Zinc in PDB 8d7w: Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation

The structure of Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation (pdb code 8d7w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation, PDB code: 8d7w:

Zinc binding site 1 out of 1 in the Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cereblon~DDB1 Bound to Cc-92480 with DDB1 in the Hinged Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:302.7 occ:1.00 SG B:CYS394 2.3 236.1 1.0 SG B:CYS326 2.3 203.7 1.0 SG B:CYS391 2.3 219.4 1.0 SG B:CYS323 2.3 190.4 1.0 CB B:CYS391 3.1 219.4 1.0 CB B:CYS326 3.4 203.7 1.0 CB B:CYS323 3.5 190.4 1.0 CB B:CYS394 3.5 236.1 1.0 OG B:SER396 3.8 221.6 1.0 N B:CYS394 4.0 236.1 1.0 N B:CYS326 4.2 203.7 1.0 CA B:CYS394 4.3 236.1 1.0 OG1 B:THR329 4.3 202.9 1.0 CA B:CYS326 4.4 203.7 1.0 CB B:GLN325 4.5 180.7 1.0 C B:GLN325 4.6 180.7 1.0 CA B:CYS391 4.6 219.4 1.0 CB B:SER396 4.7 221.6 1.0 CD1 B:ILE398 4.8 181.6 1.0 CA B:CYS323 4.9 190.4 1.0 CB B:ILE393 4.9 216.0 1.0 C B:CYS394 4.9 236.1 1.0 N B:ALA395 5.0 225.1 1.0

E.R.Watson, S.J.Novick, M.E.Matyskiela, P.P.Chamberlain, A.H.De La Pena, J.Y.Zhu, E.Tran, P.R.Griffin, I.E.Wertz, G.C.Lander. Molecular Glue Celmod Compounds Are Allosteric Regulators of Cereblon Conformation Biorxiv 2022.
DOI: 10.1101/2022.07.02.498551