Zinc in PDB 4ci3: Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide

The structure of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide, PDB code: 4ci3 was solved by E.S.Fischer, K.Boehm, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 3.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.070, 171.070, 137.930, 90.00, 90.00, 120.00
R / Rfree (%)	21.09 / 23.47

The binding sites of Zinc atom in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide (pdb code 4ci3). 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 Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide, PDB code: 4ci3:

Zinc binding site 1 out of 1 in the Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the DDB1-Crbn E3 Ubiquitin Ligase Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1428 b:95.0 occ:1.00 SG B:CYS328 2.1 89.1 1.0 SG B:CYS396 2.1 0.9 1.0 SG B:CYS325 2.3 92.5 1.0 SG B:CYS393 2.4 88.8 1.0 CB B:CYS393 3.2 83.2 1.0 CB B:CYS396 3.2 99.4 1.0 CB B:CYS325 3.3 88.6 1.0 CB B:CYS328 3.6 87.3 1.0 N B:CYS396 3.6 99.2 1.0 N B:CYS328 3.7 85.5 1.0 CA B:CYS396 4.0 98.7 1.0 CA B:CYS328 4.2 87.0 1.0 CB B:GLN327 4.4 84.6 1.0 CB B:ASN398 4.5 89.9 1.0 OG1 B:THR331 4.5 0.5 1.0 CB B:ILE395 4.6 95.7 1.0 CA B:CYS393 4.7 82.5 1.0 CA B:CYS325 4.7 87.0 1.0 CB B:THR331 4.7 94.2 1.0 C B:GLN327 4.7 88.7 1.0 C B:ILE395 4.8 0.2 1.0 N B:GLY397 4.8 90.3 1.0 C B:CYS396 4.8 96.8 1.0 CG B:GLN327 4.8 89.3 1.0 O B:CYS325 4.9 87.4 1.0 CA B:GLN327 5.0 84.4 1.0 N B:ASN398 5.0 86.3 1.0 C B:CYS325 5.0 88.6 1.0

E.S.Fischer, K.Bohm, J.R.Lydeard, H.Yang, M.B.Stadler, S.Cavadini, J.Nagel, F.Serluca, V.Acker, G.M.Lingaraju, R.B.Tichkule, M.Schebesta, W.C.Forrester, M.Schirle, U.Hassiepen, J.Ottl, M.Hild, R.E.J.Beckwith, J.W.Harper, J.L.Jenkins, N.H.Thoma. Structure of the DDB1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide. Nature V. 512 49 2014.
ISSN: ISSN 0028-0836
PubMed: 25043012
DOI: 10.1038/NATURE13527