Zinc in PDB 6r13: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7F

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7F, PDB code: 6r13 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)	48.79 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.871, 58.547, 88.283, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.4

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7F 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 7F (pdb code 6r13). 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 7F, PDB code: 6r13:
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 7F


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 7F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.3 occ:1.00 SG A:CYS93 2.3 19.2 1.0 SG A:CYS24 2.3 18.1 1.0 SG A:CYS90 2.3 18.4 1.0 SG A:CYS27 2.3 20.4 1.0 CB A:CYS90 3.1 18.1 1.0 CB A:CYS24 3.1 17.4 1.0 CB A:CYS93 3.3 20.3 1.0 CB A:CYS27 3.4 21.3 1.0 N A:CYS93 3.8 20.7 1.0 N A:CYS27 3.9 20.5 1.0 CA A:CYS93 4.1 20.8 1.0 CA A:CYS27 4.2 21.5 1.0 CB A:SER95 4.4 19.4 1.0 CB A:GLN26 4.5 23.0 1.0 CA A:CYS24 4.6 16.9 1.0 CB A:GLN29 4.6 21.9 1.0 CA A:CYS90 4.6 18.1 1.0 C A:GLN26 4.7 22.2 1.0 C A:CYS93 4.7 20.7 1.0 CB A:GLN92 4.7 21.1 1.0 N A:GLY94 4.9 20.3 1.0 N A:SER95 4.9 19.1 1.0 C A:CYS27 4.9 21.4 1.0 CA A:GLN26 4.9 21.4 1.0 C A:GLN92 4.9 21.2 1.0 N A:GLN26 4.9 19.6 1.0 N A:GLY28 4.9 20.4 1.0 C A:CYS24 5.0 17.3 1.0

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


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 7F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:40.8 occ:1.00 SG B:CYS90 2.3 34.9 1.0 SG B:CYS27 2.3 41.9 1.0 SG B:CYS24 2.3 37.5 1.0 SG B:CYS93 2.4 41.8 1.0 CB B:CYS24 3.1 35.5 1.0 CB B:CYS90 3.1 33.1 1.0 CB B:CYS27 3.4 44.1 1.0 CB B:CYS93 3.5 42.9 1.0 N B:CYS93 3.8 40.5 1.0 N B:CYS27 3.9 42.2 1.0 CA B:CYS27 4.1 44.1 1.0 CA B:CYS93 4.2 41.3 1.0 CB B:GLN92 4.5 41.6 1.0 CA B:CYS90 4.5 30.3 1.0 CA B:CYS24 4.6 33.0 1.0 CB B:GLN29 4.6 39.4 1.0 C B:GLN26 4.8 44.8 1.0 C B:CYS27 4.8 43.6 1.0 C B:GLN92 4.8 41.4 1.0 CB B:GLN26 4.8 45.7 1.0 C B:CYS93 4.8 40.2 1.0 N B:GLY28 4.8 41.5 1.0 N B:GLN29 4.9 38.8 1.0 CB B:SER95 4.9 35.1 1.0 N B:GLY94 4.9 37.8 1.0

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


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 7F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.9 occ:1.00 SG C:CYS24 2.3 38.9 1.0 SG C:CYS27 2.3 35.7 1.0 SG C:CYS93 2.3 37.6 1.0 SG C:CYS90 2.3 36.1 1.0 CB C:CYS24 3.2 39.4 1.0 CB C:CYS90 3.2 38.2 1.0 CB C:CYS27 3.3 38.1 1.0 CB C:CYS93 3.4 37.1 1.0 N C:CYS27 3.6 42.0 1.0 N C:CYS93 3.8 35.6 1.0 CA C:CYS27 4.0 40.2 1.0 CA C:CYS93 4.2 37.0 1.0 N C:GLY28 4.4 40.8 1.0 CB C:GLN26 4.4 47.9 1.0 CB C:GLN29 4.4 38.9 1.0 CB C:SER95 4.5 48.3 1.0 C C:CYS27 4.5 40.3 1.0 C C:GLN26 4.6 44.7 1.0 CA C:CYS24 4.6 41.0 1.0 CB C:GLN92 4.6 32.8 1.0 N C:GLN29 4.7 40.2 1.0 CA C:CYS90 4.7 39.0 1.0 C C:CYS93 4.8 39.2 1.0 N C:SER95 4.8 46.2 1.0 N C:GLY94 4.8 40.5 1.0 C C:GLN92 4.9 34.4 1.0 CA C:GLN26 4.9 46.6 1.0 N C:GLN26 4.9 46.4 1.0 CG C:GLN26 5.0 49.2 1.0 C C:CYS24 5.0 42.1 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