Zinc in PDB 6r0q: Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide

The structure of Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide, PDB code: 6r0q 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)	49.17 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.728, 59.163, 61.751, 90.00, 105.59, 90.00
R / Rfree (%)	15.8 / 19

The binding sites of Zinc atom in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide (pdb code 6r0q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide, PDB code: 6r0q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:12.5 occ:1.00 SG A:CYS27 2.3 13.2 1.0 SG A:CYS24 2.3 11.6 1.0 SG A:CYS93 2.3 12.4 1.0 SG A:CYS90 2.4 11.4 1.0 CB A:CYS24 3.2 11.8 1.0 CB A:CYS90 3.2 11.0 1.0 CB A:CYS27 3.4 13.8 1.0 CB A:CYS93 3.4 11.0 1.0 N A:CYS27 3.7 13.7 1.0 N A:CYS93 3.8 11.9 1.0 CA A:CYS93 4.1 12.3 1.0 CA A:CYS27 4.1 13.8 1.0 CB A:SER95 4.5 12.9 1.0 CB A:GLN26 4.6 20.7 1.0 CA A:CYS90 4.6 11.0 1.0 C A:GLN26 4.6 15.7 1.0 CB A:GLN92 4.6 15.4 1.0 CA A:CYS24 4.6 10.6 1.0 CB A:GLN29 4.7 20.2 1.0 C A:CYS93 4.7 11.2 1.0 C A:GLN92 4.8 15.3 1.0 C A:CYS27 4.8 13.7 1.0 N A:GLY94 4.8 10.6 1.0 N A:GLY28 4.9 13.5 1.0 N A:SER95 4.9 11.7 1.0 N A:GLN29 4.9 14.5 1.0

Zinc binding site 2 out of 4 in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:14.8 occ:1.00 SG B:CYS27 2.3 16.1 1.0 SG B:CYS24 2.3 14.7 1.0 SG B:CYS93 2.3 14.5 1.0 SG B:CYS90 2.4 13.9 1.0 CB B:CYS24 3.2 14.7 1.0 CB B:CYS90 3.2 11.9 1.0 CB B:CYS93 3.4 13.1 1.0 CB B:CYS27 3.4 17.1 1.0 N B:CYS27 3.8 18.8 1.0 N B:CYS93 3.8 13.8 1.0 CA B:CYS27 4.0 17.3 1.0 CA B:CYS93 4.1 13.1 1.0 CB B:GLN29 4.5 22.6 0.5 CB B:SER95 4.6 13.2 1.0 CB B:GLN29 4.6 20.5 0.5 CB B:GLN26 4.6 27.4 1.0 CB B:GLN92 4.6 18.1 1.0 CA B:CYS24 4.6 15.6 1.0 CA B:CYS90 4.6 12.1 1.0 C B:CYS93 4.7 12.6 1.0 C B:GLN26 4.7 20.4 1.0 C B:CYS27 4.8 20.3 1.0 C B:GLN92 4.8 15.2 1.0 N B:GLY28 4.8 19.3 1.0 N B:GLY94 4.9 11.3 1.0 N B:SER95 4.9 12.5 1.0 N B:GLN29 4.9 19.2 1.0

Zinc binding site 3 out of 4 in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:12.8 occ:1.00 SG C:CYS27 2.3 13.3 1.0 SG C:CYS24 2.3 11.7 1.0 SG C:CYS93 2.3 12.5 1.0 SG C:CYS90 2.4 11.7 1.0 CB C:CYS24 3.1 11.3 1.0 CB C:CYS90 3.2 11.1 1.0 CB C:CYS93 3.3 12.2 1.0 CB C:CYS27 3.3 14.5 1.0 N C:CYS27 3.8 14.3 1.0 N C:CYS93 3.8 12.0 1.0 CA C:CYS93 4.1 12.1 1.0 CA C:CYS27 4.1 13.3 1.0 CB C:GLN29 4.5 17.0 0.5 CB C:SER95 4.5 12.5 1.0 CA C:CYS90 4.6 10.9 1.0 CB C:GLN26 4.6 19.4 1.0 CA C:CYS24 4.6 10.4 1.0 CB C:GLN92 4.6 14.3 1.0 C C:GLN26 4.6 15.3 1.0 C C:CYS93 4.7 11.3 1.0 C C:GLN92 4.7 13.8 1.0 C C:CYS27 4.8 14.3 1.0 N C:GLY94 4.8 10.5 1.0 N C:GLY28 4.8 13.4 1.0 N C:SER95 4.9 10.7 1.0 CB C:GLN29 4.9 17.7 0.5 N C:GLN29 4.9 15.2 1.0

Zinc binding site 4 out of 4 in the Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide Metabolite Alpha-(O-Carboxybenzamido) Glutarimide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:14.8 occ:1.00 SG D:CYS27 2.3 15.9 1.0 SG D:CYS93 2.3 14.3 1.0 SG D:CYS24 2.3 14.9 1.0 SG D:CYS90 2.4 13.8 1.0 CB D:CYS24 3.2 13.6 1.0 CB D:CYS90 3.2 11.8 1.0 CB D:CYS93 3.3 13.7 1.0 CB D:CYS27 3.4 16.5 1.0 N D:CYS27 3.8 19.9 1.0 N D:CYS93 3.8 13.1 1.0 CA D:CYS27 4.1 17.9 1.0 CA D:CYS93 4.1 12.8 1.0 CB D:GLN29 4.5 21.8 1.0 CB D:GLN26 4.6 26.9 1.0 CB D:SER95 4.6 13.7 1.0 CB D:GLN92 4.6 18.5 1.0 CA D:CYS24 4.7 14.1 1.0 CA D:CYS90 4.7 11.8 1.0 C D:CYS93 4.7 11.4 1.0 C D:GLN26 4.8 22.6 1.0 C D:CYS27 4.8 20.6 1.0 C D:GLN92 4.8 14.6 1.0 N D:GLY28 4.9 19.3 1.0 N D:GLY94 4.9 11.7 1.0 N D:SER95 4.9 12.5 1.0 N D:GLN29 4.9 19.2 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