Zinc in PDB 7eg4: Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex

All present enzymatic activity of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex:
3.1.4.17;

The structure of Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex (pdb code 7eg4). 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 Nauclefine-Induced PDE3A-SLFN12 Complex, PDB code: 7eg4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex


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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:86.3 occ:1.00 ND1 D:HIS275 2.1 47.4 1.0 SG D:CYS312 2.4 45.9 1.0 SG D:CYS277 2.4 63.6 1.0 SG D:CYS311 2.4 50.5 1.0 CG D:HIS275 2.9 47.4 1.0 CB D:HIS275 3.0 47.4 1.0 CB D:CYS312 3.2 45.9 1.0 CA D:HIS275 3.2 47.4 1.0 CE1 D:HIS275 3.3 47.4 1.0 CB D:CYS311 3.7 50.5 1.0 CB D:CYS277 3.8 63.6 1.0 N D:PHE276 3.9 46.8 1.0 N D:CYS312 3.9 45.9 1.0 N D:CYS277 4.0 63.6 1.0 C D:HIS275 4.0 47.4 1.0 C D:CYS311 4.0 50.5 1.0 CD2 D:HIS275 4.1 47.4 1.0 CA D:CYS312 4.2 45.9 1.0 NE2 D:HIS275 4.3 47.4 1.0 N D:HIS275 4.4 47.4 1.0 O D:CYS311 4.4 50.5 1.0 CA D:CYS311 4.5 50.5 1.0 CA D:CYS277 4.5 63.6 1.0 O D:HIS274 4.6 38.5 1.0 O D:GLU279 4.7 72.3 1.0 CE2 D:PHE310 4.7 47.2 1.0 C D:HIS274 4.9 38.5 1.0 C D:PHE276 5.0 46.8 1.0 CA D:PHE276 5.0 46.8 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex


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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:86.3 occ:1.00 ND1 B:HIS275 2.1 47.4 1.0 SG B:CYS312 2.4 45.9 1.0 SG B:CYS277 2.4 63.6 1.0 SG B:CYS311 2.4 50.5 1.0 CG B:HIS275 2.9 47.4 1.0 CB B:HIS275 3.0 47.4 1.0 CB B:CYS312 3.2 45.9 1.0 CA B:HIS275 3.2 47.4 1.0 CE1 B:HIS275 3.3 47.4 1.0 CB B:CYS311 3.7 50.5 1.0 CB B:CYS277 3.8 63.6 1.0 N B:PHE276 3.9 46.8 1.0 N B:CYS312 3.9 45.9 1.0 N B:CYS277 4.0 63.6 1.0 C B:HIS275 4.0 47.4 1.0 C B:CYS311 4.0 50.5 1.0 CD2 B:HIS275 4.1 47.4 1.0 CA B:CYS312 4.2 45.9 1.0 NE2 B:HIS275 4.3 47.4 1.0 N B:HIS275 4.4 47.4 1.0 O B:CYS311 4.4 50.5 1.0 CA B:CYS311 4.5 50.5 1.0 CA B:CYS277 4.5 63.6 1.0 O B:HIS274 4.6 38.5 1.0 O B:GLU279 4.7 72.3 1.0 CE2 B:PHE310 4.7 47.2 1.0 C B:HIS274 4.9 38.5 1.0 C B:PHE276 5.0 46.8 1.0 CA B:PHE276 5.0 46.8 1.0

J.Chen, N.Liu, L.Dianrong, W.Yuanxun, S.Yuxing, W.Qingcui, H.Yinpin, H.W.Wang, H.Niu, Q.Xiangbing, X.D.Wang. Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex Nat Commun 2021.
ISSN: ESSN 2041-1723