Zinc in PDB 6r0s: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product, PDB code: 6r0s 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)	44.12 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.455, 58.824, 88.234, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A and Hydrolysis Product 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 4A and Hydrolysis Product (pdb code 6r0s). 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 4A and Hydrolysis Product, PDB code: 6r0s:
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 4A 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 4A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:17.3 occ:1.00 SG A:CYS24 2.3 16.9 1.0 SG A:CYS27 2.3 17.5 1.0 SG A:CYS93 2.3 17.6 1.0 SG A:CYS90 2.4 16.5 1.0 CB A:CYS24 3.1 16.4 1.0 CB A:CYS90 3.2 16.6 1.0 CB A:CYS93 3.3 17.9 1.0 CB A:CYS27 3.4 18.3 1.0 N A:CYS93 3.8 18.5 1.0 N A:CYS27 3.9 18.5 1.0 CA A:CYS93 4.1 18.3 1.0 CA A:CYS27 4.2 18.8 1.0 CB A:SER95 4.5 18.6 1.0 CB A:GLN26 4.5 22.2 1.0 CA A:CYS24 4.5 16.1 1.0 CB A:GLN29 4.6 19.2 1.0 CA A:CYS90 4.6 16.7 1.0 C A:GLN26 4.7 20.0 1.0 CB A:GLN92 4.7 18.6 1.0 C A:CYS93 4.8 18.1 1.0 C A:CYS27 4.8 19.2 1.0 N A:GLY94 4.9 18.3 1.0 N A:GLY28 4.9 18.5 1.0 C A:GLN92 4.9 18.8 1.0 N A:GLN26 4.9 18.9 1.0 CA A:GLN26 4.9 20.2 1.0 N A:SER95 4.9 17.8 1.0 N A:GLN29 4.9 18.0 1.0 C A:CYS24 5.0 16.9 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A 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 4A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:22.5 occ:1.00 SG B:CYS27 2.3 23.0 1.0 SG B:CYS93 2.3 23.8 1.0 SG B:CYS90 2.3 21.9 1.0 SG B:CYS24 2.4 21.3 1.0 CB B:CYS24 3.2 21.0 1.0 CB B:CYS90 3.2 21.6 1.0 CB B:CYS93 3.3 24.8 1.0 CB B:CYS27 3.4 24.4 1.0 N B:CYS93 3.7 23.1 1.0 N B:CYS27 3.8 25.1 1.0 CA B:CYS93 4.1 24.1 1.0 CA B:CYS27 4.1 24.9 1.0 CB B:GLN92 4.5 22.1 1.0 CA B:CYS90 4.6 20.6 1.0 CA B:CYS24 4.6 19.6 1.0 CB B:GLN26 4.7 29.8 1.0 CB B:SER95 4.7 23.5 1.0 C B:GLN92 4.7 22.7 1.0 C B:GLN26 4.7 27.7 1.0 CB B:GLN29 4.7 26.4 1.0 C B:CYS27 4.7 25.0 1.0 C B:CYS93 4.8 24.5 1.0 N B:GLY28 4.8 23.2 1.0 N B:GLY94 4.9 23.6 1.0 N B:GLN29 4.9 23.6 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 4A 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 4A and Hydrolysis Product within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.1 occ:1.00 SG C:CYS93 2.3 23.7 1.0 SG C:CYS27 2.3 23.3 1.0 SG C:CYS24 2.3 24.6 1.0 SG C:CYS90 2.3 21.9 1.0 CB C:CYS24 3.2 24.3 1.0 CB C:CYS90 3.2 22.1 1.0 CB C:CYS93 3.3 23.4 1.0 CB C:CYS27 3.4 25.5 1.0 N C:CYS93 3.7 22.5 1.0 N C:CYS27 3.8 28.6 1.0 CA C:CYS93 4.1 23.3 1.0 CA C:CYS27 4.2 27.9 1.0 CB C:SER95 4.4 27.7 1.0 CB C:GLN29 4.5 22.9 1.0 CB C:GLN26 4.5 34.9 1.0 CA C:CYS24 4.6 25.8 1.0 CA C:CYS90 4.6 21.8 1.0 CB C:GLN92 4.6 21.2 1.0 C C:GLN26 4.7 32.6 1.0 C C:CYS93 4.7 23.9 1.0 C C:GLN92 4.8 22.3 1.0 N C:GLY94 4.8 24.4 1.0 C C:CYS27 4.8 27.4 1.0 N C:SER95 4.8 25.9 1.0 N C:GLY28 4.8 27.0 1.0 N C:GLN29 4.9 24.3 1.0 N C:GLN26 4.9 32.1 1.0 CA C:GLN26 5.0 33.2 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