Zinc in PDB 7bqu: Cereblon in Complex with SALL4 and (S)-Thalidomide

The structure of Cereblon in Complex with SALL4 and (S)-Thalidomide, PDB code: 7bqu was solved by H.Furihata, Y.Miyauchi, A.Asano, M.Tanokura, T.Miyakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.67 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.962, 92.718, 43.986, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The binding sites of Zinc atom in the Cereblon in Complex with SALL4 and (S)-Thalidomide (pdb code 7bqu). 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 SALL4 and (S)-Thalidomide, PDB code: 7bqu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon in Complex with SALL4 and (S)-Thalidomide


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 SALL4 and (S)-Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:24.8 occ:1.00 SG A:CYS391 2.2 23.9 1.0 SG A:CYS394 2.2 29.3 1.0 SG A:CYS323 2.3 25.5 1.0 SG A:CYS326 2.4 28.8 1.0 CB A:CYS394 2.9 36.4 1.0 CB A:CYS391 3.1 22.5 1.0 CB A:CYS323 3.2 22.9 1.0 CB A:CYS326 3.2 28.4 1.0 N A:CYS326 3.7 28.7 1.0 N A:CYS394 3.7 26.3 1.0 CA A:CYS394 3.9 29.0 1.0 CA A:CYS326 4.1 24.0 1.0 CB A:ILE393 4.6 26.3 1.0 OG1 A:THR329 4.6 25.3 1.0 CA A:CYS391 4.6 24.1 1.0 CB A:THR329 4.6 29.5 1.0 CA A:CYS323 4.6 18.9 1.0 CB A:GLN325 4.7 33.8 1.0 C A:ILE393 4.7 31.9 1.0 C A:CYS394 4.8 25.6 1.0 C A:GLN325 4.8 27.8 1.0 OG A:SER396 4.8 34.3 1.0 CB A:SER396 4.9 31.0 1.0 CG2 A:THR329 4.9 28.1 1.0 N A:ILE393 5.0 27.5 1.0 CA A:ILE393 5.0 31.0 1.0 C A:CYS323 5.0 22.5 1.0

Zinc binding site 2 out of 2 in the Cereblon in Complex with SALL4 and (S)-Thalidomide


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 SALL4 and (S)-Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:22.8 occ:1.00 NE2 B:HIS432 1.9 21.3 1.0 NE2 B:HIS428 2.1 22.9 1.0 SG B:CYS415 2.2 28.4 1.0 SG B:CYS412 2.2 23.8 1.0 CD2 B:HIS432 2.9 28.2 1.0 CE1 B:HIS432 2.9 26.3 1.0 CB B:CYS415 3.0 30.6 1.0 CD2 B:HIS428 3.0 26.8 1.0 CE1 B:HIS428 3.1 30.5 1.0 CB B:CYS412 3.1 15.8 1.0 N B:CYS415 3.7 23.0 1.0 CA B:CYS415 3.9 22.0 1.0 ND1 B:HIS432 4.0 27.2 1.0 CG B:HIS432 4.0 30.2 1.0 CG B:HIS428 4.1 24.2 1.0 ND1 B:HIS428 4.1 27.8 1.0 CB B:VAL414 4.3 17.1 1.0 CB B:HIS417 4.5 26.6 1.0 C B:VAL414 4.6 22.5 1.0 CA B:CYS412 4.6 22.7 1.0 C B:CYS415 4.7 25.7 1.0 O B:HOH604 4.8 39.8 1.0 CA B:VAL414 4.8 23.1 1.0 N B:VAL414 4.8 19.2 1.0 N B:GLY416 4.9 18.8 1.0 CG1 B:VAL414 4.9 20.1 1.0 N B:HIS417 4.9 21.3 1.0 C B:CYS412 5.0 22.7 1.0

H.Furihata, S.Yamanaka, T.Honda, Y.Miyauchi, A.Asano, N.Shibata, M.Tanokura, T.Sawasaki, T.Miyakawa. Structural Bases of Imid Selectivity That Emerges By 5-Hydroxythalidomide. Nat Commun V. 11 4578 2020.
ISSN: ESSN 2041-1723
PubMed: 32929090
DOI: 10.1038/S41467-020-18488-4