Zinc in PDB 6r1d: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized, PDB code: 6r1d 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)	39.20 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.643, 52.482, 59.242, 90.00, 95.79, 90.00
R / Rfree (%)	12.2 / 15

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized (pdb code 6r1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized, PDB code: 6r1d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized


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 7D, Co-Crystallized within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:13.2 occ:1.00 SG A:CYS93 2.3 13.5 1.0 SG A:CYS27 2.3 15.4 1.0 SG A:CYS90 2.3 12.7 1.0 SG A:CYS24 2.4 12.9 1.0 CB A:CYS24 3.1 12.9 1.0 CB A:CYS90 3.2 11.2 1.0 CB A:CYS27 3.3 16.8 1.0 CB A:CYS93 3.3 15.7 1.0 N A:CYS27 3.8 15.6 1.0 N A:CYS93 3.8 14.6 1.0 CA A:CYS27 4.1 16.7 1.0 CA A:CYS93 4.1 13.9 1.0 CB A:GLN29 4.3 16.9 1.0 CB A:GLN26 4.5 16.1 0.5 CB A:GLN26 4.6 17.1 0.5 CA A:CYS90 4.6 10.6 1.0 CA A:CYS24 4.6 11.9 1.0 CB A:SER95 4.6 12.6 0.5 CB A:GLN92 4.6 20.8 1.0 CB A:SER95 4.7 13.8 0.5 OG A:SER95 4.7 14.6 0.5 C A:GLN26 4.7 17.7 1.0 C A:CYS27 4.8 16.5 1.0 C A:CYS93 4.8 13.2 1.0 C A:GLN92 4.8 19.8 1.0 N A:GLY28 4.9 15.0 1.0 N A:GLN29 4.9 14.4 1.0 N A:GLY94 4.9 12.1 1.0

Zinc binding site 2 out of 2 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7D, Co-Crystallized


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 7D, Co-Crystallized within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:12.7 occ:1.00 SG B:CYS93 2.3 13.6 1.0 SG B:CYS27 2.3 14.1 1.0 SG B:CYS24 2.3 11.7 1.0 SG B:CYS90 2.3 11.9 1.0 CB B:CYS24 3.2 10.7 1.0 CB B:CYS90 3.2 10.8 1.0 CB B:CYS27 3.3 16.4 1.0 CB B:CYS93 3.3 14.9 1.0 N B:CYS93 3.7 13.3 1.0 N B:CYS27 3.8 14.8 1.0 CA B:CYS93 4.0 14.4 1.0 CA B:CYS27 4.1 15.2 1.0 CB B:GLN29 4.4 16.6 0.5 CB B:GLN29 4.5 13.6 0.5 CA B:CYS90 4.6 10.6 1.0 CA B:CYS24 4.6 10.1 1.0 CB B:GLN92 4.7 16.0 1.0 CB B:GLN26 4.7 19.0 0.5 CB B:GLN26 4.7 17.3 0.5 CB B:SER95 4.7 15.5 0.5 C B:CYS93 4.7 12.8 1.0 C B:GLN26 4.8 16.7 1.0 C B:CYS27 4.8 14.9 1.0 C B:GLN92 4.8 14.7 1.0 N B:GLY94 4.9 12.2 1.0 N B:GLN29 4.9 13.4 1.0 N B:GLY28 4.9 13.4 1.0 CB B:SER95 4.9 14.1 0.5 OG B:SER95 5.0 16.4 0.5

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