Zinc in PDB 5ebe: Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with 5' Cmp

The structure of Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with 5' Cmp, PDB code: 5ebe 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)	47.56 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.654, 147.654, 142.298, 90.00, 90.00, 120.00
R / Rfree (%)	25.1 / 29.5

The binding sites of Zinc atom in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with 5' Cmp (pdb code 5ebe). 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 5' Cmp, PDB code: 5ebe:
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 5' Cmp


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:27.7 occ:1.00 O1P A:C5P607 2.0 51.0 1.0 NE2 A:HIS252 2.1 14.6 1.0 OD2 A:ASP110 2.2 15.4 1.0 OD1 A:ASN151 2.2 23.5 1.0 ND1 A:HIS293 2.3 16.6 1.0 P A:C5P607 2.9 50.4 1.0 CE1 A:HIS252 2.9 14.6 1.0 O2P A:C5P607 3.0 48.1 1.0 CG A:ASP110 3.1 15.9 1.0 CD2 A:HIS252 3.2 14.7 1.0 CE1 A:HIS293 3.2 16.8 1.0 O5' A:C5P607 3.2 62.0 1.0 CG A:ASN151 3.2 22.4 1.0 OD1 A:ASP110 3.4 15.2 1.0 CG A:HIS293 3.4 16.1 1.0 ZN A:ZN606 3.6 14.2 1.0 ND2 A:ASN151 3.6 22.8 1.0 CA A:HIS293 3.7 14.8 1.0 CB A:HIS293 3.8 15.1 1.0 OD2 A:ASP45 3.9 11.1 1.0 ND1 A:HIS252 4.1 14.7 1.0 O A:HIS293 4.1 14.9 1.0 C5' A:C5P607 4.2 72.5 1.0 CG A:HIS252 4.2 14.7 1.0 O3P A:C5P607 4.3 52.3 1.0 NE2 A:HIS293 4.4 17.1 1.0 C A:HIS293 4.4 14.4 1.0 CB A:ASP110 4.4 16.4 1.0 CD2 A:HIS293 4.5 16.8 1.0 N A:ASN151 4.5 19.9 1.0 CD2 A:HIS152 4.6 20.8 1.0 CB A:ASN151 4.6 21.5 1.0 N A:HIS293 4.8 15.1 1.0 NE2 A:HIS47 5.0 13.4 1.0

Zinc binding site 2 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with 5' Cmp


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:14.2 occ:1.00 O2P A:C5P607 1.7 48.1 1.0 NE2 A:HIS47 2.1 13.4 1.0 NE2 A:HIS295 2.3 13.5 1.0 OD2 A:ASP110 2.4 15.4 1.0 OD2 A:ASP45 2.4 11.1 1.0 CD2 A:HIS47 3.0 13.8 1.0 P A:C5P607 3.1 50.4 1.0 CD2 A:HIS295 3.1 13.4 1.0 CG A:ASP45 3.1 11.4 1.0 CE1 A:HIS47 3.2 13.5 1.0 CG A:ASP110 3.3 15.9 1.0 CE1 A:HIS295 3.4 13.9 1.0 CB A:ASP45 3.4 11.6 1.0 CB A:ASP110 3.5 16.4 1.0 ZN A:ZN605 3.6 27.7 1.0 O1P A:C5P607 3.7 51.0 1.0 O A:HIS293 4.0 14.9 1.0 O5' A:C5P607 4.1 62.0 1.0 O3P A:C5P607 4.1 52.3 1.0 CG A:HIS47 4.2 13.9 1.0 ND1 A:HIS47 4.2 13.9 1.0 OD1 A:ASP45 4.2 11.0 1.0 C5' A:C5P607 4.2 72.5 1.0 CE1 A:HIS252 4.3 14.6 1.0 CG A:HIS295 4.3 13.7 1.0 ND1 A:HIS295 4.4 14.0 1.0 CA A:ASP45 4.4 11.8 1.0 NE2 A:HIS114 4.5 15.4 1.0 CE1 A:HIS114 4.5 15.7 1.0 OD1 A:ASP110 4.5 15.2 1.0 CA A:HIS293 4.6 14.8 1.0 NE2 A:HIS252 4.6 14.6 1.0 C A:HIS293 4.7 14.4 1.0

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


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn606 b:35.8 occ:1.00 O3X B:RP5611 2.3 68.9 1.0 OD2 B:ASP45 2.3 42.6 1.0 OD2 B:ASP110 2.3 25.3 1.0 NE2 B:HIS47 2.4 23.9 1.0 NE2 B:HIS295 2.4 29.8 1.0 CD2 B:HIS295 3.1 30.4 1.0 CD2 B:HIS47 3.1 24.8 1.0 CG B:ASP45 3.2 37.5 1.0 CG B:ASP110 3.3 28.3 1.0 P' B:RP5611 3.5 75.0 1.0 O2X B:RP5611 3.5 78.2 1.0 CE1 B:HIS47 3.5 24.8 1.0 ZN B:ZN607 3.5 40.1 1.0 CE1 B:HIS295 3.6 30.1 1.0 CB B:ASP110 3.6 29.2 1.0 CB B:ASP45 3.7 33.2 1.0 O B:HIS293 4.1 33.9 1.0 O B:HOH701 4.2 21.1 1.0 OD1 B:ASP45 4.2 41.1 1.0 CE1 B:HIS252 4.3 41.6 1.0 CG B:HIS47 4.3 26.5 1.0 CG B:HIS295 4.3 29.8 1.0 OD1 B:ASP110 4.4 29.8 1.0 O1X B:RP5611 4.5 81.3 1.0 NE2 B:HIS252 4.5 42.7 1.0 ND1 B:HIS47 4.5 26.8 1.0 CA B:HIS293 4.5 35.2 1.0 NE2 B:HIS114 4.5 36.0 1.0 ND1 B:HIS295 4.5 31.4 1.0 O5' B:RP5611 4.6 76.8 1.0 C5' B:RP5611 4.6 73.2 1.0 CE1 B:HIS114 4.6 36.8 1.0 CA B:ASP45 4.6 32.8 1.0 C B:HIS293 4.7 33.1 1.0 N B:HIS293 5.0 37.5 1.0

Zinc binding site 4 out of 6 in the Structure of Human Sphingomyelinase Phosphodiesterase Like 3A (SMPDL3A) with 5' Cmp


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn607 b:40.1 occ:1.00 O2X B:RP5611 1.7 78.2 1.0 NE2 B:HIS252 2.2 42.7 1.0 OD2 B:ASP110 2.4 25.3 1.0 OD1 B:ASN151 2.5 64.7 1.0 ND1 B:HIS293 2.7 42.1 1.0 P' B:RP5611 3.2 75.0 1.0 CE1 B:HIS252 3.2 41.6 1.0 CG B:ASP110 3.2 28.3 1.0 CD2 B:HIS252 3.2 41.9 1.0 OD1 B:ASP110 3.3 29.8 1.0 O3X B:RP5611 3.5 68.9 1.0 ZN B:ZN606 3.5 35.8 1.0 CG B:ASN151 3.5 54.9 1.0 CG B:HIS293 3.6 41.2 1.0 CE1 B:HIS293 3.7 42.6 1.0 CB B:HIS293 3.8 36.9 1.0 CA B:HIS293 3.8 35.2 1.0 ND2 B:ASN151 3.9 55.4 1.0 O5' B:RP5611 4.0 76.8 1.0 O1X B:RP5611 4.1 81.3 1.0 ND1 B:HIS252 4.3 41.3 1.0 OD2 B:ASP45 4.3 42.6 1.0 O B:HIS293 4.3 33.9 1.0 CG B:HIS252 4.3 41.0 1.0 C5' B:RP5611 4.5 73.2 1.0 CB B:ASP110 4.5 29.2 1.0 C B:HIS293 4.6 33.1 1.0 N B:ASN151 4.7 41.0 1.0 CD2 B:HIS152 4.7 35.7 1.0 NE2 B:HIS293 4.8 42.9 1.0 CD2 B:HIS293 4.8 44.4 1.0 N B:HIS293 4.9 37.5 1.0 CB B:ASN151 4.9 51.1 1.0

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


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn605 b:50.7 occ:1.00 NE2 C:HIS252 1.9 31.5 1.0 O2P C:C5P607 1.9 61.9 1.0 OD1 C:ASN151 2.3 43.5 1.0 OD2 C:ASP110 2.4 40.6 1.0 ND1 C:HIS293 2.5 25.0 1.0 CE1 C:HIS252 2.7 31.0 1.0 CD2 C:HIS252 3.0 31.8 1.0 P C:C5P607 3.1 56.8 1.0 CG C:ASN151 3.1 42.5 1.0 CE1 C:HIS293 3.2 25.3 1.0 O1P C:C5P607 3.3 59.3 1.0 ND2 C:ASN151 3.3 43.2 1.0 CG C:HIS293 3.4 25.3 1.0 CG C:ASP110 3.5 39.3 1.0 CB C:HIS293 3.8 26.4 1.0 O3P C:C5P607 3.8 53.5 1.0 OD1 C:ASP110 3.9 37.0 1.0 ZN C:ZN606 3.9 32.2 1.0 ND1 C:HIS252 3.9 31.3 1.0 CA C:HIS293 4.0 26.1 1.0 CG C:HIS252 4.1 32.2 1.0 NE2 C:HIS293 4.3 26.3 1.0 N C:ASN151 4.3 43.8 1.0 CD2 C:HIS293 4.4 25.6 1.0 O5' C:C5P607 4.4 68.3 1.0 OD2 C:ASP45 4.4 23.9 1.0 CB C:ASN151 4.5 42.7 1.0 O C:HIS293 4.6 26.2 1.0 CD2 C:HIS152 4.7 36.5 1.0 CB C:ASP110 4.7 38.3 1.0 C C:HIS293 4.8 25.8 1.0 CA C:ASN151 5.0 44.1 1.0

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


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 5' Cmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn606 b:32.2 occ:1.00 O3P C:C5P607 1.7 53.5 1.0 OD2 C:ASP45 2.1 23.9 1.0 NE2 C:HIS47 2.3 35.6 1.0 NE2 C:HIS295 2.4 24.5 1.0 OD2 C:ASP110 2.6 40.6 1.0 P C:C5P607 2.8 56.8 1.0 O2P C:C5P607 2.9 61.9 1.0 CG C:ASP45 3.0 27.6 1.0 CD2 C:HIS295 3.2 25.8 1.0 CD2 C:HIS47 3.2 35.7 1.0 CE1 C:HIS47 3.3 35.6 1.0 CG C:ASP110 3.4 39.3 1.0 CB C:ASP110 3.4 38.3 1.0 CB C:ASP45 3.5 30.6 1.0 CE1 C:HIS295 3.5 25.0 1.0 ZN C:ZN605 3.9 50.7 1.0 CE1 C:HIS252 3.9 31.0 1.0 O5' C:C5P607 3.9 68.3 1.0 O1P C:C5P607 3.9 59.3 1.0 OD1 C:ASP45 4.1 26.5 1.0 O C:HIS293 4.1 26.2 1.0 C5' C:C5P607 4.3 72.7 1.0 CA C:ASP45 4.4 32.4 1.0 CG C:HIS47 4.4 36.0 1.0 ND1 C:HIS47 4.4 36.1 1.0 CG C:HIS295 4.4 25.8 1.0 NE2 C:HIS252 4.5 31.5 1.0 CA C:HIS293 4.5 26.1 1.0 ND1 C:HIS295 4.5 26.1 1.0 OD1 C:ASP110 4.6 37.0 1.0 NE2 C:HIS114 4.8 45.1 1.0 C C:HIS293 4.8 25.8 1.0 CE1 C:HIS114 4.8 45.3 1.0 CA C:ASP110 4.9 35.5 1.0 N C:HIS293 5.0 25.6 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