Zinc in PDB 8w6r: Murine SMPDL3A Bound to Sulfate

The structure of Murine SMPDL3A Bound to Sulfate, PDB code: 8w6r was solved by C.Zhang, P.Liu, S.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.54 / 1.95
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	86.374, 86.374, 79.886, 90, 90, 90
R / Rfree (%)	22.1 / 25.2

The binding sites of Zinc atom in the Murine SMPDL3A Bound to Sulfate (pdb code 8w6r). 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 SMPDL3A Bound to Sulfate, PDB code: 8w6r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Murine SMPDL3A Bound to Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine SMPDL3A Bound to Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:25.8 occ:1.00 OD1 A:ASN148 2.1 15.9 1.0 O A:HOH663 2.1 17.0 1.0 OD2 A:ASP107 2.2 15.0 1.0 O2 A:SO4506 2.2 22.9 1.0 NE2 A:HIS249 2.3 17.5 1.0 ND1 A:HIS290 2.4 15.1 1.0 CE1 A:HIS290 3.2 18.4 1.0 CG A:ASN148 3.2 14.3 1.0 CD2 A:HIS249 3.2 16.6 1.0 CG A:ASP107 3.2 16.4 1.0 CE1 A:HIS249 3.3 16.1 1.0 S A:SO4506 3.3 28.8 1.0 ZN A:ZN505 3.4 20.3 1.0 CG A:HIS290 3.5 15.2 1.0 O1 A:SO4506 3.5 18.0 1.0 OD1 A:ASP107 3.6 13.6 1.0 ND2 A:ASN148 3.6 16.4 1.0 CB A:HIS290 3.9 14.9 1.0 O3 A:SO4506 3.9 25.2 1.0 CA A:HIS290 3.9 15.2 1.0 OD1 A:ASP42 4.0 15.9 1.0 O A:HIS290 4.2 13.9 1.0 CD2 A:HIS149 4.3 13.7 1.0 NE2 A:HIS290 4.3 15.5 1.0 CG A:HIS249 4.4 13.4 1.0 ND1 A:HIS249 4.4 13.0 1.0 N A:ASN148 4.4 13.7 1.0 CD2 A:HIS290 4.5 14.4 1.0 CB A:ASN148 4.5 13.3 1.0 O4 A:SO4506 4.5 21.8 1.0 C A:HIS290 4.6 14.6 1.0 CB A:ASP107 4.6 14.5 1.0 NE2 A:HIS149 5.0 17.7 1.0 O A:HOH653 5.0 29.6 1.0 N A:HIS290 5.0 10.8 1.0

Zinc binding site 2 out of 2 in the Murine SMPDL3A Bound to Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine SMPDL3A Bound to Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:20.3 occ:1.00 OD1 A:ASP42 2.1 15.9 1.0 O A:HOH663 2.1 17.0 1.0 NE2 A:HIS44 2.2 16.4 1.0 NE2 A:HIS292 2.3 15.9 1.0 OD2 A:ASP107 2.3 15.0 1.0 O1 A:SO4506 2.4 18.0 1.0 CE1 A:HIS44 3.2 13.9 1.0 CE1 A:HIS292 3.2 15.0 1.0 CG A:ASP42 3.2 16.6 1.0 CG A:ASP107 3.3 16.4 1.0 CD2 A:HIS44 3.3 15.3 1.0 CD2 A:HIS292 3.3 13.6 1.0 ZN A:ZN504 3.4 25.8 1.0 CB A:ASP107 3.5 14.5 1.0 S A:SO4506 3.6 28.8 1.0 O2 A:SO4506 3.8 22.9 1.0 CB A:ASP42 3.8 12.0 1.0 O3 A:SO4506 4.1 25.2 1.0 CE1 A:HIS249 4.2 16.1 1.0 OD2 A:ASP42 4.2 16.3 1.0 O A:HIS290 4.2 13.9 1.0 NE2 A:HIS249 4.3 17.5 1.0 ND1 A:HIS44 4.3 14.5 1.0 ND1 A:HIS292 4.3 14.3 1.0 OD1 A:ASP107 4.3 13.6 1.0 CG A:HIS44 4.4 16.0 1.0 NE2 A:HIS111 4.4 19.9 1.0 CE1 A:HIS111 4.4 15.8 1.0 CG A:HIS292 4.4 11.9 1.0 CA A:ASP42 4.5 13.5 1.0 CA A:HIS290 4.6 15.2 1.0 O4 A:SO4506 4.7 21.8 1.0 CD2 A:HIS149 4.8 13.7 1.0 C A:HIS290 4.8 14.6 1.0

Y.Hou, Z.Wang, P.Liu, X.Wei, Z.Zhang, S.Fan, L.Zhang, F.Han, Y.Song, L.Chu, C.Zhang. SMPDL3A Is A Cgamp-Degrading Enzyme Induced By Lxr-Mediated Lipid Metabolism to Restrict Cgas-Sting Dna Sensing. Immunity V. 56 2492 2023.
ISSN: ISSN 1074-7613
PubMed: 37890481
DOI: 10.1016/J.IMMUNI.2023.10.001