Zinc in PDB 8c3h: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex A Long Aspartimide Degron Peptide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex A Long Aspartimide Degron Peptide, PDB code: 8c3h was solved by C.Heim, 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)	47.53 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.256, 58.821, 88.858, 90, 90, 90
R / Rfree (%)	17.9 / 21

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex A Long Aspartimide Degron Peptide (pdb code 8c3h). 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 A Long Aspartimide Degron Peptide, PDB code: 8c3h:
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 A Long 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 A Long Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:31.3 occ:1.00 SG A:CYS27 2.3 31.3 1.0 SG A:CYS24 2.3 31.0 1.0 SG A:CYS93 2.3 32.7 1.0 SG A:CYS90 2.4 30.6 1.0 CB A:CYS24 3.1 30.6 1.0 CB A:CYS90 3.1 30.6 1.0 CB A:CYS93 3.3 32.2 1.0 CB A:CYS27 3.4 31.2 1.0 N A:CYS93 3.8 33.5 1.0 N A:CYS27 3.9 32.5 1.0 CA A:CYS93 4.0 33.4 1.0 CA A:CYS27 4.2 32.8 1.0 CB A:GLN26 4.5 37.7 1.0 CB A:GLN29 4.5 31.3 0.5 CA A:CYS24 4.5 29.0 1.0 CB A:GLN29 4.6 32.1 0.5 CA A:CYS90 4.6 29.6 1.0 CB A:SER95 4.6 33.0 0.5 C A:GLN26 4.6 36.9 1.0 CB A:GLN92 4.7 31.2 1.0 C A:CYS93 4.8 33.4 1.0 OG A:SER95 4.8 36.0 0.5 C A:CYS27 4.9 33.1 1.0 CB A:SER95 4.9 33.2 0.5 C A:GLN92 4.9 31.9 1.0 CA A:GLN26 4.9 35.3 1.0 N A:GLN26 4.9 31.4 1.0 N A:GLY28 4.9 31.0 1.0 N A:GLY94 4.9 32.1 1.0 N A:GLN29 5.0 29.5 1.0 C A:CYS24 5.0 28.2 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex A Long 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 A Long Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.9 occ:1.00 SG B:CYS90 2.3 39.0 1.0 SG B:CYS27 2.3 44.5 1.0 SG B:CYS93 2.4 43.9 1.0 SG B:CYS24 2.4 39.2 1.0 CB B:CYS24 3.1 39.4 1.0 CB B:CYS90 3.1 35.8 1.0 CB B:CYS93 3.4 46.7 1.0 CB B:CYS27 3.4 48.5 1.0 N B:CYS93 3.8 42.8 1.0 N B:CYS27 3.9 46.0 1.0 CA B:CYS93 4.1 46.2 1.0 CA B:CYS27 4.2 47.9 1.0 CA B:CYS24 4.6 37.5 1.0 CA B:CYS90 4.6 34.9 1.0 CB B:GLN26 4.6 52.2 1.0 CB B:GLN92 4.6 45.0 1.0 C B:GLN26 4.7 50.1 1.0 C B:GLN92 4.8 42.0 1.0 CB B:GLN29 4.8 45.9 1.0 C B:CYS27 4.8 47.2 1.0 C B:CYS93 4.8 44.3 1.0 N B:GLY28 4.9 42.6 1.0 N B:GLY94 4.9 40.8 1.0 CB B:SER95 4.9 42.2 1.0 N B:GLN29 5.0 42.1 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex A Long 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 A Long Aspartimide Degron Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:46.3 occ:1.00 SG C:CYS93 2.3 50.2 1.0 SG C:CYS27 2.3 46.2 1.0 SG C:CYS24 2.4 52.5 1.0 SG C:CYS90 2.4 47.0 1.0 CB C:CYS24 3.1 51.2 1.0 CB C:CYS90 3.2 48.8 1.0 CB C:CYS27 3.2 50.6 1.0 CB C:CYS93 3.3 49.9 1.0 N C:CYS93 3.8 45.3 1.0 N C:CYS27 3.9 59.2 1.0 CA C:CYS93 4.1 47.5 1.0 CA C:CYS27 4.1 54.1 1.0 CB C:GLN29 4.4 41.8 1.0 CB C:GLN26 4.4 68.8 1.0 CB C:GLN92 4.5 42.9 1.0 CB C:SER95 4.5 60.6 1.0 CA C:CYS24 4.6 51.8 1.0 CA C:CYS90 4.6 45.7 1.0 C C:CYS93 4.7 50.9 1.0 N C:GLY28 4.7 49.1 1.0 C C:CYS27 4.7 52.9 1.0 C C:GLN26 4.7 65.1 1.0 C C:GLN92 4.8 45.0 1.0 N C:GLY94 4.8 47.0 1.0 N C:GLN29 4.8 44.5 1.0 N C:SER95 4.9 56.0 1.0

C.Heim, A.K.Spring, S.Kirchgassner, D.Schwarzer, M.D.Hartmann. Cereblon Neo-Substrate Binding Mimics the Recognition of the Cyclic Imide Degron. Biochem.Biophys.Res.Commun. V. 646 30 2023.
ISSN: ESSN 1090-2104
PubMed: 36701892
DOI: 10.1016/J.BBRC.2023.01.051