Zinc in PDB 5fqd: Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase

All present enzymatic activity of Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase:
6.3.2.19;

The structure of Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase, PDB code: 5fqd was solved by G.Petzold, E.S.Fischer, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.30 / 2.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	87.970, 109.930, 112.400, 106.02, 93.19, 101.63
R / Rfree (%)	18.1 / 21

The binding sites of Zinc atom in the Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase (pdb code 5fqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase, PDB code: 5fqd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1437 b:94.2 occ:1.00 SG B:CYS394 2.4 78.6 1.0 SG B:CYS323 2.4 75.0 1.0 SG B:CYS391 2.5 75.8 1.0 SG B:CYS326 2.5 85.5 1.0 CB B:CYS391 3.2 70.0 1.0 CB B:CYS326 3.2 80.5 1.0 CB B:CYS323 3.3 71.2 1.0 CB B:CYS394 3.6 76.8 1.0 N B:CYS326 3.9 79.0 1.0 N B:CYS394 3.9 79.0 1.0 CA B:CYS326 4.1 80.0 1.0 CA B:CYS394 4.4 77.9 1.0 CB B:THR329 4.5 82.5 1.0 OG1 B:THR329 4.6 88.8 1.0 CB B:GLN325 4.6 75.9 1.0 CB B:ILE393 4.7 82.3 1.0 CA B:CYS391 4.7 70.6 1.0 CA B:CYS323 4.7 70.7 1.0 C B:GLN325 4.7 82.3 1.0 CG2 B:THR329 4.9 78.5 1.0 C B:ILE393 4.9 84.0 1.0 OG B:SER396 4.9 87.9 1.0 CB B:SER396 5.0 74.7 1.0

Zinc binding site 2 out of 2 in the Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Lenalidomide Induced CK1A Degradation By the CRL4CRBN Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1437 b:0.2 occ:1.00 SG E:CYS394 2.3 90.5 1.0 SG E:CYS326 2.4 0.3 1.0 SG E:CYS391 2.5 81.6 1.0 SG E:CYS323 2.5 91.2 1.0 CB E:CYS391 3.1 77.7 1.0 CB E:CYS326 3.4 99.7 1.0 CB E:CYS323 3.4 86.5 1.0 CB E:CYS394 3.5 87.3 1.0 N E:CYS394 3.7 86.9 1.0 N E:CYS326 3.9 97.9 1.0 CA E:CYS394 4.2 86.8 1.0 CA E:CYS326 4.2 99.6 1.0 CB E:ILE393 4.6 89.4 1.0 CA E:CYS391 4.6 77.8 1.0 CB E:GLN325 4.6 94.1 1.0 CB E:THR329 4.7 84.4 1.0 OG1 E:THR329 4.7 88.1 1.0 C E:ILE393 4.8 92.7 1.0 C E:GLN325 4.8 99.7 1.0 OG E:SER396 4.9 97.5 1.0 CA E:CYS323 4.9 86.3 1.0 C E:CYS394 4.9 89.8 1.0 CB E:SER396 4.9 86.7 1.0 N E:ILE393 4.9 85.3 1.0 CA E:ILE393 4.9 86.1 1.0

G.Petzold, E.S.Fischer, N.H.Thoma. Structural Basis of Lenalidomide-Induced CK1ALPHA Degradation By the CRL4(Crbn) Ubiquitin Ligase. Nature V. 532 127 2016.
ISSN: ISSN 0028-0836
PubMed: 26909574
DOI: 10.1038/NATURE16979