Zinc in PDB 8tzx: Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1

The structure of Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1, PDB code: 8tzx was solved by M.C.Clifton, X.Ma, E.Ornelas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.31 / 3.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.669, 137.742, 136.628, 90, 96.92, 90
R / Rfree (%)	21.3 / 25.2

The binding sites of Zinc atom in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 (pdb code 8tzx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1, PDB code: 8tzx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:84.0 occ:1.00 SG A:CYS394 2.3 91.3 1.0 SG A:CYS391 2.4 102.5 1.0 SG A:CYS326 2.4 101.3 1.0 SG A:CYS323 2.7 120.0 1.0 CB A:CYS391 3.1 103.1 1.0 CB A:CYS326 3.1 101.2 1.0 CB A:CYS323 3.3 104.7 1.0 CB A:CYS394 3.4 108.9 1.0 N A:CYS394 3.8 91.2 1.0 N A:CYS326 3.8 93.6 1.0 CA A:CYS326 4.0 95.2 1.0 CA A:CYS394 4.2 91.7 1.0 OG1 A:THR329 4.5 103.2 1.0 CA A:CYS391 4.6 92.3 1.0 CB A:ILE393 4.7 90.8 1.0 CB A:THR329 4.7 109.9 1.0 CA A:CYS323 4.8 100.4 1.0 C A:CYS394 4.8 92.3 1.0 CB A:GLN325 4.8 109.3 1.0 C A:ILE393 4.8 92.7 1.0 C A:CYS326 4.9 107.7 1.0 C A:GLN325 4.9 101.4 1.0 CB A:SER396 4.9 87.3 1.0 N A:ALA395 4.9 92.4 1.0 CG2 A:THR329 5.0 85.0 1.0 N A:ILE393 5.0 91.9 1.0

Zinc binding site 2 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:97.9 occ:1.00 NE2 C:HIS892 2.0 91.8 1.0 NE2 C:HIS888 2.1 104.4 1.0 SG C:CYS875 2.3 90.0 1.0 SG C:CYS872 2.3 104.6 1.0 CD2 C:HIS888 2.8 100.7 1.0 CE1 C:HIS892 2.9 90.4 1.0 CB C:CYS872 3.0 105.8 1.0 CD2 C:HIS892 3.1 93.7 1.0 CE1 C:HIS888 3.2 104.4 1.0 CB C:CYS875 3.3 109.7 1.0 N C:CYS875 3.5 93.8 1.0 CA C:CYS875 3.9 96.9 1.0 CG C:HIS888 4.0 101.2 1.0 ND1 C:HIS892 4.0 96.4 1.0 CG C:HIS892 4.2 99.2 1.0 ND1 C:HIS888 4.2 109.1 1.0 CB C:VAL874 4.3 94.5 1.0 C C:VAL874 4.4 110.1 1.0 CA C:CYS872 4.5 102.4 1.0 N C:GLY876 4.5 119.7 1.0 C C:CYS875 4.6 115.8 1.0 N C:VAL874 4.6 93.5 1.0 CA C:VAL874 4.7 102.2 1.0 CB C:ALA877 4.7 117.5 1.0 N C:ALA877 4.8 118.0 1.0 C C:CYS872 4.8 115.6 1.0 CG2 C:VAL874 4.9 92.2 1.0

Zinc binding site 3 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:118.8 occ:1.00 SG D:CYS394 2.3 113.3 1.0 SG D:CYS326 2.3 85.9 1.0 SG D:CYS391 2.4 77.5 1.0 SG D:CYS323 2.4 118.0 1.0 CB D:CYS326 3.0 104.4 1.0 CB D:CYS323 3.1 99.7 1.0 CB D:CYS391 3.2 92.1 1.0 N D:CYS326 3.4 103.6 1.0 CB D:CYS394 3.5 107.3 1.0 CA D:CYS326 3.8 103.5 1.0 N D:CYS394 4.0 85.7 1.0 CA D:CYS394 4.3 81.3 1.0 CB D:GLN325 4.5 113.6 1.0 C D:GLN325 4.6 103.6 1.0 C D:CYS326 4.6 107.3 1.0 CA D:CYS323 4.6 96.1 1.0 OG1 D:THR329 4.6 113.8 1.0 CA D:CYS391 4.7 84.2 1.0 CB D:SER396 4.7 87.1 1.0 CB D:THR329 4.8 104.2 1.0 OG D:SER396 4.8 108.9 1.0 C D:CYS394 4.9 84.7 1.0 N D:GLN325 4.9 108.0 1.0 CA D:GLN325 4.9 106.8 1.0 C D:CYS323 4.9 92.9 1.0 CB D:ILE393 5.0 84.6 1.0

Zinc binding site 4 out of 4 in the Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn901 b:89.7 occ:1.00 NE2 F:HIS892 2.1 91.2 1.0 NE2 F:HIS888 2.2 114.5 1.0 SG F:CYS875 2.4 94.6 1.0 SG F:CYS872 2.4 109.9 1.0 CB F:CYS875 3.0 108.2 1.0 CD2 F:HIS892 3.0 86.5 1.0 CD2 F:HIS888 3.0 92.8 1.0 CE1 F:HIS892 3.1 99.6 1.0 CB F:CYS872 3.1 112.9 1.0 CE1 F:HIS888 3.3 120.6 1.0 N F:CYS875 3.3 99.6 1.0 CA F:CYS875 3.7 92.9 1.0 ND1 F:HIS892 4.2 108.6 1.0 CG F:HIS892 4.2 94.6 1.0 CB F:VAL874 4.2 100.9 1.0 CG F:HIS888 4.2 96.4 1.0 C F:VAL874 4.3 104.9 1.0 ND1 F:HIS888 4.3 118.3 1.0 N F:GLY876 4.4 111.4 1.0 C F:CYS875 4.5 103.7 1.0 CA F:CYS872 4.5 108.4 1.0 CA F:VAL874 4.6 102.4 1.0 N F:VAL874 4.6 98.9 1.0 N F:ALA877 4.9 120.2 1.0 C F:CYS872 4.9 115.0 1.0 CB F:ALA877 4.9 134.6 1.0 CG1 F:VAL874 5.0 108.4 1.0

P.Ting, A.Reyes, B.D.Fodor, F.Wu, M.S.Belew, X.Mao, J.Wang, S.Chitnis, W.Niu, A.Hachey, J.S.Cobb, N.A.Savage, A.Burke, J.Paulk, D.Dovala, J.Lin, M.C.Clifton, E.Ornelas, X.Ma, N.F.Ware, C.C.Sanchez, J.Trarszka, R.Terranova, J.Knehr, M.Altorfer, S.W.Barnes, R.E.J.Beckwith, J.M.Solomon, N.A.Dales, A.W.Patterson, J.Wagner, T.Bouwmeester, G.Dranoff, S.C.Stevenson, J.E.Bradner. Ternary Complex Structure of Cereblon-DDB1 Bound to Wiz(ZF7) and the Molecular Glue Dwiz-1 Science 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADK6129