Zinc in PDB 5fca: Murine SMPDL3A in Presence of Excess Zinc

The structure of Murine SMPDL3A in Presence of Excess Zinc, PDB code: 5fca was solved by A.Gorelik, K.Illes, G.Superti-Furga, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.32 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.137, 123.588, 131.608, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.4

The binding sites of Zinc atom in the Murine SMPDL3A in Presence of Excess Zinc (pdb code 5fca). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Murine SMPDL3A in Presence of Excess Zinc, PDB code: 5fca:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.7 occ:1.00 OD2 A:ASP42 2.1 30.6 1.0 NE2 A:HIS44 2.1 34.3 1.0 NE2 A:HIS292 2.2 32.9 1.0 OD2 A:ASP107 2.4 37.3 1.0 CD2 A:HIS44 3.0 33.9 1.0 CE1 A:HIS44 3.1 37.8 1.0 CE1 A:HIS292 3.1 34.0 1.0 CG A:ASP42 3.1 32.8 1.0 HB3 A:ASP42 3.1 39.6 1.0 HB3 A:ASP107 3.2 41.7 1.0 CD2 A:HIS292 3.2 31.6 1.0 HD2 A:HIS44 3.2 40.7 1.0 HE1 A:HIS292 3.3 40.8 1.0 HE1 A:HIS44 3.3 45.4 1.0 HD2 A:HIS292 3.4 37.9 1.0 CG A:ASP107 3.4 34.8 1.0 ZN A:ZN502 3.5 48.1 1.0 HE1 A:HIS249 3.6 40.9 1.0 CB A:ASP42 3.6 33.0 1.0 CB A:ASP107 3.6 34.7 1.0 HA A:HIS290 3.7 35.4 1.0 HB2 A:ASP107 3.7 41.7 1.0 HE1 A:HIS111 3.9 50.0 1.0 HA A:ASP42 3.9 40.7 1.0 HD2 A:HIS149 4.0 43.4 1.0 OD1 A:ASP42 4.2 27.7 1.0 ND1 A:HIS44 4.2 37.0 1.0 CG A:HIS44 4.2 37.3 1.0 O A:HIS290 4.2 31.3 1.0 CE1 A:HIS249 4.2 34.1 1.0 ND1 A:HIS292 4.2 30.1 1.0 NE2 A:HIS249 4.3 31.4 1.0 CG A:HIS292 4.3 31.4 1.0 CA A:ASP42 4.4 33.9 1.0 ZN A:ZN503 4.4 74.9 1.0 HB2 A:ASP42 4.4 39.6 1.0 CA A:HIS290 4.6 29.5 1.0 OD1 A:ASP107 4.6 33.2 1.0 CE1 A:HIS111 4.6 41.6 1.0 CD2 A:HIS149 4.7 36.2 1.0 C A:HIS290 4.8 31.3 1.0 H A:HIS290 4.8 36.3 1.0 NE2 A:HIS111 4.8 45.7 1.0 HG21 A:THR317 4.9 41.4 1.0 HD1 A:HIS44 5.0 44.4 1.0

Zinc binding site 2 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:48.1 occ:1.00 NE2 A:HIS249 2.1 31.4 1.0 OD1 A:ASN148 2.1 34.9 1.0 ND1 A:HIS290 2.2 31.2 1.0 OD2 A:ASP107 2.4 37.3 1.0 CD2 A:HIS249 3.0 29.8 1.0 CE1 A:HIS290 3.0 31.9 1.0 HA A:HIS290 3.0 35.4 1.0 HD2 A:HIS249 3.1 35.8 1.0 HE1 A:HIS290 3.1 38.3 1.0 CE1 A:HIS249 3.2 34.1 1.0 CG A:ASP107 3.2 34.8 1.0 CG A:ASN148 3.2 34.5 1.0 CG A:HIS290 3.3 28.4 1.0 HD21 A:ASN148 3.4 38.9 1.0 HE1 A:HIS249 3.4 40.9 1.0 HD2 A:HIS149 3.5 43.4 1.0 OD1 A:ASP107 3.5 33.2 1.0 ZN A:ZN501 3.5 42.7 1.0 H A:ASN148 3.5 41.2 1.0 HB2 A:HIS290 3.5 36.9 1.0 ND2 A:ASN148 3.7 32.4 1.0 CB A:HIS290 3.7 30.7 1.0 CA A:HIS290 3.8 29.5 1.0 OD2 A:ASP42 4.0 30.6 1.0 O A:HIS290 4.1 31.3 1.0 CG A:HIS249 4.2 30.6 1.0 NE2 A:HIS290 4.2 32.5 1.0 ND1 A:HIS249 4.2 32.8 1.0 ZN A:ZN503 4.2 74.9 1.0 N A:ASN148 4.3 34.3 1.0 CD2 A:HIS290 4.4 29.9 1.0 HB2 A:ASP107 4.4 41.7 1.0 CD2 A:HIS149 4.4 36.2 1.0 CB A:ASP107 4.4 34.7 1.0 H A:HIS149 4.4 41.9 1.0 CB A:ASN148 4.5 35.2 1.0 C A:HIS290 4.5 31.3 1.0 HG22 A:VAL250 4.5 38.4 1.0 HD22 A:ASN148 4.6 38.9 1.0 HB3 A:ASN148 4.6 42.3 1.0 HB3 A:HIS290 4.7 36.9 1.0 HB3 A:ASP107 4.7 41.7 1.0 HE1 A:HIS44 4.8 45.4 1.0 H A:HIS290 4.8 36.3 1.0 HA3 A:GLY147 4.9 37.5 1.0 N A:HIS290 4.9 30.2 1.0 HE2 A:HIS290 4.9 39.1 1.0 CA A:ASN148 5.0 33.0 1.0

Zinc binding site 3 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:74.9 occ:1.00 NE2 A:HIS149 2.7 41.9 1.0 NE2 A:HIS111 2.8 45.7 1.0 HD2 A:HIS149 3.1 43.4 1.0 CD2 A:HIS149 3.2 36.2 1.0 HD21 A:ASN148 3.3 38.9 1.0 HD2 A:HIS111 3.5 51.1 1.0 CD2 A:HIS111 3.6 42.5 1.0 O A:HOH814 3.6 44.2 1.0 O A:HOH874 3.7 51.4 1.0 CE1 A:HIS111 3.8 41.6 1.0 CE1 A:HIS149 3.9 42.5 1.0 HE1 A:HIS111 4.1 50.0 1.0 ND2 A:ASN148 4.1 32.4 1.0 HE1 A:HIS290 4.1 38.3 1.0 O A:HOH929 4.2 56.5 1.0 ZN A:ZN502 4.2 48.1 1.0 HE1 A:HIS44 4.2 45.4 1.0 HE1 A:HIS149 4.2 51.0 1.0 ZN A:ZN501 4.4 42.7 1.0 OD2 A:ASP107 4.4 37.3 1.0 CG A:HIS149 4.6 36.7 1.0 HD22 A:ASN148 4.6 38.9 1.0 O A:HOH807 4.6 51.4 1.0 CE1 A:HIS290 4.7 31.9 1.0 CE1 A:HIS44 4.7 37.8 1.0 HE22 A:GLN154 4.8 51.6 1.0 CG A:HIS111 4.8 45.2 1.0 ND1 A:HIS149 4.8 41.4 1.0 OD1 A:ASN148 4.8 34.9 1.0 NE2 A:HIS44 4.9 34.3 1.0 ND1 A:HIS111 4.9 43.5 1.0 CG A:ASN148 5.0 34.5 1.0 HO3 A:GOL518 5.0 85.0 1.0

Zinc binding site 4 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:44.9 occ:0.24 NE2 B:HIS420 2.2 38.4 1.0 OD2 A:ASP260 2.4 38.3 1.0 OD2 A:ASP438 2.4 42.5 1.0 OD1 A:ASP438 2.6 39.4 1.0 O A:HOH639 2.7 43.6 1.0 OD1 A:ASP260 2.7 37.3 1.0 HD2 B:HIS420 2.8 48.5 1.0 CG A:ASP438 2.8 37.2 1.0 CD2 B:HIS420 2.8 40.4 1.0 CG A:ASP260 2.8 36.0 1.0 CE1 B:HIS420 3.3 39.5 1.0 HD22 B:LEU445 3.7 49.6 1.0 HE1 B:HIS420 3.7 47.4 1.0 HD21 B:LEU445 3.9 49.6 1.0 CG B:HIS420 4.0 41.4 1.0 HG1 B:THR259 4.1 37.0 1.0 O A:HOH849 4.2 48.5 1.0 CB A:ASP260 4.2 32.7 1.0 ND1 B:HIS420 4.2 41.8 1.0 CD2 B:LEU445 4.3 41.4 1.0 CB A:ASP438 4.3 33.0 1.0 HB2 A:ASP260 4.3 39.2 1.0 OG A:SER434 4.4 37.0 0.7 HG A:SER434 4.5 44.4 0.7 HB3 A:ASP438 4.6 39.6 1.0 HB3 A:ASP260 4.6 39.2 1.0 HD1 A:TYR437 4.6 36.3 1.0 HB2 A:SER434 4.7 43.0 0.3 HB2 A:ASP438 4.7 39.6 1.0 HD23 B:LEU445 4.8 49.6 1.0 HA A:ASP438 4.8 41.6 1.0 OG1 B:THR259 4.8 30.8 1.0 HD13 B:LEU445 4.8 51.1 1.0 HH A:TYR254 4.9 40.7 1.0 HG21 B:THR259 4.9 38.3 1.0

Zinc binding site 5 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn524 b:44.6 occ:0.26 NE2 A:HIS420 2.3 39.3 1.0 OD2 B:ASP438 2.4 39.5 1.0 OD2 B:ASP260 2.5 38.2 1.0 OD1 B:ASP438 2.5 39.6 1.0 O B:HOH612 2.7 44.6 1.0 OD1 B:ASP260 2.7 39.8 1.0 CG B:ASP438 2.8 34.7 1.0 CG B:ASP260 2.9 37.7 1.0 CD2 A:HIS420 2.9 39.0 1.0 HD2 A:HIS420 3.0 46.8 1.0 CE1 A:HIS420 3.3 36.6 1.0 HE1 A:HIS420 3.6 43.9 1.0 HD22 A:LEU445 3.7 47.4 1.0 CG A:HIS420 4.0 38.2 1.0 HG1 A:THR259 4.1 36.0 1.0 ND1 A:HIS420 4.1 39.9 1.0 O B:HOH797 4.1 46.9 1.0 OG B:SER434 4.2 37.5 0.6 HG B:SER434 4.3 45.0 0.6 HD21 A:LEU445 4.3 47.4 1.0 CB B:ASP438 4.3 33.7 1.0 CB B:ASP260 4.3 31.8 1.0 HB2 B:ASP260 4.4 38.1 1.0 CD2 A:LEU445 4.4 39.5 1.0 HB2 B:SER434 4.5 43.7 0.4 HB3 B:ASP438 4.6 40.4 1.0 HB2 B:ASP438 4.7 40.4 1.0 HB3 B:ASP260 4.8 38.1 1.0 HD1 B:TYR437 4.8 33.0 1.0 HA B:ASP438 4.8 38.4 1.0 HD13 A:LEU445 4.8 52.2 1.0 HH B:TYR254 4.9 41.0 1.0 OG1 A:THR259 4.9 30.0 1.0 HG21 A:THR259 5.0 36.6 1.0 HD23 A:LEU445 5.0 47.4 1.0

Zinc binding site 6 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:47.4 occ:1.00 NE2 B:HIS292 2.2 36.5 1.0 OD2 B:ASP42 2.2 32.5 1.0 NE2 B:HIS44 2.2 41.9 1.0 OD2 B:ASP107 2.3 40.6 1.0 CD2 B:HIS44 3.0 38.0 1.0 HD2 B:HIS44 3.1 45.6 1.0 HB3 B:ASP42 3.1 42.9 1.0 CE1 B:HIS292 3.1 39.5 1.0 HB3 B:ASP107 3.1 49.6 1.0 CD2 B:HIS292 3.2 35.4 1.0 CG B:ASP42 3.2 33.5 1.0 CG B:ASP107 3.3 35.4 1.0 HE1 B:HIS292 3.3 47.4 1.0 HD2 B:HIS292 3.3 42.4 1.0 CE1 B:HIS44 3.3 41.6 1.0 ZN B:ZN502 3.5 48.7 1.0 CB B:ASP107 3.6 41.3 1.0 HE1 B:HIS249 3.6 40.5 1.0 HE1 B:HIS44 3.6 49.9 1.0 CB B:ASP42 3.6 35.7 1.0 HB2 B:ASP107 3.7 49.6 1.0 HA B:HIS290 3.7 36.4 1.0 HE1 B:HIS111 3.8 57.6 1.0 HA B:ASP42 4.0 43.6 1.0 HD2 B:HIS149 4.1 54.9 1.0 O B:HIS290 4.1 36.2 1.0 CE1 B:HIS249 4.2 33.8 1.0 ND1 B:HIS292 4.2 37.3 1.0 CG B:HIS44 4.3 40.0 1.0 OD1 B:ASP42 4.3 36.1 1.0 CG B:HIS292 4.3 37.1 1.0 NE2 B:HIS249 4.3 32.6 1.0 ND1 B:HIS44 4.4 42.6 1.0 OD1 B:ASP107 4.4 34.7 1.0 HB2 B:ASP42 4.4 42.9 1.0 CA B:ASP42 4.4 36.4 1.0 CE1 B:HIS111 4.5 48.0 1.0 CA B:HIS290 4.6 30.4 1.0 HO2 B:GOL521 4.7 70.0 1.0 C B:HIS290 4.7 33.3 1.0 H B:HIS290 4.8 37.1 1.0 NE2 B:HIS111 4.8 50.3 1.0 CD2 B:HIS149 4.8 45.7 1.0 HO3 B:GOL521 4.8 70.0 1.0 ZN B:ZN503 4.9 75.0 1.0 HG21 B:THR317 5.0 44.9 1.0

Zinc binding site 7 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:48.7 occ:1.00 OD1 B:ASN148 2.0 39.5 1.0 NE2 B:HIS249 2.1 32.6 1.0 ND1 B:HIS290 2.3 32.1 1.0 OD2 B:ASP107 2.4 40.6 1.0 HA B:HIS290 3.0 36.4 1.0 CE1 B:HIS290 3.0 33.2 1.0 CD2 B:HIS249 3.1 31.4 1.0 HE1 B:HIS290 3.1 39.9 1.0 CG B:ASN148 3.1 37.6 1.0 CG B:ASP107 3.2 35.4 1.0 CE1 B:HIS249 3.2 33.8 1.0 HD2 B:HIS249 3.2 37.7 1.0 HD21 B:ASN148 3.2 43.1 1.0 HE1 B:HIS249 3.4 40.5 1.0 OD1 B:ASP107 3.4 34.7 1.0 CG B:HIS290 3.4 32.4 1.0 HD2 B:HIS149 3.4 54.9 1.0 ZN B:ZN501 3.5 47.4 1.0 ND2 B:ASN148 3.5 35.9 1.0 H B:ASN148 3.6 45.9 1.0 HB2 B:HIS290 3.7 37.9 1.0 CA B:HIS290 3.8 30.4 1.0 CB B:HIS290 3.8 31.6 1.0 OD2 B:ASP42 4.0 32.5 1.0 O B:HIS290 4.1 36.2 1.0 NE2 B:HIS290 4.2 34.0 1.0 CG B:HIS249 4.2 33.5 1.0 ND1 B:HIS249 4.3 34.9 1.0 CD2 B:HIS149 4.3 45.7 1.0 H B:HIS149 4.4 44.7 1.0 CB B:ASN148 4.4 33.8 1.0 N B:ASN148 4.4 38.2 1.0 HD22 B:ASN148 4.4 43.1 1.0 HB2 B:ASP107 4.4 49.6 1.0 CD2 B:HIS290 4.4 30.7 1.0 CB B:ASP107 4.4 41.3 1.0 C B:HIS290 4.5 33.3 1.0 HB3 B:ASN148 4.5 40.6 1.0 HG22 B:VAL250 4.6 39.1 1.0 ZN B:ZN503 4.6 75.0 1.0 H B:HIS290 4.8 37.1 1.0 HB3 B:ASP107 4.8 49.6 1.0 HB3 B:HIS290 4.8 37.9 1.0 N B:HIS290 4.9 31.0 1.0 HA3 B:GLY147 4.9 44.9 1.0 NE2 B:HIS149 4.9 51.4 1.0 CA B:ASN148 5.0 38.2 1.0 NE2 B:HIS44 5.0 41.9 1.0 HE2 B:HIS290 5.0 40.8 1.0 HE1 B:HIS44 5.0 49.9 1.0

Zinc binding site 8 out of 8 in the Murine SMPDL3A in Presence of Excess Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Murine SMPDL3A in Presence of Excess Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:75.0 occ:1.00 NE2 B:HIS149 2.3 51.4 1.0 NE2 B:HIS111 2.6 50.3 1.0 HD2 B:HIS111 3.1 59.1 1.0 CD2 B:HIS111 3.2 49.2 1.0 CD2 B:HIS149 3.2 45.7 1.0 HD21 B:ASN148 3.2 43.1 1.0 CE1 B:HIS149 3.3 50.8 1.0 HD2 B:HIS149 3.3 54.9 1.0 HE1 B:HIS149 3.5 60.9 1.0 CE1 B:HIS111 3.8 48.0 1.0 ND2 B:ASN148 4.0 35.9 1.0 HE22 B:GLN154 4.2 60.1 1.0 HE1 B:HIS111 4.2 57.6 1.0 O2 B:GOL521 4.2 58.3 1.0 O B:HOH877 4.2 46.7 1.0 HD22 B:ASN148 4.4 43.1 1.0 CG B:HIS149 4.4 45.1 1.0 ND1 B:HIS149 4.4 46.7 1.0 HE1 B:HIS44 4.4 49.9 1.0 CG B:HIS111 4.5 50.3 1.0 HE1 B:HIS290 4.5 39.9 1.0 HO2 B:GOL521 4.6 70.0 1.0 H32 B:GOL522 4.6 86.6 1.0 O B:HOH928 4.6 53.8 1.0 ZN B:ZN502 4.6 48.7 1.0 ND1 B:HIS111 4.7 49.4 1.0 OD2 B:ASP107 4.8 40.6 1.0 NE2 B:GLN154 4.8 50.1 1.0 ZN B:ZN501 4.9 47.4 1.0 HH B:TYR211 4.9 50.0 1.0 CE1 B:HIS44 5.0 41.6 1.0

A.Gorelik, K.Illes, G.Superti-Furga, B.Nagar. Structural Basis For Nucleotide Hydrolysis By the Acid Sphingomyelinase-Like Phosphodiesterase SMPDL3A. J.Biol.Chem. V. 291 6376 2016.
ISSN: ESSN 1083-351X
PubMed: 26792860
DOI: 10.1074/JBC.M115.711085