Zinc in PDB 6r12: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B, PDB code: 6r12 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)	48.93 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.417, 58.795, 88.234, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 23.4

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B (pdb code 6r12). 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 Compound 7B, PDB code: 6r12:
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 Compound 7B


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 Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:20.8 occ:1.00 SG A:CYS93 2.3 21.2 1.0 SG A:CYS24 2.3 19.1 1.0 SG A:CYS27 2.3 20.8 1.0 SG A:CYS90 2.4 20.3 1.0 CB A:CYS24 3.1 19.8 1.0 CB A:CYS90 3.2 21.7 1.0 CB A:CYS93 3.3 20.8 1.0 CB A:CYS27 3.4 22.5 1.0 N A:CYS93 3.7 21.2 1.0 N A:CYS27 3.9 21.4 1.0 CA A:CYS93 4.0 21.9 1.0 CA A:CYS27 4.2 23.4 1.0 CB A:GLN26 4.5 25.7 1.0 CB A:SER95 4.5 22.1 1.0 CA A:CYS24 4.6 19.4 1.0 CA A:CYS90 4.6 20.0 1.0 CB A:GLN29 4.6 23.2 1.0 C A:GLN26 4.7 24.7 1.0 CB A:GLN92 4.7 22.0 1.0 C A:CYS93 4.7 21.7 1.0 C A:CYS27 4.9 22.9 1.0 C A:GLN92 4.9 21.6 1.0 CA A:GLN26 4.9 23.0 1.0 N A:GLY94 4.9 23.5 1.0 N A:GLN26 4.9 19.6 1.0 N A:SER95 4.9 20.9 1.0 N A:GLY28 4.9 21.2 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B


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 Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:27.3 occ:1.00 SG B:CYS93 2.2 28.5 1.0 SG B:CYS90 2.3 25.1 1.0 SG B:CYS24 2.4 24.9 1.0 SG B:CYS27 2.5 28.4 1.0 CB B:CYS90 3.1 26.9 1.0 CB B:CYS24 3.2 24.1 1.0 CB B:CYS93 3.3 28.9 1.0 CB B:CYS27 3.4 32.7 1.0 N B:CYS93 3.7 26.0 1.0 N B:CYS27 3.8 27.7 1.0 CA B:CYS93 4.1 27.3 1.0 CA B:CYS27 4.1 31.0 1.0 CA B:CYS90 4.6 23.9 1.0 CB B:GLN92 4.6 26.6 1.0 CA B:CYS24 4.6 22.2 1.0 CB B:GLN29 4.7 33.0 1.0 CB B:SER95 4.7 27.1 1.0 C B:GLN92 4.7 26.1 1.0 C B:GLN26 4.7 33.3 1.0 C B:CYS93 4.7 29.1 1.0 C B:CYS27 4.7 29.9 1.0 CB B:GLN26 4.8 37.2 1.0 N B:GLY28 4.8 27.3 1.0 N B:GLY94 4.8 26.0 1.0 N B:GLN29 5.0 26.7 1.0 N B:SER95 5.0 26.3 1.0 CG B:GLN26 5.0 40.4 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7B


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 Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.1 occ:1.00 SG C:CYS24 2.3 31.4 1.0 SG C:CYS93 2.3 32.5 1.0 SG C:CYS90 2.3 29.9 1.0 SG C:CYS27 2.4 31.7 1.0 CB C:CYS24 3.1 32.7 1.0 CB C:CYS90 3.1 29.4 1.0 CB C:CYS93 3.4 30.0 1.0 CB C:CYS27 3.4 35.7 1.0 N C:CYS93 3.8 29.7 1.0 N C:CYS27 3.8 39.3 1.0 CA C:CYS93 4.1 29.7 1.0 CA C:CYS27 4.2 37.1 1.0 CB C:GLN29 4.4 29.1 1.0 CB C:SER95 4.5 33.9 1.0 CB C:GLN26 4.5 46.5 1.0 CA C:CYS24 4.6 32.6 1.0 CA C:CYS90 4.6 28.5 1.0 CB C:GLN92 4.7 28.6 1.0 C C:GLN26 4.7 42.6 1.0 C C:CYS93 4.8 31.9 1.0 C C:CYS27 4.8 32.6 1.0 N C:GLY94 4.8 32.5 1.0 C C:GLN92 4.8 29.9 1.0 N C:GLY28 4.8 30.3 1.0 N C:SER95 4.8 33.5 1.0 N C:GLN29 4.8 31.4 1.0 N C:GLN26 5.0 40.0 1.0 CA C:GLN26 5.0 43.8 1.0

C.Heim, D.Pliatsika, F.Mousavizadeh, K.Bar, B.Hernandez Alvarez, A.Giannis, M.D.Hartmann. De-Novo Design of Cereblon (Crbn) Effectors Guided By Natural Hydrolysis Products of Thalidomide Derivatives. J.Med.Chem. V. 62 6615 2019.
ISSN: ISSN 0022-2623
PubMed: 31251063
DOI: 10.1021/ACS.JMEDCHEM.9B00454