Zinc in PDB 8jul: Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid

The binding sites of Zinc atom in the Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid (pdb code 8jul). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid, PDB code: 8jul:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:38.5 occ:1.00 NE2 A:HIS795 2.0 24.0 1.0 O A:HOH1001 2.0 27.5 1.0 NE2 A:HIS563 2.0 21.5 1.0 NE2 A:HIS791 2.1 24.7 1.0 CE1 A:HIS795 2.4 24.0 1.0 CD2 A:HIS791 2.8 24.7 1.0 CE1 A:HIS563 2.9 21.5 1.0 CD2 A:HIS563 3.1 21.5 1.0 CE1 A:HIS791 3.2 24.7 1.0 CD2 A:HIS795 3.3 24.0 1.0 ND1 A:HIS795 3.7 24.0 1.0 CG A:HIS791 4.0 24.7 1.0 ND1 A:HIS563 4.1 21.5 1.0 CG A:HIS795 4.1 24.0 1.0 CG A:HIS563 4.2 21.5 1.0 ND1 A:HIS791 4.2 24.7 1.0 OG A:SER559 4.2 21.2 1.0 O2 A:PX2902 4.3 43.0 1.0 O3 A:PX2902 4.4 43.0 1.0 P1 A:PX2902 4.9 43.0 1.0 CD1 A:TRP794 5.0 26.2 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of SIDT1 in Complex with Phosphatidic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:38.6 occ:1.00 NE2 B:HIS795 2.0 24.4 1.0 O B:HOH1001 2.0 27.4 1.0 NE2 B:HIS563 2.0 21.5 1.0 NE2 B:HIS791 2.1 24.9 1.0 CE1 B:HIS795 2.4 24.4 1.0 CD2 B:HIS791 2.8 24.9 1.0 CE1 B:HIS563 2.9 21.5 1.0 CD2 B:HIS563 3.1 21.5 1.0 CE1 B:HIS791 3.2 24.9 1.0 CD2 B:HIS795 3.3 24.4 1.0 ND1 B:HIS795 3.7 24.4 1.0 CG B:HIS791 4.0 24.9 1.0 ND1 B:HIS563 4.1 21.5 1.0 CG B:HIS795 4.1 24.4 1.0 CG B:HIS563 4.2 21.5 1.0 ND1 B:HIS791 4.2 24.9 1.0 O2 B:PX2902 4.2 42.9 1.0 OG B:SER559 4.2 21.2 1.0 O3 B:PX2902 4.4 42.9 1.0 P1 B:PX2902 4.8 42.9 1.0 CD1 B:TRP794 5.0 26.3 1.0

C.R.Sun, D.Xu, F.Yang, Z.Hou, Y.Luo, C.Y.Zhang, G.Shan, G.Huang, X.Yao, Y.Chen, Q.Li, C.Z.Zhou. Human SIDT1 Mediates Dsrna Uptake Via Its Phospholipase Activity. Cell Res. 2023.
ISSN: ISSN 1001-0602
PubMed: 37932444
DOI: 10.1038/S41422-023-00889-X