Zinc in PDB 8bc6: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aspartimide Degron Peptide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aspartimide Degron Peptide, PDB code: 8bc6 was solved by C.Heim, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.23 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.966, 59.015, 88.651, 90, 90, 90
R / Rfree (%)	19.5 / 22.3

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aspartimide Degron Peptide (pdb code 8bc6). 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 Aspartimide Degron Peptide, PDB code: 8bc6:
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 Aspartimide 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 Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.0 occ:1.00 SG A:CYS24 2.3 22.9 1.0 SG A:CYS27 2.3 24.9 1.0 SG A:CYS93 2.3 24.9 1.0 SG A:CYS90 2.4 23.1 1.0 CB A:CYS24 3.1 23.2 1.0 CB A:CYS90 3.1 21.5 1.0 CB A:CYS93 3.3 24.8 1.0 CB A:CYS27 3.4 26.6 1.0 N A:CYS93 3.8 26.2 1.0 N A:CYS27 3.9 26.5 1.0 CA A:CYS93 4.0 26.2 1.0 CA A:CYS27 4.2 27.1 1.0 CB A:GLN29 4.5 26.7 1.0 CB A:SER95 4.5 26.7 1.0 CA A:CYS24 4.5 22.5 1.0 CB A:GLN26 4.6 31.6 1.0 CA A:CYS90 4.6 21.5 1.0 C A:GLN26 4.6 29.3 1.0 C A:CYS93 4.7 25.1 1.0 CB A:GLN92 4.8 24.5 1.0 N A:GLY94 4.8 25.9 1.0 C A:CYS27 4.9 27.8 1.0 N A:SER95 4.9 25.0 1.0 CA A:GLN26 4.9 28.9 1.0 C A:GLN92 4.9 25.7 1.0 N A:GLN26 4.9 26.1 1.0 N A:GLY28 4.9 26.7 1.0 N A:GLN29 4.9 25.8 1.0 C A:CYS24 5.0 23.3 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aspartimide 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 Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.5 occ:1.00 SG B:CYS27 2.2 45.8 1.0 SG B:CYS90 2.3 37.5 1.0 SG B:CYS24 2.4 39.0 1.0 SG B:CYS93 2.4 44.1 1.0 CB B:CYS24 3.1 38.1 1.0 CB B:CYS90 3.1 33.6 1.0 CB B:CYS27 3.3 45.5 1.0 CB B:CYS93 3.4 46.6 1.0 N B:CYS27 3.8 44.1 1.0 N B:CYS93 3.8 42.2 1.0 CA B:CYS27 4.1 45.8 1.0 CA B:CYS93 4.2 44.8 1.0 CA B:CYS90 4.5 31.8 1.0 CA B:CYS24 4.5 34.6 1.0 CB B:GLN92 4.6 42.9 1.0 C B:GLN26 4.6 47.0 1.0 CB B:GLN26 4.7 49.2 1.0 C B:CYS27 4.7 44.8 1.0 N B:GLY28 4.7 42.0 1.0 C B:GLN92 4.8 42.1 1.0 CB B:GLN29 4.8 43.4 1.0 C B:CYS93 4.8 41.6 1.0 N B:GLN29 4.9 40.9 1.0 N B:GLY94 4.9 39.6 1.0 CA B:GLN26 5.0 47.6 1.0 CB B:SER95 5.0 38.2 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex An Aspartimide 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 Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:38.9 occ:1.00 SG C:CYS93 2.3 42.0 1.0 SG C:CYS27 2.3 38.9 1.0 SG C:CYS24 2.4 42.6 1.0 SG C:CYS90 2.4 38.9 1.0 CB C:CYS24 3.0 42.2 1.0 CB C:CYS90 3.2 39.9 1.0 CB C:CYS93 3.4 41.5 1.0 CB C:CYS27 3.4 42.7 1.0 N C:CYS93 3.8 37.9 1.0 N C:CYS27 3.8 47.7 1.0 CA C:CYS93 4.1 39.2 1.0 CA C:CYS27 4.1 44.3 1.0 CB C:GLN26 4.3 59.5 1.0 CB C:GLN29 4.4 35.6 1.0 CB C:SER95 4.4 49.7 1.0 CA C:CYS24 4.5 44.3 1.0 CB C:GLN92 4.6 34.2 1.0 N C:GLY28 4.7 39.9 1.0 CA C:CYS90 4.7 39.2 1.0 C C:CYS93 4.7 41.3 1.0 C C:GLN26 4.7 53.0 1.0 C C:CYS27 4.7 42.1 1.0 C C:GLN92 4.8 36.9 1.0 N C:GLY94 4.8 40.8 1.0 N C:GLN29 4.8 37.3 1.0 N C:SER95 4.8 47.3 1.0 CA C:GLN26 4.9 55.7 1.0 C C:CYS24 5.0 46.2 1.0 N C:GLN26 5.0 55.8 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