Zinc in PDB 5kar: Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B)

The structure of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B), PDB code: 5kar 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)	36.83 / 1.14
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.892, 47.031, 93.861, 90.00, 98.07, 90.00
R / Rfree (%)	13.5 / 15.2

The binding sites of Zinc atom in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) (pdb code 5kar). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B), PDB code: 5kar:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.3 occ:1.00 O A:HOH613 2.0 13.3 1.0 OD1 A:ASN134 2.1 14.0 1.0 NE2 A:HIS236 2.1 10.8 1.0 ND1 A:HIS277 2.1 11.3 1.0 OD2 A:ASP93 2.2 12.4 1.0 HA A:HIS277 2.9 11.4 1.0 CE1 A:HIS277 3.0 11.9 1.0 CG A:ASP93 3.1 11.7 1.0 HE1 A:HIS277 3.1 14.2 1.0 CE1 A:HIS236 3.1 10.7 1.0 CD2 A:HIS236 3.1 10.7 1.0 CG A:ASN134 3.2 11.7 1.0 CG A:HIS277 3.2 10.6 1.0 HE1 A:HIS236 3.3 12.9 1.0 HD2 A:HIS236 3.3 12.8 1.0 HD2 A:HIS135 3.4 15.7 1.0 HD21 A:ASN134 3.4 14.9 1.0 ZN A:ZN502 3.4 11.8 1.0 OD1 A:ASP93 3.4 14.2 1.0 HB2 A:HIS277 3.6 12.6 1.0 H A:ASN134 3.6 13.1 1.0 CB A:HIS277 3.7 10.5 1.0 ND2 A:ASN134 3.7 12.5 1.0 CA A:HIS277 3.7 9.5 1.0 OD1 A:ASP28 3.8 11.5 1.0 O A:HIS277 4.1 11.8 1.0 NE2 A:HIS277 4.2 12.1 1.0 ND1 A:HIS236 4.2 10.8 1.0 CG A:HIS236 4.2 10.0 1.0 CD2 A:HIS135 4.2 13.1 1.0 HB2 A:ASP93 4.3 14.5 1.0 CB A:ASP93 4.3 12.1 1.0 CD2 A:HIS277 4.3 11.8 1.0 HG22 A:VAL237 4.3 13.9 1.0 N A:ASN134 4.4 10.9 1.0 C A:HIS277 4.4 10.8 1.0 CB A:ASN134 4.4 12.4 1.0 H A:HIS135 4.5 14.0 1.0 HD22 A:ASN134 4.5 14.9 1.0 HB3 A:ASN134 4.6 14.8 1.0 HE1 A:HIS30 4.6 12.1 1.0 HB3 A:ASP93 4.6 14.5 1.0 H A:HIS277 4.6 12.4 1.0 HB3 A:HIS277 4.6 12.6 1.0 N A:HIS277 4.7 10.3 1.0 NE2 A:HIS30 4.9 10.8 1.0 HA3 A:GLY133 4.9 14.4 1.0 HE2 A:HIS277 4.9 14.5 1.0 NE2 A:HIS135 4.9 14.2 1.0 HO1 A:GOL515 4.9 40.1 1.0 CA A:ASN134 4.9 11.1 1.0 HD1 A:HIS236 5.0 12.9 1.0

Zinc binding site 2 out of 2 in the Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine Acid Sphingomyelinase-Like Phosphodiesterase 3B (SMPDL3B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.8 occ:1.00 O A:HOH613 2.0 13.3 1.0 OD1 A:ASP28 2.0 11.5 1.0 NE2 A:HIS30 2.1 10.8 1.0 NE2 A:HIS279 2.1 11.4 1.0 OD2 A:ASP93 2.3 12.4 1.0 CE1 A:HIS30 3.0 10.1 1.0 CE1 A:HIS279 3.1 11.6 1.0 CD2 A:HIS30 3.1 10.2 1.0 CG A:ASP28 3.1 10.2 1.0 HB3 A:ASP93 3.1 14.5 1.0 CD2 A:HIS279 3.1 10.7 1.0 HB3 A:ASP28 3.1 12.8 1.0 HE1 A:HIS30 3.2 12.1 1.0 HE1 A:HIS279 3.2 13.9 1.0 HD2 A:HIS30 3.3 12.2 1.0 HD2 A:HIS279 3.3 12.9 1.0 CG A:ASP93 3.3 11.7 1.0 HO1 A:GOL515 3.3 40.1 1.0 ZN A:ZN501 3.4 12.3 1.0 CB A:ASP93 3.6 12.1 1.0 HA A:HIS277 3.6 11.4 1.0 HE1 A:HIS236 3.6 12.9 1.0 CB A:ASP28 3.6 10.7 1.0 HB2 A:ASP93 3.6 14.5 1.0 O A:HIS277 3.9 11.8 1.0 HA A:ASP28 3.9 13.3 1.0 HE1 A:HIS97 4.1 15.5 1.0 OD2 A:ASP28 4.1 10.9 1.0 ND1 A:HIS30 4.2 11.1 1.0 HD2 A:HIS135 4.2 15.7 1.0 O1 A:GOL515 4.2 33.4 1.0 ND1 A:HIS279 4.2 11.3 1.0 CG A:HIS30 4.2 10.5 1.0 CG A:HIS279 4.2 10.7 1.0 CE1 A:HIS236 4.3 10.7 1.0 NE2 A:HIS236 4.3 10.8 1.0 CA A:ASP28 4.4 11.1 1.0 HB2 A:ASP28 4.4 12.8 1.0 CA A:HIS277 4.4 9.5 1.0 OD1 A:ASP93 4.4 14.2 1.0 NE2 A:HIS97 4.5 12.7 1.0 C A:HIS277 4.5 10.8 1.0 CE1 A:HIS97 4.6 12.9 1.0 H A:HIS277 4.6 12.4 1.0 CD2 A:HIS135 4.8 13.1 1.0 ND1 A:HIS277 4.8 11.3 1.0 HG21 A:THR304 4.9 14.0 1.0 HD1 A:HIS30 4.9 13.3 1.0 HD1 A:HIS279 5.0 13.5 1.0

A.Gorelik, L.X.Heinz, K.Illes, G.Superti-Furga, B.Nagar. Crystal Structure of the Acid Sphingomyelinase-Like Phosphodiesterase SMPDL3B Provides Insights Into Determinants of Substrate Specificity. J.Biol.Chem. V. 291 24054 2016.
ISSN: ESSN 1083-351X
PubMed: 27687724
DOI: 10.1074/JBC.M116.755801