Zinc in PDB 8d7z: Cereblon-DDB1 Bound to Cc-92480 and Ikaros ZF1-2-3

The structure of Cereblon-DDB1 Bound to Cc-92480 and Ikaros ZF1-2-3 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Cereblon-DDB1 Bound to Cc-92480 and Ikaros ZF1-2-3 (pdb code 8d7z). 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 Cc-92480 and Ikaros ZF1-2-3, PDB code: 8d7z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon-DDB1 Bound to Cc-92480 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 Cc-92480 and Ikaros ZF1-2-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:352.5 occ:1.00 SG B:CYS394 2.3 228.6 1.0 SG B:CYS391 2.3 218.8 1.0 SG B:CYS323 2.3 236.3 1.0 SG B:CYS326 2.3 238.8 1.0 CB B:CYS394 3.4 228.6 1.0 CB B:CYS326 3.4 238.8 1.0 CB B:CYS391 3.5 218.8 1.0 N B:CYS394 3.8 228.6 1.0 CB B:CYS323 4.1 236.3 1.0 CA B:CYS394 4.2 228.6 1.0 O B:LYS324 4.3 225.1 1.0 CA B:CYS326 4.6 238.8 1.0 N B:CYS326 4.6 238.8 1.0 CB B:ILE393 4.8 201.7 1.0 O B:CYS323 4.9 236.3 1.0 CA B:CYS391 4.9 218.8 1.0 CD1 B:ILE398 4.9 192.2 1.0 C B:ILE393 4.9 201.7 1.0 CG2 B:THR329 4.9 201.4 1.0 C B:CYS394 4.9 228.6 1.0

Zinc binding site 2 out of 2 in the Cereblon-DDB1 Bound to Cc-92480 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 Cc-92480 and Ikaros ZF1-2-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:251.0 occ:1.00 NE2 C:HIS163 2.0 239.3 1.0 NE2 C:HIS167 2.0 221.3 1.0 CB C:CYS150 2.2 205.4 1.0 SG C:CYS147 2.3 216.6 1.0 CD2 C:HIS167 2.5 221.3 1.0 CE1 C:HIS163 2.7 239.3 1.0 CD2 C:HIS163 2.8 239.3 1.0 N C:CYS150 2.9 205.4 1.0 CA C:CYS150 3.1 205.4 1.0 CE1 C:HIS167 3.3 221.3 1.0 CB C:CYS147 3.5 216.6 1.0 ND1 C:HIS163 3.6 239.3 1.0 CG C:HIS163 3.6 239.3 1.0 SG C:CYS150 3.7 205.4 1.0 CG C:HIS167 3.8 221.3 1.0 C C:GLN149 3.8 193.4 1.0 CB C:GLN149 3.9 193.4 1.0 ND1 C:HIS167 4.1 221.3 1.0 N C:GLN149 4.1 193.4 1.0 CA C:GLN149 4.1 193.4 1.0 N C:GLY151 4.2 189.2 1.0 C C:CYS150 4.2 205.4 1.0 O C:GLN149 4.7 193.4 1.0 N C:ALA152 4.8 205.8 1.0 N C:ASN148 4.8 194.7 1.0 CG C:GLN149 4.8 193.4 1.0 O C:HIS163 4.9 239.3 1.0 CA C:CYS147 4.9 216.6 1.0 CB C:HIS163 4.9 239.3 1.0 C C:ASN148 5.0 194.7 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