Zinc in PDB 6r0v: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Hydrolysis Product of Compound 4B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Hydrolysis Product of Compound 4B, PDB code: 6r0v 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)	47.78 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.747, 58.815, 88.568, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.9

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Hydrolysis Product of Compound 4B 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 Hydrolysis Product of Compound 4B (pdb code 6r0v). 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 Hydrolysis Product of Compound 4B, PDB code: 6r0v:
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 Hydrolysis Product of Compound 4B


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 Hydrolysis Product of Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.9 occ:1.00 SG A:CYS24 2.3 17.7 1.0 SG A:CYS93 2.3 19.3 1.0 SG A:CYS90 2.3 18.7 1.0 SG A:CYS27 2.3 19.5 1.0 CB A:CYS24 3.1 17.4 1.0 CB A:CYS90 3.2 18.0 1.0 CB A:CYS93 3.3 20.3 1.0 CB A:CYS27 3.4 20.2 1.0 N A:CYS93 3.8 20.5 1.0 N A:CYS27 3.9 20.4 1.0 CA A:CYS93 4.1 20.4 1.0 CA A:CYS27 4.2 20.9 1.0 CB A:GLN26 4.5 24.1 1.0 CB A:SER95 4.5 19.8 1.0 CB A:GLN29 4.6 20.7 0.4 CA A:CYS24 4.6 17.0 1.0 CA A:CYS90 4.6 17.9 1.0 CB A:GLN29 4.6 22.0 0.6 C A:GLN26 4.7 22.7 1.0 CB A:GLN92 4.7 20.6 1.0 C A:CYS93 4.7 20.2 1.0 C A:CYS27 4.8 21.4 1.0 N A:GLY94 4.9 19.9 1.0 N A:SER95 4.9 19.1 1.0 C A:GLN92 4.9 20.2 1.0 N A:GLY28 4.9 20.5 1.0 CA A:GLN26 4.9 21.9 1.0 N A:GLN26 4.9 19.6 1.0 C A:CYS24 5.0 17.8 1.0 N A:GLN29 5.0 21.0 1.0

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


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 Hydrolysis Product of Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:35.1 occ:1.00 SG B:CYS27 2.3 37.1 1.0 SG B:CYS90 2.3 30.1 1.0 SG B:CYS93 2.3 35.8 1.0 SG B:CYS24 2.4 31.6 1.0 CB B:CYS24 3.2 30.9 1.0 CB B:CYS27 3.3 38.8 1.0 CB B:CYS90 3.3 29.9 1.0 CB B:CYS93 3.3 37.7 1.0 N B:CYS27 3.7 36.6 1.0 N B:CYS93 3.8 34.7 1.0 CA B:CYS27 4.0 38.6 1.0 CA B:CYS93 4.1 36.3 1.0 CB B:GLN92 4.5 35.0 1.0 CA B:CYS24 4.6 28.7 1.0 C B:GLN26 4.6 38.8 1.0 CB B:GLN26 4.7 40.0 1.0 CB B:GLN29 4.7 35.2 1.0 C B:CYS27 4.7 37.9 1.0 CA B:CYS90 4.7 27.2 1.0 C B:GLN92 4.7 35.0 1.0 N B:GLY28 4.8 35.4 1.0 C B:CYS93 4.8 35.8 1.0 N B:GLN29 4.9 33.8 1.0 N B:GLY94 5.0 33.6 1.0 CB B:SER95 5.0 31.8 1.0

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


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 Hydrolysis Product of Compound 4B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:28.2 occ:1.00 SG C:CYS93 2.3 29.8 1.0 SG C:CYS24 2.3 27.9 1.0 SG C:CYS27 2.3 27.5 1.0 SG C:CYS90 2.4 28.7 1.0 CB C:CYS90 3.1 29.4 1.0 CB C:CYS24 3.2 28.4 1.0 CB C:CYS93 3.3 29.8 1.0 CB C:CYS27 3.5 30.1 1.0 N C:CYS93 3.8 28.4 1.0 N C:CYS27 3.9 31.6 1.0 CA C:CYS93 4.1 30.2 1.0 CA C:CYS27 4.2 31.5 1.0 CB C:SER95 4.4 35.1 1.0 CB C:GLN26 4.5 38.3 1.0 CB C:GLN29 4.5 27.9 1.0 CA C:CYS90 4.6 29.1 1.0 CA C:CYS24 4.6 29.0 1.0 CB C:GLN92 4.7 26.4 1.0 C C:CYS93 4.7 32.3 1.0 C C:GLN26 4.8 35.8 1.0 N C:SER95 4.8 34.9 1.0 N C:GLY94 4.8 33.2 1.0 C C:GLN92 4.8 28.0 1.0 C C:CYS27 4.8 31.3 1.0 N C:GLY28 4.9 30.1 1.0 N C:GLN29 5.0 28.7 1.0 CA C:GLN26 5.0 35.8 1.0 N C:GLN26 5.0 35.4 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