Zinc in PDB 5v3o: Cereblon in Complex with DDB1 and Cc-220

The structure of Cereblon in Complex with DDB1 and Cc-220, PDB code: 5v3o was solved by M.Matyskiela, B.Pagarigan, P.Chamberlain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.029, 126.886, 172.487, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.7

The binding sites of Zinc atom in the Cereblon in Complex with DDB1 and Cc-220 (pdb code 5v3o). 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 Cereblon in Complex with DDB1 and Cc-220, PDB code: 5v3o:

Zinc binding site 1 out of 1 in the Cereblon in Complex with DDB1 and Cc-220


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cereblon in Complex with DDB1 and Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:0.0 occ:1.00 SG C:CYS391 1.8 77.0 1.0 SG C:CYS323 2.2 78.8 1.0 SG C:CYS326 2.3 0.3 1.0 SG C:CYS394 2.4 67.3 1.0 CB C:CYS391 3.0 75.1 1.0 CB C:CYS326 3.1 1.0 1.0 CB C:CYS323 3.1 78.1 1.0 CB C:CYS394 3.5 71.7 1.0 N C:CYS326 3.8 0.6 1.0 N C:CYS394 3.9 69.3 1.0 CA C:CYS326 4.0 0.9 1.0 OG1 C:THR329 4.2 0.8 1.0 CA C:CYS394 4.3 70.9 1.0 CB C:ILE393 4.4 74.8 1.0 CA C:CYS391 4.4 74.0 1.0 CA C:CYS323 4.6 78.2 1.0 CB C:THR329 4.6 99.7 1.0 C C:ILE393 4.9 71.3 1.0 C C:GLN325 4.9 98.2 1.0 C C:CYS391 4.9 76.1 1.0 CB C:SER396 4.9 72.9 1.0 N C:ILE393 5.0 71.8 1.0 O C:CYS323 5.0 84.0 1.0 CA C:ILE393 5.0 73.1 1.0 C C:CYS323 5.0 80.7 1.0 OG C:SER396 5.0 77.0 1.0

M.E.Matyskiela, W.Zhang, H.W.Man, G.Muller, G.Khambatta, F.Baculi, M.Hickman, L.Lebrun, B.Pagarigan, G.Carmel, C.C.Lu, G.Lu, M.Riley, Y.Satoh, P.Schafer, T.O.Daniel, J.Carmichael, B.E.Cathers, P.P.Chamberlain. A Cereblon Modulator (Cc-220) with Improved Degradation of Ikaros and Aiolos. J. Med. Chem. V. 61 535 2018.
ISSN: ISSN 1520-4804
PubMed: 28425720
DOI: 10.1021/ACS.JMEDCHEM.6B01921