Zinc in PDB 6bn8: Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET55 Protac.

The structure of Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET55 Protac., PDB code: 6bn8 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)	99.77 / 3.99
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	115.204, 115.204, 597.135, 90.00, 90.00, 120.00
R / Rfree (%)	28.9 / 33.3

The binding sites of Zinc atom in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET55 Protac. (pdb code 6bn8). 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 DBET55 Protac., PDB code: 6bn8:

Zinc binding site 1 out of 1 in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET55 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 DBET55 Protac. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.8 occ:1.00 SG B:CYS394 2.3 0.9 1.0 SG B:CYS326 2.5 1.0 1.0 SG B:CYS323 2.5 0.6 1.0 SG B:CYS391 2.5 0.0 1.0 CB B:CYS326 2.9 0.6 1.0 CB B:CYS323 3.0 0.7 1.0 CB B:CYS391 3.3 0.5 1.0 CB B:CYS394 3.6 0.1 1.0 N B:CYS326 3.7 0.8 1.0 CA B:CYS326 3.9 0.6 1.0 N B:CYS394 4.0 0.5 1.0 CA B:CYS394 4.4 0.3 1.0 CA B:CYS323 4.5 0.6 1.0 C B:GLN325 4.7 0.5 1.0 CB B:THR329 4.7 0.1 1.0 CA B:CYS391 4.7 0.4 1.0 OG1 B:THR329 4.8 0.0 1.0 CB B:GLN325 4.9 0.2 1.0 C B:CYS323 4.9 0.4 1.0 CB B:SER396 4.9 0.1 1.0 CB B:ILE393 5.0 0.1 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