 29.8 1.0 HE1 B:HIS455 2.6 41.4 1.0 CE1 B:HIS455 2.7 34.5 1.0 P12 B:NT8717 2.8 31.8 1.0 CD2 B:HIS423 3.0 28.2 1.0 CG B:ASP276 3.0 26.0 1.0 HD21 B:ASN316 3.1 34.3 1.0 CG B:ASN316 3.1 27.6 1.0 CE1 B:HIS423 3.1 25.4 1.0 HA B:HIS455 3.1 32.9 1.0 HD2 B:HIS423 3.1 33.9 1.0 OD2 B:ASP276 3.3 28.4 1.0 HE1 B:HIS423 3.3 30.5 1.0 HD2 B:HIS317 3.3 38.4 1.0 CG B:HIS455 3.4 28.8 1.0 ND2 B:ASN316 3.4 28.6 1.0 H011 B:NT8717 3.5 43.3 1.0 ZN B:ZN701 3.5 36.9 1.0 H B:ASN316 3.7 38.1 1.0 O13 B:NT8717 3.8 32.3 1.0 OD1 B:ASP204 3.8 25.9 1.0 CA B:HIS455 3.9 27.4 1.0 NE2 B:HIS455 4.0 28.1 1.0 CB B:HIS455 4.0 29.1 1.0 HB2 B:HIS455 4.0 35.0 1.0 CG B:HIS423 4.2 27.4 1.0 ND1 B:HIS423 4.2 27.2 1.0 C02 B:NT8717 4.2 38.6 1.0 CD2 B:HIS317 4.2 32.0 1.0 N01 B:NT8717 4.3 36.1 1.0 CD2 B:HIS455 4.3 25.2 1.0 HD22 B:ASN316 4.3 34.3 1.0 O B:HIS455 4.3 34.6 1.0 CB B:ASP276 4.3 24.4 1.0 HB2 B:ASP276 4.4 29.2 1.0 CB B:ASN316 4.5 26.4 1.0 N B:ASN316 4.6 31.7 1.0 O17 B:NT8717 4.6 43.0 1.0 HB3 B:ASN316 4.6 31.7 1.0 HE1 B:HIS206 4.6 31.8 1.0 C B:HIS455 4.6 27.9 1.0 HE2 B:HIS455 4.7 33.7 1.0 HB3 B:ASP276 4.7 29.2 1.0 HG12 B:ILE424 4.7 34.1 1.0 H B:HIS317 4.7 37.0 1.0 H012 B:NT8717 4.8 43.3 1.0 HE2 B:HIS317 4.8 39.2 1.0 NE2 B:HIS317 4.9 32.6 1.0 HB3 B:HIS455 4.9 35.0 1.0 H B:HIS455 5.0 29.6 1.0 HD1 B:HIS423 5.0 32.6 1.0 N B:HIS455 5.0 24.7 1.0 HG13 B:ILE424 5.0 34.1 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