Zinc in PDB 8rqc: Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2

The structure of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2, PDB code: 8rqc was solved by H.Furihata, A.Kroupova, D.Zollman, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.44 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.585, 142.842, 56.693, 90, 112.34, 90
R / Rfree (%)	26.1 / 28.6

The structure of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 (pdb code 8rqc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2, PDB code: 8rqc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


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 Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:52.9 occ:1.00 SG A:CYS394 2.3 52.2 1.0 SG A:CYS323 2.3 50.7 1.0 SG A:CYS326 2.3 51.2 1.0 SG A:CYS391 2.3 55.1 1.0 CB A:CYS323 3.0 52.4 1.0 CB A:CYS391 3.1 48.4 1.0 CB A:CYS394 3.4 55.2 1.0 CB A:CYS326 3.4 59.2 1.0 OG1 A:THR329 3.6 58.3 1.0 N A:CYS326 3.8 63.7 1.0 N A:CYS394 3.9 57.2 1.0 OG A:SER396 3.9 64.7 1.0 CA A:CYS326 4.2 57.7 1.0 CA A:CYS394 4.2 57.2 1.0 CA A:CYS323 4.4 56.3 1.0 CA A:CYS391 4.6 52.0 1.0 C A:CYS323 4.7 59.3 1.0 N A:GLN327 4.7 59.6 1.0 O A:CYS323 4.7 60.4 1.0 C A:GLN325 4.8 68.0 1.0 CB A:ILE393 4.8 54.6 1.0 C A:CYS326 4.8 58.2 1.0 C A:CYS394 4.9 58.5 1.0 C A:ILE393 4.9 56.6 1.0 CB A:THR329 4.9 58.2 1.0 N A:GLN325 4.9 65.3 1.0 N A:ALA395 5.0 59.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:46.0 occ:1.00 NE2 B:HIS167 1.8 57.3 1.0 NE2 B:HIS163 2.0 55.2 1.0 SG B:CYS150 2.3 47.2 1.0 SG B:CYS147 2.3 40.3 1.0 CD2 B:HIS167 2.8 53.6 1.0 CE1 B:HIS167 2.8 53.1 1.0 CE1 B:HIS163 2.9 49.4 1.0 CD2 B:HIS163 3.1 51.7 1.0 CB B:CYS147 3.2 52.5 1.0 CB B:CYS150 3.4 51.0 1.0 N B:CYS150 3.6 50.6 1.0 ND1 B:HIS167 3.9 50.9 1.0 CG B:HIS167 3.9 52.7 1.0 ND1 B:HIS163 4.0 51.0 1.0 CA B:CYS150 4.1 44.9 1.0 CG B:HIS163 4.2 54.0 1.0 CB B:GLN149 4.2 49.2 1.0 C B:GLN149 4.5 50.3 1.0 CB B:ALA152 4.5 50.0 1.0 CA B:CYS147 4.7 51.1 1.0 CA B:GLN149 4.7 48.7 1.0 N B:GLN149 4.8 44.8 1.0 C B:CYS150 4.8 44.6 1.0 N B:GLY151 4.8 46.2 1.0 N B:ALA152 4.9 47.5 1.0 CG B:GLN149 5.0 52.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:69.5 occ:1.00 SG D:CYS394 2.4 58.6 1.0 SG D:CYS326 2.4 78.7 1.0 SG D:CYS391 2.4 61.2 1.0 SG D:CYS323 2.4 67.2 1.0 CB D:CYS323 3.0 62.0 1.0 CB D:CYS391 3.1 51.2 1.0 CB D:CYS394 3.5 60.8 1.0 CB D:CYS326 3.5 75.2 1.0 CG2 D:THR329 3.7 70.4 1.0 N D:CYS394 4.0 50.3 1.0 N D:CYS326 4.1 72.6 1.0 CA D:CYS394 4.3 52.9 1.0 CA D:CYS323 4.4 61.0 1.0 CA D:CYS326 4.4 85.3 1.0 CA D:CYS391 4.6 48.9 1.0 C D:CYS323 4.7 69.2 1.0 O D:CYS323 4.9 71.0 1.0 N D:GLN325 5.0 73.4 1.0 CB D:ILE393 5.0 61.2 1.0 C D:CYS394 5.0 51.2 1.0 C D:GLN325 5.0 74.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Crbn-Midi in Complex with Mezigdomide and IKZF1 ZF2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:45.0 occ:1.00 NE2 E:HIS167 1.8 55.3 1.0 NE2 E:HIS163 2.1 52.7 1.0 SG E:CYS147 2.3 41.5 1.0 SG E:CYS150 2.3 46.2 1.0 CD2 E:HIS167 2.8 53.0 1.0 CE1 E:HIS167 2.9 46.2 1.0 CD2 E:HIS163 3.0 48.6 1.0 CE1 E:HIS163 3.1 51.1 1.0 CB E:CYS147 3.1 47.9 1.0 CB E:CYS150 3.4 45.4 1.0 N E:CYS150 3.8 48.6 1.0 ND1 E:HIS167 3.9 44.3 1.0 CG E:HIS167 4.0 51.2 1.0 ND1 E:HIS163 4.1 53.6 1.0 CG E:HIS163 4.2 53.5 1.0 CA E:CYS150 4.2 46.4 1.0 CB E:GLN149 4.3 46.5 1.0 CA E:CYS147 4.6 46.6 1.0 C E:GLN149 4.8 50.3 1.0 CB E:ALA152 4.8 48.7 1.0 N E:GLN149 4.8 43.9 1.0 CA E:GLN149 4.9 47.5 1.0 N E:GLY151 4.9 41.0 1.0 C E:CYS150 4.9 43.8 1.0

A.Kroupova, V.Spiteri, H.Furihata, D.Darren, S.Ramachandran, Z.Rutter, S.Chakraborti, K.Haubrich, J.Pethe, D.Gonzales, A.Wijaya, M.Rodriguez-Rios, D.Lynch, W.Farnaby, M.Nakasone, D.Zollman, A.Ciulli. Design of A Cereblon Construct For Crystallographic and Biophysical Studies of Protein Degraders To Be Published.