Zinc in PDB 7bqv: Cereblon in Complex with SALL4 and (S)-5-Hydroxythalidomide

The structure of Cereblon in Complex with SALL4 and (S)-5-Hydroxythalidomide, PDB code: 7bqv 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)	35.79 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	83.621, 93.895, 43.682, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.3

The binding sites of Zinc atom in the Cereblon in Complex with SALL4 and (S)-5-Hydroxythalidomide (pdb code 7bqv). 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)-5-Hydroxythalidomide, PDB code: 7bqv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon in Complex with SALL4 and (S)-5-Hydroxythalidomide


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)-5-Hydroxythalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:31.1 occ:1.00 SG A:CYS391 2.3 28.8 1.0 SG A:CYS323 2.3 29.1 1.0 SG A:CYS394 2.3 30.4 1.0 SG A:CYS326 2.3 36.9 1.0 CB A:CYS391 3.1 28.4 1.0 CB A:CYS326 3.2 37.8 1.0 CB A:CYS323 3.2 31.1 1.0 CB A:CYS394 3.4 33.3 1.0 N A:CYS326 3.7 34.9 1.0 N A:CYS394 3.8 32.4 1.0 CA A:CYS326 4.0 38.4 1.0 CA A:CYS394 4.2 33.4 1.0 OG1 A:THR329 4.5 34.4 1.0 CB A:GLN325 4.5 38.2 1.0 CB A:THR329 4.5 33.5 1.0 CA A:CYS391 4.6 29.7 1.0 CA A:CYS323 4.7 28.4 1.0 CB A:ILE393 4.7 31.9 1.0 C A:GLN325 4.7 36.4 1.0 C A:ILE393 4.7 33.1 1.0 C A:CYS394 4.9 29.9 1.0 CB A:SER396 5.0 31.9 1.0 CG2 A:THR329 5.0 33.0 1.0 N A:ILE393 5.0 29.6 1.0

Zinc binding site 2 out of 2 in the Cereblon in Complex with SALL4 and (S)-5-Hydroxythalidomide


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)-5-Hydroxythalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:28.6 occ:1.00 NE2 B:HIS432 2.0 28.6 1.0 NE2 B:HIS428 2.1 27.9 1.0 SG B:CYS415 2.2 26.8 1.0 SG B:CYS412 2.3 27.5 1.0 CD2 B:HIS432 3.0 29.2 1.0 CE1 B:HIS432 3.1 27.0 1.0 CD2 B:HIS428 3.1 30.4 1.0 CE1 B:HIS428 3.1 28.5 1.0 CB B:CYS412 3.2 26.1 1.0 CB B:CYS415 3.4 25.3 1.0 N B:CYS415 3.7 27.8 1.0 CA B:CYS415 4.1 24.7 1.0 CG B:HIS432 4.1 30.9 1.0 ND1 B:HIS432 4.1 28.2 1.0 ND1 B:HIS428 4.2 29.3 1.0 CG B:HIS428 4.2 29.6 1.0 CB B:VAL414 4.3 31.0 1.0 CB B:HIS417 4.4 27.9 1.0 O B:HOH606 4.4 35.4 1.0 CA B:CYS412 4.6 26.3 1.0 C B:VAL414 4.6 28.1 1.0 C B:CYS415 4.8 24.2 1.0 CA B:VAL414 4.8 29.0 1.0 N B:VAL414 4.8 28.7 1.0 CG1 B:VAL414 4.8 30.3 1.0 N B:GLY416 4.9 26.0 1.0 N B:HIS417 4.9 25.5 1.0 C B:CYS412 5.0 26.6 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