Zinc in PDB 7eg1: Cryo-Em Structure of Dnmdp-Induced PDE3A-SLFN12 Complex

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

The structure of Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex (pdb code 7eg1). 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 Dnmdp-Induced PDE3A-SLFN12 Complex, PDB code: 7eg1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:49.5 occ:1.00 ND1 B:HIS275 2.1 28.9 1.0 SG B:CYS277 2.4 40.5 1.0 SG B:CYS311 2.4 33.9 1.0 SG B:CYS312 2.8 28.4 1.0 CG B:HIS275 3.1 28.9 1.0 CE1 B:HIS275 3.2 28.9 1.0 CB B:HIS275 3.3 28.9 1.0 CB B:CYS312 3.3 28.4 1.0 CA B:HIS275 3.7 28.9 1.0 CB B:CYS311 3.8 33.9 1.0 CB B:CYS277 4.0 40.5 1.0 N B:CYS312 4.1 28.4 1.0 C B:CYS311 4.2 33.9 1.0 CD2 B:HIS275 4.2 28.9 1.0 NE2 B:HIS275 4.3 28.9 1.0 CA B:CYS312 4.4 28.4 1.0 O B:GLU279 4.4 52.5 1.0 O B:CYS311 4.5 33.9 1.0 N B:PHE276 4.5 29.8 1.0 CA B:CYS311 4.5 33.9 1.0 N B:CYS277 4.6 40.5 1.0 C B:HIS275 4.6 28.9 1.0 CE2 B:PHE310 4.7 30.3 1.0 N B:HIS275 4.9 28.9 1.0 CA B:CYS277 4.9 40.5 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:50.9 occ:1.00 ND1 D:HIS275 2.2 28.5 1.0 SG D:CYS277 2.4 41.5 1.0 SG D:CYS311 2.4 33.1 1.0 SG D:CYS312 2.9 27.4 1.0 CG D:HIS275 3.1 28.5 1.0 CE1 D:HIS275 3.2 28.5 1.0 CB D:HIS275 3.3 28.5 1.0 CB D:CYS312 3.5 27.4 1.0 CB D:CYS311 3.8 33.1 1.0 CA D:HIS275 3.8 28.5 1.0 CB D:CYS277 3.9 41.5 1.0 O D:GLU279 4.2 49.6 1.0 CD2 D:HIS275 4.3 28.5 1.0 NE2 D:HIS275 4.3 28.5 1.0 C D:CYS311 4.3 33.1 1.0 N D:CYS312 4.3 27.4 1.0 N D:CYS277 4.5 41.5 1.0 N D:PHE276 4.5 29.8 1.0 CA D:CYS312 4.6 27.4 1.0 O D:CYS311 4.6 33.1 1.0 C D:HIS275 4.6 28.5 1.0 CA D:CYS311 4.6 33.1 1.0 CA D:CYS277 4.8 41.5 1.0 CE2 D:PHE310 4.9 29.6 1.0 N D:LYS281 5.0 41.8 1.0 N D:HIS275 5.0 28.5 1.0

J.Chen, N.Liu, D.R.Li, Y.X.Wang, Y.X.Sun, Q.C.Wu, Y.P.Huang, H.W.Wang, N.Huang, X.B.Qi, X.D.Wang. Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex To Be Published.