Zinc in PDB 5hxb: Cereblon in Complex with DDB1, Cc-885, and GSPT1

The structure of Cereblon in Complex with DDB1, Cc-885, and GSPT1, PDB code: 5hxb was solved by P.P.Chamberlain, M.Matyskiela, B.Pagarigan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.60
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.747, 111.522, 175.057, 90.00, 95.81, 90.00
R / Rfree (%)	22.4 / 27.3

The structure of Cereblon in Complex with DDB1, Cc-885, and GSPT1 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Cereblon in Complex with DDB1, Cc-885, and GSPT1 (pdb code 5hxb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cereblon in Complex with DDB1, Cc-885, and GSPT1, PDB code: 5hxb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon in Complex with DDB1, Cc-885, and GSPT1


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, Cc-885, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ Z:Zn501 b:0.8 occ:1.00 SG Z:CYS394 1.9 86.2 1.0 SG Z:CYS323 2.0 95.2 1.0 SG Z:CYS391 2.2 0.7 1.0 SG Z:CYS326 2.4 0.1 1.0 CB Z:CYS394 3.0 92.8 1.0 CB Z:CYS391 3.2 0.2 1.0 CB Z:CYS323 3.4 0.7 1.0 CB Z:CYS326 3.4 0.6 1.0 N Z:CYS394 3.7 0.8 1.0 N Z:CYS326 3.9 0.5 1.0 CA Z:CYS394 3.9 99.0 1.0 CA Z:CYS326 4.3 0.3 1.0 OG Z:SER396 4.3 0.8 1.0 CB Z:ILE393 4.3 0.2 1.0 CG1 Z:ILE393 4.4 0.5 1.0 CG Z:GLN325 4.5 0.9 1.0 OG1 Z:THR329 4.7 95.0 1.0 CA Z:CYS391 4.7 0.8 1.0 CA Z:CYS323 4.7 0.6 1.0 CB Z:GLN325 4.8 0.8 1.0 C Z:CYS394 4.8 0.6 1.0 C Z:ILE393 4.8 0.4 1.0 CB Z:THR329 4.9 0.0 1.0 CA Z:ILE393 5.0 0.9 1.0

Zinc binding site 2 out of 2 in the Cereblon in Complex with DDB1, Cc-885, and GSPT1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cereblon in Complex with DDB1, Cc-885, and GSPT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.8 occ:1.00 SG C:CYS394 1.7 92.9 1.0 SG C:CYS323 2.1 83.8 1.0 SG C:CYS391 2.5 0.2 1.0 SG C:CYS326 2.6 0.6 1.0 CB C:CYS394 2.7 0.1 1.0 CB C:CYS391 3.3 0.6 1.0 CB C:CYS326 3.4 0.1 1.0 N C:CYS394 3.7 0.8 1.0 CB C:CYS323 3.7 92.8 1.0 CA C:CYS394 3.7 0.6 1.0 N C:CYS326 3.8 0.3 1.0 OG C:SER396 3.9 96.3 1.0 CG C:GLN325 4.0 0.0 1.0 CA C:CYS326 4.2 0.6 1.0 CB C:GLN325 4.4 0.1 1.0 C C:CYS394 4.5 0.7 1.0 CB C:ILE393 4.6 0.2 1.0 CG1 C:ILE393 4.8 0.3 1.0 CB C:SER396 4.8 98.7 1.0 N C:ALA395 4.8 1.0 1.0 CA C:CYS391 4.8 0.3 1.0 C C:GLN325 4.8 0.4 1.0 C C:ILE393 4.8 0.8 1.0 CA C:CYS323 4.9 99.0 1.0 N C:SER396 5.0 0.7 1.0

M.E.Matyskiela, G.Lu, T.Ito, B.Pagarigan, C.C.Lu, K.Miller, W.Fang, N.Y.Wang, D.Nguyen, J.Houston, G.Carmel, T.Tran, M.Riley, L.Nosaka, G.C.Lander, S.Gaidarova, S.Xu, A.L.Ruchelman, H.Handa, J.Carmichael, T.O.Daniel, B.E.Cathers, A.Lopez-Girona, P.P.Chamberlain. A Novel Cereblon Modulator Recruits GSPT1 to the CRL4(Crbn) Ubiquitin Ligase. Nature V. 535 252 2016.
ISSN: ESSN 1476-4687
PubMed: 27338790
DOI: 10.1038/NATURE18611