Zinc in PDB 6bn9: Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac

The structure of Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac, PDB code: 6bn9 was solved by R.P.Nowak, S.L.Deangelo, D.Buckley, J.E.Bradner, E.S.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.40 / 4.38
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	117.604, 117.604, 597.157, 90.00, 90.00, 120.00
R / Rfree (%)	27.5 / 30.1

The binding sites of Zinc atom in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac (pdb code 6bn9). 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 Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac, PDB code: 6bn9:

Zinc binding site 1 out of 1 in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET70 Protac within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.1 occ:1.00 SG B:CYS326 2.3 0.9 1.0 SG B:CYS391 2.3 0.9 1.0 SG B:CYS394 2.6 0.3 1.0 SG B:CYS323 2.6 0.3 1.0 CB B:CYS323 2.9 0.6 1.0 CB B:CYS326 2.9 0.0 1.0 CB B:CYS391 3.2 0.5 1.0 N B:CYS326 3.7 0.8 1.0 CB B:CYS394 3.8 0.5 1.0 CA B:CYS326 3.9 0.4 1.0 N B:CYS394 4.0 0.6 1.0 CB B:THR329 4.3 0.8 1.0 CA B:CYS323 4.3 0.6 1.0 OG1 B:THR329 4.4 0.6 1.0 CA B:CYS394 4.5 0.3 1.0 CG2 B:THR329 4.6 0.9 1.0 CA B:CYS391 4.6 0.9 1.0 C B:GLN325 4.7 1.0 1.0 CB B:ILE393 4.7 0.7 1.0 CB B:GLN325 4.9 0.8 1.0 C B:CYS323 4.9 0.6 1.0

R.P.Nowak, S.L.Deangelo, D.Buckley, Z.He, K.A.Donovan, J.An, N.Safaee, M.P.Jedrychowski, C.M.Ponthier, M.Ishoey, T.Zhang, J.D.Mancias, N.S.Gray, J.E.Bradner, E.S.Fischer. Plasticity in Binding Confers Selectivity in Ligand-Induced Protein Degradation. Nat. Chem. Biol. V. 14 706 2018.
ISSN: ESSN 1552-4469
PubMed: 29892083
DOI: 10.1038/S41589-018-0055-Y