Zinc in PDB 7ps9: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Iberdomide (Cc-220)

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Iberdomide (Cc-220), PDB code: 7ps9 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)	34.76 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.001, 58.85, 88.583, 90, 90, 90
R / Rfree (%)	19.3 / 24.6

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Iberdomide (Cc-220) (pdb code 7ps9). 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 with Iberdomide (Cc-220), PDB code: 7ps9:
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 with Iberdomide (Cc-220)


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 with Iberdomide (Cc-220) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.1 occ:1.00 SG A:CYS24 2.3 25.7 1.0 SG A:CYS93 2.3 25.1 1.0 SG A:CYS27 2.3 26.0 1.0 SG A:CYS90 2.4 23.3 1.0 CB A:CYS90 3.1 24.4 1.0 CB A:CYS24 3.1 23.8 1.0 CB A:CYS93 3.3 25.9 1.0 CB A:CYS27 3.4 27.6 1.0 N A:CYS93 3.8 25.4 1.0 N A:CYS27 3.9 26.1 1.0 CA A:CYS93 4.0 25.6 1.0 CA A:CYS27 4.2 27.6 1.0 CB A:GLN26 4.4 31.3 1.0 CA A:CYS90 4.5 23.6 1.0 CB A:SER95 4.5 31.0 1.0 CA A:CYS24 4.5 25.6 1.0 CB A:GLN29 4.6 27.2 1.0 C A:GLN26 4.7 27.9 1.0 CB A:GLN92 4.7 26.1 1.0 C A:CYS93 4.8 27.6 1.0 C A:GLN92 4.9 26.0 1.0 N A:GLY94 4.9 26.6 1.0 C A:CYS27 4.9 26.6 1.0 CA A:GLN26 4.9 28.4 1.0 N A:GLN26 4.9 24.9 1.0 N A:SER95 4.9 26.0 1.0 N A:GLY28 5.0 23.6 1.0 C A:CYS24 5.0 24.4 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Iberdomide (Cc-220)


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 with Iberdomide (Cc-220) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:31.6 occ:1.00 SG B:CYS93 2.3 30.1 1.0 SG B:CYS90 2.3 30.0 1.0 SG B:CYS27 2.3 34.4 1.0 SG B:CYS24 2.4 28.4 1.0 CB B:CYS90 3.1 29.1 1.0 CB B:CYS24 3.1 28.8 1.0 CB B:CYS93 3.2 35.8 1.0 CB B:CYS27 3.3 37.4 1.0 N B:CYS93 3.7 32.1 1.0 N B:CYS27 3.9 35.0 1.0 CA B:CYS93 4.0 34.2 1.0 CA B:CYS27 4.2 35.2 1.0 CA B:CYS90 4.5 26.1 1.0 CA B:CYS24 4.6 25.7 1.0 CB B:GLN92 4.6 31.3 1.0 CB B:GLN26 4.6 39.9 1.0 CB B:SER95 4.7 32.7 1.0 C B:GLN92 4.7 31.6 1.0 C B:CYS93 4.7 31.4 1.0 C B:GLN26 4.8 37.2 1.0 CB B:GLN29 4.8 36.8 1.0 C B:CYS27 4.8 34.5 1.0 N B:GLY94 4.9 31.4 1.0 N B:GLY28 4.9 31.5 1.0 N B:GLN29 5.0 33.8 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Iberdomide (Cc-220)


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 with Iberdomide (Cc-220) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.1 occ:1.00 SG C:CYS93 2.3 35.8 1.0 SG C:CYS24 2.3 38.8 1.0 SG C:CYS27 2.3 36.3 1.0 SG C:CYS90 2.3 36.2 1.0 CB C:CYS24 3.1 39.4 1.0 CB C:CYS90 3.1 34.9 1.0 CB C:CYS93 3.3 36.9 1.0 CB C:CYS27 3.4 42.8 1.0 N C:CYS93 3.8 38.6 1.0 N C:CYS27 3.9 48.0 1.0 CA C:CYS93 4.1 40.0 1.0 CA C:CYS27 4.1 40.7 1.0 CB C:GLN29 4.4 34.9 1.0 CB C:GLN26 4.5 50.3 1.0 CA C:CYS24 4.5 41.2 1.0 CA C:CYS90 4.6 33.1 1.0 CB C:SER95 4.6 43.3 1.0 CB C:GLN92 4.6 32.7 1.0 C C:GLN26 4.7 46.9 1.0 C C:CYS27 4.7 40.7 1.0 C C:CYS93 4.7 42.1 1.0 N C:GLY28 4.8 37.3 1.0 C C:GLN92 4.8 38.9 1.0 N C:GLY94 4.8 36.6 1.0 N C:GLN29 4.9 32.4 1.0 N C:SER95 4.9 41.6 1.0 N C:GLN26 5.0 47.7 1.0 CA C:GLN26 5.0 49.6 1.0

C.Heim, M.D.Hartmann. High-Resolution Structures of the Bound Effectors Avadomide (Cc-122) and Iberdomide (Cc-220) Highlight Advantages and Limitations of the MSCI4 Soaking System. Acta Crystallogr D Struct V. 78 290 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35234143
DOI: 10.1107/S2059798322000092