Zinc in PDB 8oiz: Crystal Structure of Human Crbn-DDB1 in Complex with Pomalidomide

The structure of Crystal Structure of Human Crbn-DDB1 in Complex with Pomalidomide, PDB code: 8oiz was solved by Y.-V.Le Bihan, M.P.Cabry, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.59 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.841, 128.508, 198.377, 90, 90, 90
R / Rfree (%)	21.3 / 26.2

The binding sites of Zinc atom in the Crystal Structure of Human Crbn-DDB1 in Complex with Pomalidomide (pdb code 8oiz). 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 Human Crbn-DDB1 in Complex with Pomalidomide, PDB code: 8oiz:

Zinc binding site 1 out of 1 in the Crystal Structure of Human Crbn-DDB1 in Complex with Pomalidomide


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 Human Crbn-DDB1 in Complex with Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:62.0 occ:0.97 SG B:CYS394 2.2 56.9 1.0 SG B:CYS326 2.3 70.9 1.0 SG B:CYS391 2.3 60.4 1.0 SG B:CYS323 2.4 64.6 1.0 CB B:CYS326 3.0 70.2 1.0 CB B:CYS391 3.1 54.6 1.0 CB B:CYS323 3.2 66.0 1.0 CB B:CYS394 3.4 55.4 1.0 N B:CYS326 3.7 70.0 1.0 N B:CYS394 3.7 55.1 1.0 CA B:CYS326 3.9 70.4 1.0 CA B:CYS394 4.1 55.5 1.0 CA B:CYS391 4.5 53.5 1.0 CB B:GLN325 4.5 71.8 1.0 CB B:ILE393 4.6 53.2 1.0 CA B:CYS323 4.6 66.6 1.0 C B:GLN325 4.7 70.0 1.0 CB B:THR329 4.7 78.1 1.0 C B:ILE393 4.8 54.6 1.0 C B:CYS394 4.8 56.0 1.0 OG1 B:THR329 4.9 79.8 1.0 OG B:SER396 4.9 64.7 1.0 CG2 B:THR329 4.9 77.9 1.0

H.Bouguenina, A.Scarpino, J.O'hanlon, J.Warne, H.Z.Wang, L.Chan Wah Hak, A.Sadok, P.C.Mcandrew, M.Stubbs, O.A.Pierrat, T.Hahner, M.P.Cabry, Y.V.Le Bihan, C.Mitsopoulos, F.J.Sialana, T.I.Roumeliotis, R.Burke, R.L.M.Van Montfort, J.Choudhary, R.Chopra, J.J.Caldwell, I.Collins. A Degron Blocking Strategy Towards Improved CRL4CRBN Recruiting Protac Selectivity. Chembiochem 00351 2023.
ISSN: ESSN 1439-7633
PubMed: 37418539
DOI: 10.1002/CBIC.202300351