Zinc in PDB 8d80: Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3

The binding sites of Zinc atom in the Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3 (pdb code 8d80). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3, PDB code: 8d80:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3


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 Iberdomide and Ikaros ZF1-2-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:351.9 occ:1.00 SG B:CYS394 2.3 195.4 1.0 SG B:CYS326 2.3 195.8 1.0 SG B:CYS391 2.3 187.3 1.0 SG B:CYS323 2.3 192.5 1.0 CB B:CYS394 3.4 195.4 1.0 N B:CYS394 3.5 195.4 1.0 CB B:CYS326 3.6 195.8 1.0 CB B:CYS391 3.6 187.3 1.0 CB B:CYS323 3.7 192.5 1.0 O B:CYS323 3.9 192.5 1.0 CA B:CYS394 3.9 195.4 1.0 N B:CYS326 4.3 195.8 1.0 N B:ALA395 4.5 184.6 1.0 C B:CYS394 4.5 195.4 1.0 CA B:CYS326 4.6 195.8 1.0 C B:ILE393 4.7 183.7 1.0 CB B:ILE393 4.7 183.7 1.0 N B:ILE393 4.7 183.7 1.0 C B:CYS323 4.8 192.5 1.0 CB B:GLN325 4.8 173.1 1.0 CA B:CYS323 4.8 192.5 1.0 CA B:ILE393 4.9 183.7 1.0 CA B:CYS391 5.0 187.3 1.0 N B:SER396 5.0 183.6 1.0

Zinc binding site 2 out of 2 in the Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cereblon~DDB1 Bound to Iberdomide and Ikaros ZF1-2-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:299.9 occ:1.00 NE2 C:HIS167 2.0 259.2 1.0 NE2 C:HIS163 2.1 293.2 1.0 CB C:CYS150 2.3 242.0 1.0 SG C:CYS147 2.3 246.8 1.0 CD2 C:HIS167 2.6 259.2 1.0 CD2 C:HIS163 2.7 293.2 1.0 CE1 C:HIS163 2.8 293.2 1.0 N C:CYS150 2.8 242.0 1.0 SG C:CYS150 3.0 242.0 1.0 CA C:CYS150 3.1 242.0 1.0 CE1 C:HIS167 3.3 259.2 1.0 CG C:HIS163 3.6 293.2 1.0 ND1 C:HIS163 3.6 293.2 1.0 CB C:CYS147 3.7 246.8 1.0 CG C:HIS167 3.9 259.2 1.0 C C:GLN149 3.9 215.0 1.0 C C:CYS150 4.1 242.0 1.0 N C:GLY151 4.1 219.3 1.0 ND1 C:HIS167 4.2 259.2 1.0 CB C:GLN149 4.2 215.0 1.0 CA C:GLN149 4.5 215.0 1.0 N C:GLN149 4.7 215.0 1.0 N C:ALA152 4.8 241.1 1.0 CB C:HIS163 4.9 293.2 1.0 O C:GLN149 4.9 215.0 1.0 O C:HIS163 4.9 293.2 1.0 CB C:ALA152 4.9 241.1 1.0 CA C:CYS147 5.0 246.8 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