Zinc in PDB 7pso: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Avadomide (Cc-122)

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Avadomide (Cc-122), PDB code: 7pso 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)	44.24 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.562, 60.162, 88.406, 90, 90, 90
R / Rfree (%)	18.5 / 21.7

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Avadomide (Cc-122) (pdb code 7pso). 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 Avadomide (Cc-122), PDB code: 7pso:
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 Avadomide (Cc-122)


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 Avadomide (Cc-122) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.2 occ:1.00 SG A:CYS27 2.3 19.7 1.0 SG A:CYS24 2.3 19.5 1.0 SG A:CYS93 2.3 20.5 1.0 SG A:CYS90 2.4 19.5 1.0 CB A:CYS24 3.1 17.0 1.0 CB A:CYS90 3.1 18.2 1.0 CB A:CYS93 3.3 19.4 1.0 CB A:CYS27 3.5 20.9 1.0 N A:CYS93 3.8 19.3 1.0 N A:CYS27 3.9 19.2 1.0 CA A:CYS93 4.1 19.9 1.0 CA A:CYS27 4.2 21.2 1.0 CB A:SER95 4.5 22.0 1.0 CA A:CYS24 4.5 16.6 1.0 CB A:GLN29 4.5 20.4 1.0 CB A:GLN26 4.5 25.0 1.0 CA A:CYS90 4.6 18.6 1.0 C A:GLN26 4.6 25.6 1.0 CB A:GLN92 4.7 20.5 1.0 C A:CYS93 4.8 21.5 1.0 C A:CYS27 4.8 25.3 1.0 C A:GLN92 4.9 20.5 1.0 N A:GLY94 4.9 19.3 1.0 CA A:GLN26 4.9 22.8 1.0 N A:GLN26 4.9 19.6 1.0 N A:GLY28 4.9 20.9 1.0 C A:CYS24 4.9 19.4 1.0 N A:SER95 4.9 20.8 1.0 N A:GLN29 5.0 21.0 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Avadomide (Cc-122)


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 Avadomide (Cc-122) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.6 occ:1.00 SG B:CYS90 2.3 22.3 1.0 SG B:CYS93 2.3 26.5 1.0 SG B:CYS27 2.3 25.2 1.0 SG B:CYS24 2.4 22.4 1.0 CB B:CYS90 3.1 23.9 1.0 CB B:CYS24 3.2 23.3 1.0 CB B:CYS93 3.3 27.2 1.0 CB B:CYS27 3.3 27.3 1.0 N B:CYS93 3.8 24.2 1.0 N B:CYS27 3.8 25.5 1.0 CA B:CYS93 4.1 23.2 1.0 CA B:CYS27 4.1 24.6 1.0 CA B:CYS90 4.5 20.0 1.0 CB B:GLN92 4.6 24.3 1.0 CA B:CYS24 4.6 21.1 1.0 CB B:SER95 4.7 24.1 1.0 CB B:GLN29 4.7 29.0 1.0 C B:GLN26 4.7 31.0 1.0 C B:GLN92 4.7 23.9 1.0 C B:CYS27 4.7 26.6 1.0 CB B:GLN26 4.8 31.1 1.0 C B:CYS93 4.8 28.1 1.0 N B:GLY28 4.9 23.2 1.0 N B:GLY94 4.9 24.1 1.0 N B:GLN29 4.9 23.9 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Avadomide (Cc-122)


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 Avadomide (Cc-122) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.0 occ:1.00 SG C:CYS93 2.3 23.9 1.0 SG C:CYS27 2.3 24.4 1.0 SG C:CYS24 2.3 22.2 1.0 SG C:CYS90 2.3 22.0 1.0 CB C:CYS24 3.1 23.0 1.0 CB C:CYS90 3.1 21.6 1.0 CB C:CYS93 3.3 23.4 1.0 CB C:CYS27 3.4 23.9 1.0 N C:CYS93 3.7 22.9 1.0 N C:CYS27 3.8 26.6 1.0 CA C:CYS93 4.1 23.9 1.0 CA C:CYS27 4.2 27.7 1.0 CB C:GLN29 4.4 22.9 1.0 CB C:SER95 4.5 26.2 1.0 CA C:CYS24 4.6 24.1 1.0 CB C:GLN26 4.6 32.4 1.0 CA C:CYS90 4.6 21.6 1.0 CB C:GLN92 4.6 23.4 1.0 C C:CYS93 4.7 26.4 1.0 C C:GLN26 4.7 31.9 1.0 C C:GLN92 4.8 22.7 1.0 C C:CYS27 4.8 28.2 1.0 N C:GLY94 4.8 24.5 1.0 N C:GLY28 4.8 26.8 1.0 N C:GLN29 4.9 24.0 1.0 N C:SER95 4.9 24.6 1.0 CA C:GLN26 5.0 31.1 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