Zinc in PDB 8bc7: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide, PDB code: 8bc7 was solved by C.Heim, R.Albrecht, A.K.Spring, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.606, 59.45, 89.059, 90, 90, 90
R / Rfree (%)	17.4 / 21.1

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide (pdb code 8bc7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide, PDB code: 8bc7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:26.4 occ:1.00 SG A:CYS24 2.3 25.9 1.0 SG A:CYS93 2.3 27.7 1.0 SG A:CYS27 2.3 27.5 1.0 SG A:CYS90 2.4 25.8 1.0 CB A:CYS24 3.1 26.4 1.0 CB A:CYS90 3.2 26.0 1.0 CB A:CYS93 3.3 27.3 1.0 CB A:CYS27 3.5 27.4 1.0 N A:CYS93 3.8 26.7 1.0 N A:CYS27 3.9 28.5 1.0 CA A:CYS93 4.0 27.7 1.0 CA A:CYS27 4.2 28.1 1.0 CB A:GLN26 4.4 38.5 1.0 CB A:GLN29 4.4 26.8 0.5 CA A:CYS24 4.5 25.8 1.0 CB A:SER95 4.6 36.7 1.0 CA A:CYS90 4.6 23.9 1.0 CB A:GLN29 4.6 26.2 0.5 C A:GLN26 4.7 33.2 1.0 CB A:GLN92 4.7 26.3 1.0 C A:CYS93 4.7 29.0 1.0 C A:GLN92 4.9 26.9 1.0 N A:GLY94 4.9 28.9 1.0 C A:CYS27 4.9 30.9 1.0 N A:GLY28 4.9 28.5 1.0 N A:GLN26 5.0 29.6 1.0 CA A:GLN26 5.0 34.1 1.0 N A:GLN29 5.0 25.6 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.8 occ:1.00 SG B:CYS93 2.3 36.2 1.0 SG B:CYS90 2.3 33.6 1.0 SG B:CYS27 2.3 37.5 1.0 SG B:CYS24 2.4 32.3 1.0 CB B:CYS90 3.1 30.7 1.0 CB B:CYS24 3.1 34.2 1.0 CB B:CYS27 3.3 39.9 1.0 CB B:CYS93 3.3 38.3 1.0 N B:CYS93 3.8 34.0 1.0 N B:CYS27 3.9 39.3 1.0 CA B:CYS93 4.1 36.8 1.0 CA B:CYS27 4.2 39.4 1.0 CA B:CYS90 4.6 27.9 1.0 CB B:GLN26 4.6 42.4 1.0 CA B:CYS24 4.6 31.0 1.0 CB B:GLN92 4.7 34.7 1.0 CB B:SER95 4.7 35.2 1.0 C B:CYS93 4.7 36.0 1.0 C B:GLN26 4.7 42.5 1.0 C B:GLN92 4.8 35.5 1.0 CB B:GLN29 4.8 37.6 1.0 C B:CYS27 4.8 37.5 1.0 N B:GLY28 4.8 36.1 1.0 N B:GLY94 4.9 34.3 1.0 N B:GLN29 5.0 34.1 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aminoglutarimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:37.7 occ:1.00 SG C:CYS93 2.3 40.5 1.0 SG C:CYS27 2.3 39.0 1.0 SG C:CYS90 2.3 36.7 1.0 SG C:CYS24 2.4 40.3 1.0 CB C:CYS24 3.1 37.9 1.0 CB C:CYS90 3.2 37.2 1.0 CB C:CYS93 3.3 40.9 1.0 CB C:CYS27 3.3 43.7 1.0 N C:CYS93 3.8 36.8 1.0 N C:CYS27 3.9 46.9 1.0 CA C:CYS93 4.1 38.4 1.0 CA C:CYS27 4.2 45.6 1.0 CB C:GLN29 4.4 33.9 1.0 CB C:GLN26 4.5 53.1 1.0 CA C:CYS24 4.6 39.7 1.0 CB C:SER95 4.6 47.7 1.0 CA C:CYS90 4.6 36.7 1.0 CB C:GLN92 4.7 35.0 1.0 C C:CYS93 4.7 39.0 1.0 C C:GLN26 4.8 50.5 1.0 C C:CYS27 4.8 42.8 1.0 N C:GLY28 4.8 38.8 1.0 C C:GLN92 4.8 36.3 1.0 N C:GLY94 4.8 38.3 1.0 N C:GLN29 4.9 36.3 1.0 N C:SER95 4.9 44.6 1.0 N C:GLN26 5.0 49.8 1.0

C.Heim, A.K.Spring, S.Kirchgassner, D.Schwarzer, M.D.Hartmann. Identification and Structural Basis of C-Terminal Cyclic Imides As Natural Degrons For Cereblon. Biochem.Biophys.Res.Commun. V. 637 66 2022.
ISSN: ESSN 1090-2104
PubMed: 36375252
DOI: 10.1016/J.BBRC.2022.11.001