Zinc in PDB 5ebb: Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+

The structure of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+, PDB code: 5ebb was solved by S.M.Lim, K.Yeung, L.Tresaugues, H.L.Teo, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.790, 147.790, 139.900, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 25.5

The binding sites of Zinc atom in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ (pdb code 5ebb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+, PDB code: 5ebb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:14.9 occ:1.00 O7 A:MLI706 1.9 22.5 1.0 OD1 A:ASN151 2.1 9.2 1.0 NE2 A:HIS252 2.1 4.9 1.0 ND1 A:HIS293 2.3 5.6 1.0 OD2 A:ASP110 2.3 6.4 1.0 C2 A:MLI706 3.0 33.7 1.0 CG A:ASP110 3.1 6.3 1.0 CE1 A:HIS252 3.1 4.9 1.0 CD2 A:HIS252 3.1 5.0 1.0 CE1 A:HIS293 3.2 5.8 1.0 O8 A:MLI706 3.2 41.5 1.0 CG A:ASN151 3.2 9.2 1.0 OD1 A:ASP110 3.3 6.3 1.0 CG A:HIS293 3.3 5.5 1.0 ZN A:ZN702 3.3 7.2 1.0 CB A:HIS293 3.6 5.2 1.0 CA A:HIS293 3.7 5.1 1.0 ND2 A:ASN151 3.8 9.3 1.0 OD2 A:ASP45 3.8 5.0 1.0 C1 A:MLI706 3.9 35.6 1.0 O6 A:MLI706 3.9 41.4 1.0 C3 A:MLI706 3.9 39.3 1.0 O A:HIS293 4.1 5.7 1.0 ND1 A:HIS252 4.2 5.0 1.0 CG A:HIS252 4.3 5.0 1.0 NE2 A:HIS293 4.3 5.8 1.0 N A:ASN151 4.3 8.2 1.0 CB A:ASP110 4.3 6.2 1.0 C A:HIS293 4.4 5.2 1.0 CD2 A:HIS152 4.4 8.1 1.0 CD2 A:HIS293 4.4 5.6 1.0 CB A:ASN151 4.4 8.7 1.0 N A:HIS293 4.8 5.2 1.0 NE2 A:HIS47 4.9 5.1 1.0 CA A:ASN151 4.9 8.4 1.0 CG A:ASP45 5.0 4.6 1.0

Zinc binding site 2 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:7.2 occ:1.00 OD2 A:ASP45 2.0 5.0 1.0 O7 A:MLI706 2.1 22.5 1.0 OD2 A:ASP110 2.1 6.4 1.0 NE2 A:HIS47 2.2 5.1 1.0 NE2 A:HIS295 2.2 5.3 1.0 O6 A:MLI706 2.3 41.4 1.0 C2 A:MLI706 2.5 33.7 1.0 CG A:ASP45 3.0 4.6 1.0 CE1 A:HIS47 3.1 5.1 1.0 CD2 A:HIS295 3.2 5.3 1.0 CG A:ASP110 3.2 6.3 1.0 CD2 A:HIS47 3.2 5.3 1.0 CE1 A:HIS295 3.2 5.2 1.0 ZN A:ZN701 3.3 14.9 1.0 CB A:ASP110 3.5 6.2 1.0 CB A:ASP45 3.5 4.6 1.0 O A:HIS293 3.9 5.7 1.0 C1 A:MLI706 4.0 35.6 1.0 OD1 A:ASP45 4.1 4.5 1.0 CE1 A:HIS252 4.2 4.9 1.0 ND1 A:HIS47 4.3 4.9 1.0 NE2 A:HIS252 4.3 4.9 1.0 OD1 A:ASP110 4.3 6.3 1.0 ND1 A:HIS295 4.3 5.4 1.0 CG A:HIS47 4.3 5.0 1.0 CG A:HIS295 4.3 5.2 1.0 CA A:ASP45 4.4 4.5 1.0 CA A:HIS293 4.4 5.1 1.0 C A:HIS293 4.6 5.2 1.0 NE2 A:HIS114 4.6 7.9 1.0 O8 A:MLI706 4.7 41.5 1.0 CE1 A:HIS114 4.7 7.7 1.0 C3 A:MLI706 4.9 39.3 1.0 ND1 A:HIS293 5.0 5.6 1.0 CA A:ASP110 5.0 6.1 1.0 OD1 A:ASN151 5.0 9.2 1.0

Zinc binding site 3 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:19.0 occ:1.00 O8 B:MLI706 1.5 21.3 1.0 NE2 B:HIS47 2.0 17.2 1.0 NE2 B:HIS295 2.2 13.1 1.0 OD2 B:ASP110 2.3 19.8 1.0 OD2 B:ASP45 2.4 13.7 1.0 C3 B:MLI706 2.6 27.9 1.0 CD2 B:HIS47 2.9 17.9 1.0 CG B:ASP45 3.1 12.4 1.0 CE1 B:HIS47 3.1 16.6 1.0 CE1 B:HIS295 3.1 13.1 1.0 CD2 B:HIS295 3.2 12.6 1.0 C1 B:MLI706 3.2 28.7 1.0 CG B:ASP110 3.2 16.6 1.0 CB B:ASP45 3.2 13.9 1.0 CB B:ASP110 3.5 16.7 1.0 O9 B:MLI706 3.7 35.5 1.0 ZN B:ZN702 3.7 23.5 1.0 OD1 B:ASP45 4.0 10.9 1.0 CG B:HIS47 4.1 16.5 1.0 O B:HIS293 4.1 10.8 1.0 ND1 B:HIS47 4.1 16.6 1.0 CA B:ASP45 4.2 14.0 1.0 ND1 B:HIS295 4.3 13.2 1.0 CG B:HIS295 4.3 12.4 1.0 OD1 B:ASP110 4.3 16.9 1.0 NE2 B:HIS114 4.4 20.6 1.0 CE1 B:HIS252 4.4 9.3 1.0 CE1 B:HIS114 4.5 19.9 1.0 NE2 B:HIS252 4.5 9.2 1.0 CA B:HIS293 4.5 10.8 1.0 C2 B:MLI706 4.7 32.9 1.0 C B:HIS293 4.7 10.0 1.0 C B:ASP45 5.0 14.5 1.0 N B:HIS293 5.0 11.6 1.0

Zinc binding site 4 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:23.5 occ:1.00 O9 B:MLI706 1.7 35.5 1.0 OD1 B:ASN151 2.0 18.6 1.0 C3 B:MLI706 2.3 27.9 1.0 NE2 B:HIS252 2.3 9.2 1.0 O8 B:MLI706 2.4 21.3 1.0 ND1 B:HIS293 2.4 14.5 1.0 OD2 B:ASP110 2.6 19.8 1.0 CG B:ASN151 3.1 18.0 1.0 CD2 B:HIS252 3.2 9.2 1.0 CG B:ASP110 3.2 16.6 1.0 OD1 B:ASP110 3.2 16.9 1.0 CE1 B:HIS293 3.3 16.0 1.0 CE1 B:HIS252 3.3 9.3 1.0 CG B:HIS293 3.5 15.1 1.0 ND2 B:ASN151 3.6 17.7 1.0 ZN B:ZN701 3.7 19.0 1.0 C1 B:MLI706 3.7 28.7 1.0 CA B:HIS293 3.8 10.8 1.0 CB B:HIS293 3.8 12.2 1.0 OD2 B:ASP45 3.9 13.7 1.0 C2 B:MLI706 4.0 32.9 1.0 O B:HIS293 4.1 10.8 1.0 O6 B:MLI706 4.2 31.8 1.0 N B:ASN151 4.2 16.3 1.0 CG B:HIS252 4.3 9.7 1.0 CB B:ASN151 4.3 16.7 1.0 C B:HIS293 4.4 10.0 1.0 ND1 B:HIS252 4.4 9.5 1.0 O7 B:MLI706 4.4 36.0 1.0 CD2 B:HIS152 4.5 20.5 1.0 NE2 B:HIS293 4.5 18.0 1.0 CB B:ASP110 4.5 16.7 1.0 CD2 B:HIS293 4.6 16.9 1.0 CA B:ASN151 4.9 16.2 1.0 N B:HIS293 4.9 11.6 1.0 NE2 B:HIS47 4.9 17.2 1.0

Zinc binding site 5 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:13.8 occ:1.00 OD1 C:ASP45 2.0 14.7 1.0 O9 C:MLI706 2.1 38.4 1.0 OD2 C:ASP110 2.3 9.8 1.0 NE2 C:HIS47 2.3 12.3 1.0 O8 C:MLI706 2.4 54.0 1.0 NE2 C:HIS295 2.5 15.8 1.0 C3 C:MLI706 2.5 49.0 1.0 CG C:ASP45 3.1 12.6 1.0 ZN C:ZN702 3.1 23.6 1.0 CE1 C:HIS47 3.2 12.1 1.0 CG C:ASP110 3.3 10.3 1.0 CD2 C:HIS47 3.4 12.5 1.0 CE1 C:HIS295 3.4 15.0 1.0 CD2 C:HIS295 3.4 14.8 1.0 CB C:ASP110 3.5 11.3 1.0 CB C:ASP45 3.6 12.1 1.0 O C:HIS293 3.9 19.8 1.0 C1 C:MLI706 4.1 49.4 1.0 CE1 C:HIS252 4.2 15.6 1.0 OD2 C:ASP45 4.2 12.1 1.0 NE2 C:HIS252 4.2 17.4 1.0 OD1 C:ASN151 4.2 19.9 1.0 ND1 C:HIS47 4.4 11.2 1.0 CA C:ASP45 4.4 10.9 1.0 CA C:HIS293 4.5 18.1 1.0 OD1 C:ASP110 4.5 9.3 1.0 CG C:HIS47 4.5 11.7 1.0 ND1 C:HIS295 4.5 14.7 1.0 CG C:HIS295 4.6 14.0 1.0 C C:HIS293 4.6 17.1 1.0 NE2 C:HIS114 4.6 21.0 1.0 CE1 C:HIS114 4.6 19.4 1.0 O6 C:MLI706 4.7 49.2 1.0 C2 C:MLI706 4.9 50.3 1.0 ND1 C:HIS293 5.0 18.3 1.0 CA C:ASP110 5.0 11.9 1.0 CD2 C:HIS152 5.0 18.1 1.0 N C:HIS293 5.0 20.3 1.0

Zinc binding site 6 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:23.6 occ:1.00 OD1 C:ASN151 1.9 19.9 1.0 NE2 C:HIS252 2.1 17.4 1.0 O9 C:MLI706 2.1 38.4 1.0 ND1 C:HIS293 2.4 18.3 1.0 OD2 C:ASP110 2.4 9.8 1.0 CE1 C:HIS252 3.0 15.6 1.0 CD2 C:HIS252 3.1 15.7 1.0 CG C:ASN151 3.1 19.1 1.0 ZN C:ZN701 3.1 13.8 1.0 C3 C:MLI706 3.1 49.0 1.0 CG C:ASP110 3.2 10.3 1.0 CE1 C:HIS293 3.3 18.8 1.0 CG C:HIS293 3.4 18.2 1.0 O6 C:MLI706 3.5 49.2 1.0 OD1 C:ASP110 3.5 9.3 1.0 CA C:HIS293 3.6 18.1 1.0 OD1 C:ASP45 3.6 14.7 1.0 CB C:HIS293 3.7 17.9 1.0 O C:HIS293 3.9 19.8 1.0 CB C:ASN151 4.0 18.9 1.0 O8 C:MLI706 4.0 54.0 1.0 C1 C:MLI706 4.0 49.4 1.0 C2 C:MLI706 4.1 50.3 1.0 ND2 C:ASN151 4.1 19.2 1.0 ND1 C:HIS252 4.1 16.8 1.0 CG C:HIS252 4.2 15.4 1.0 C C:HIS293 4.2 17.1 1.0 CB C:ASP110 4.2 11.3 1.0 N C:ASN151 4.4 18.1 1.0 NE2 C:HIS293 4.5 19.0 1.0 CD2 C:HIS152 4.5 18.1 1.0 CD2 C:HIS293 4.5 18.4 1.0 N C:HIS293 4.6 20.3 1.0 CA C:ASN151 4.8 18.4 1.0 CG C:ASP45 4.8 12.6 1.0 NE2 C:HIS47 5.0 12.3 1.0 N C:HIS152 5.0 15.1 1.0

S.M.Lim, K.Yeung, L.Tresaugues, T.H.Ling, P.Nordlund. The Structure and Catalytic Mechanism of Human Sphingomyelin Phosphodiesterase Like 3A - An Acid Sphingomyelinase Homologue with A Novel Nucleotide Hydrolase Activity. Febs J. V. 283 1107 2016.
ISSN: ISSN 1742-464X
PubMed: 26783088
DOI: 10.1111/FEBS.13655