Zinc in PDB 6r18: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A, PDB code: 6r18 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)	44.45 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.630, 59.592, 88.894, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.7

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A (pdb code 6r18). 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 11A, PDB code: 6r18:
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 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:11.9 occ:1.00 SG A:CYS27 2.3 12.6 1.0 SG A:CYS24 2.3 11.7 1.0 SG A:CYS93 2.3 12.3 1.0 SG A:CYS90 2.3 11.5 1.0 CB A:CYS24 3.1 11.2 1.0 CB A:CYS90 3.2 10.9 1.0 CB A:CYS93 3.3 12.8 1.0 CB A:CYS27 3.4 12.6 1.0 N A:CYS93 3.8 12.0 1.0 N A:CYS27 3.9 13.9 1.0 CA A:CYS93 4.1 12.3 1.0 CA A:CYS27 4.2 13.9 1.0 CB A:GLN29 4.5 12.2 0.5 CB A:SER95 4.5 13.4 1.0 CA A:CYS24 4.5 10.7 1.0 CB A:GLN29 4.5 13.3 0.5 CB A:GLN26 4.5 17.2 1.0 C A:GLN26 4.6 16.1 1.0 CA A:CYS90 4.6 11.2 1.0 C A:CYS93 4.7 12.9 1.0 CB A:GLN92 4.8 12.6 1.0 N A:GLY94 4.8 12.4 1.0 C A:CYS27 4.9 14.5 1.0 C A:GLN92 4.9 12.9 1.0 N A:GLN26 4.9 13.7 1.0 CA A:GLN26 4.9 15.6 1.0 N A:SER95 4.9 12.3 1.0 N A:GLY28 4.9 13.2 1.0 N A:GLN29 4.9 13.0 1.0 C A:CYS24 5.0 11.4 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.0 occ:1.00 SG B:CYS27 2.3 15.8 1.0 SG B:CYS90 2.3 13.9 1.0 SG B:CYS93 2.3 16.7 1.0 SG B:CYS24 2.4 14.5 1.0 CB B:CYS90 3.2 13.4 1.0 CB B:CYS24 3.2 14.1 1.0 CB B:CYS93 3.3 16.6 1.0 CB B:CYS27 3.3 16.6 1.0 N B:CYS27 3.7 17.1 1.0 N B:CYS93 3.8 15.7 1.0 CA B:CYS27 4.1 16.3 1.0 CA B:CYS93 4.1 15.8 1.0 CA B:CYS90 4.6 12.7 1.0 C B:GLN26 4.6 20.0 1.0 CA B:CYS24 4.7 13.3 1.0 CB B:SER95 4.7 15.4 1.0 CB B:GLN26 4.7 21.0 1.0 CB B:GLN92 4.7 16.0 1.0 C B:CYS27 4.7 15.5 1.0 CB B:GLN29 4.8 18.1 1.0 C B:GLN92 4.8 15.6 1.0 C B:CYS93 4.8 16.6 1.0 N B:GLY28 4.8 15.0 1.0 N B:GLY94 4.9 15.0 1.0 N B:GLN29 5.0 15.4 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 11A


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 11A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:15.6 occ:1.00 SG C:CYS24 2.3 15.9 1.0 SG C:CYS93 2.3 16.3 1.0 SG C:CYS27 2.3 16.4 1.0 SG C:CYS90 2.3 15.0 1.0 CB C:CYS90 3.2 14.9 1.0 CB C:CYS24 3.2 14.7 1.0 CB C:CYS93 3.3 15.5 1.0 CB C:CYS27 3.4 18.2 1.0 N C:CYS93 3.8 14.8 1.0 N C:CYS27 3.8 20.5 1.0 CA C:CYS93 4.1 15.5 1.0 CA C:CYS27 4.2 19.9 1.0 CB C:GLN29 4.4 15.9 1.0 CB C:SER95 4.5 17.3 1.0 CB C:GLN26 4.5 25.3 1.0 CA C:CYS90 4.6 14.9 1.0 CA C:CYS24 4.6 16.6 1.0 C C:GLN26 4.7 24.0 1.0 C C:CYS93 4.7 15.8 1.0 CB C:GLN92 4.7 13.9 1.0 C C:GLN92 4.8 14.6 1.0 C C:CYS27 4.8 20.5 1.0 N C:GLY94 4.8 16.0 1.0 N C:GLY28 4.8 19.8 1.0 N C:SER95 4.9 16.3 1.0 N C:GLN29 4.9 17.0 1.0 CA C:GLN26 5.0 23.2 1.0 N C:GLN26 5.0 22.2 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