Zinc in PDB 6r0u: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product, PDB code: 6r0u 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)	47.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.952, 59.583, 89.053, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product 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 5A and Hydrolysis Product (pdb code 6r0u). 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 5A and Hydrolysis Product, PDB code: 6r0u:
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 5A and Hydrolysis Product


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 5A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:21.6 occ:1.00 SG A:CYS24 2.3 20.7 1.0 SG A:CYS27 2.3 21.8 1.0 SG A:CYS93 2.3 21.1 1.0 SG A:CYS90 2.3 19.9 1.0 CB A:CYS24 3.1 21.5 1.0 CB A:CYS90 3.1 19.2 1.0 CB A:CYS93 3.3 21.9 1.0 CB A:CYS27 3.5 22.6 1.0 N A:CYS93 3.9 22.7 1.0 N A:CYS27 3.9 23.4 1.0 CA A:CYS93 4.1 22.9 1.0 CA A:CYS27 4.2 23.6 1.0 CB A:SER95 4.5 22.7 1.0 CB A:GLN29 4.5 23.7 1.0 CB A:GLN26 4.5 27.9 1.0 CA A:CYS24 4.5 20.2 1.0 CA A:CYS90 4.6 19.2 1.0 C A:GLN26 4.6 26.2 1.0 CB A:GLN92 4.7 21.7 1.0 C A:CYS93 4.8 23.6 1.0 N A:GLY94 4.9 22.7 1.0 C A:CYS27 4.9 24.4 1.0 N A:SER95 4.9 21.8 1.0 CA A:GLN26 4.9 25.9 1.0 N A:GLN26 4.9 22.4 1.0 N A:GLY28 4.9 24.1 1.0 C A:GLN92 4.9 22.9 1.0 C A:CYS24 5.0 20.3 1.0 N A:GLN29 5.0 22.4 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product


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 5A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:35.5 occ:1.00 SG B:CYS90 2.3 31.3 1.0 SG B:CYS27 2.3 35.7 1.0 SG B:CYS24 2.3 33.6 1.0 SG B:CYS93 2.4 35.2 1.0 CB B:CYS90 3.1 30.7 1.0 CB B:CYS24 3.2 33.0 1.0 CB B:CYS27 3.3 38.0 1.0 CB B:CYS93 3.5 36.8 1.0 N B:CYS93 3.8 33.9 1.0 N B:CYS27 3.8 38.4 1.0 CA B:CYS27 4.1 37.7 1.0 CA B:CYS93 4.2 35.6 1.0 CB B:GLN92 4.5 36.4 1.0 CA B:CYS90 4.5 26.9 1.0 CB B:GLN29 4.7 38.5 1.0 CA B:CYS24 4.7 30.2 1.0 C B:GLN26 4.7 43.2 1.0 C B:CYS27 4.7 36.9 1.0 C B:GLN92 4.8 35.4 1.0 CB B:GLN26 4.8 46.0 1.0 C B:CYS93 4.8 34.6 1.0 N B:GLY28 4.9 36.5 1.0 N B:GLN29 4.9 35.0 1.0 N B:GLY94 4.9 34.0 1.0 CB B:SER95 5.0 34.3 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5A and Hydrolysis Product


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 5A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:28.9 occ:1.00 SG C:CYS93 2.3 30.7 1.0 SG C:CYS27 2.3 27.9 1.0 SG C:CYS90 2.3 28.9 1.0 SG C:CYS24 2.3 30.0 1.0 CB C:CYS90 3.1 28.9 1.0 CB C:CYS24 3.2 32.5 1.0 CB C:CYS93 3.3 30.9 1.0 CB C:CYS27 3.4 31.2 1.0 N C:CYS93 3.8 29.3 1.0 N C:CYS27 3.8 34.4 1.0 CA C:CYS93 4.1 31.2 1.0 CA C:CYS27 4.2 32.2 1.0 CB C:GLN29 4.4 28.1 1.0 CB C:SER95 4.5 37.4 1.0 CA C:CYS90 4.6 28.0 1.0 CA C:CYS24 4.6 32.4 1.0 CB C:GLN92 4.6 26.1 1.0 CB C:GLN26 4.6 42.5 1.0 C C:GLN26 4.7 39.8 1.0 C C:CYS93 4.7 33.4 1.0 N C:GLY94 4.8 31.4 1.0 C C:CYS27 4.8 31.9 1.0 N C:SER95 4.8 36.7 1.0 N C:GLN29 4.8 30.2 1.0 C C:GLN92 4.8 26.1 1.0 N C:GLY28 4.9 31.4 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