Zinc in PDB 6r11: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5B, PDB code: 6r11 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)	47.64 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.660, 58.709, 88.013, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.7

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5B 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 5B (pdb code 6r11). 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 5B, PDB code: 6r11:
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 5B


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 5B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.7 occ:1.00 SG A:CYS24 2.3 22.6 1.0 SG A:CYS93 2.3 24.8 1.0 SG A:CYS27 2.3 25.1 1.0 SG A:CYS90 2.3 23.5 1.0 CB A:CYS24 3.2 22.2 1.0 CB A:CYS90 3.2 23.9 1.0 CB A:CYS93 3.3 25.9 1.0 CB A:CYS27 3.4 26.8 1.0 N A:CYS93 3.9 25.1 1.0 N A:CYS27 3.9 26.4 1.0 CA A:CYS93 4.1 26.5 1.0 CA A:CYS27 4.2 27.3 1.0 CB A:GLN26 4.5 30.8 1.0 CB A:SER95 4.5 26.2 1.0 CA A:CYS24 4.6 22.0 1.0 CB A:GLN29 4.6 25.6 0.5 CA A:CYS90 4.6 23.6 1.0 C A:GLN26 4.7 29.3 1.0 CB A:GLN92 4.7 25.9 1.0 CB A:GLN29 4.7 26.9 0.5 C A:CYS93 4.8 26.6 1.0 C A:CYS27 4.9 27.6 1.0 CA A:GLN26 4.9 28.8 1.0 N A:GLY94 4.9 26.2 1.0 N A:SER95 4.9 23.9 1.0 N A:GLN26 4.9 25.6 1.0 C A:GLN92 4.9 25.8 1.0 N A:GLY28 4.9 25.8 1.0 N A:GLN29 5.0 25.4 1.0 C A:CYS24 5.0 24.0 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5B


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 5B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:41.1 occ:1.00 SG B:CYS90 2.3 39.5 1.0 SG B:CYS27 2.3 43.5 1.0 SG B:CYS24 2.3 38.7 1.0 SG B:CYS93 2.4 42.7 1.0 CB B:CYS24 3.1 37.2 1.0 CB B:CYS90 3.1 38.5 1.0 CB B:CYS27 3.4 45.1 1.0 CB B:CYS93 3.4 45.3 1.0 N B:CYS93 3.8 41.7 1.0 N B:CYS27 3.9 42.8 1.0 CA B:CYS93 4.1 43.0 1.0 CA B:CYS27 4.1 44.6 1.0 CB B:GLN92 4.5 41.3 1.0 CA B:CYS90 4.5 35.0 1.0 CA B:CYS24 4.5 33.4 1.0 CB B:GLN29 4.7 43.5 1.0 C B:GLN92 4.8 41.5 1.0 C B:CYS27 4.8 44.2 1.0 C B:GLN26 4.8 47.2 1.0 C B:CYS93 4.8 43.2 1.0 CB B:GLN26 4.8 49.4 1.0 N B:GLY28 4.8 41.6 1.0 N B:GLN29 4.9 40.4 1.0 N B:GLY94 4.9 41.9 1.0 CB B:SER95 5.0 37.1 1.0 CA B:GLN92 5.0 40.7 1.0 N B:GLN92 5.0 38.2 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 5B


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 5B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:35.6 occ:1.00 SG C:CYS24 2.3 36.9 1.0 SG C:CYS93 2.3 38.2 1.0 SG C:CYS27 2.3 35.9 1.0 SG C:CYS90 2.3 35.5 1.0 CB C:CYS90 3.1 36.6 1.0 CB C:CYS24 3.2 37.8 1.0 CB C:CYS93 3.4 37.4 1.0 CB C:CYS27 3.5 39.8 1.0 N C:CYS93 3.8 36.2 1.0 N C:CYS27 3.8 44.4 1.0 CA C:CYS93 4.1 36.6 1.0 CA C:CYS27 4.2 42.5 1.0 CB C:SER95 4.4 45.3 1.0 CB C:GLN29 4.5 34.0 1.0 CB C:GLN26 4.5 53.1 1.0 CA C:CYS90 4.6 35.7 1.0 CB C:GLN92 4.6 31.0 1.0 CA C:CYS24 4.6 38.8 1.0 C C:GLN26 4.7 49.5 1.0 C C:CYS93 4.8 38.6 1.0 C C:CYS27 4.8 40.0 1.0 N C:GLY28 4.8 39.6 1.0 N C:SER95 4.8 42.4 1.0 C C:GLN92 4.8 33.4 1.0 N C:GLN29 4.9 37.5 1.0 N C:GLY94 4.9 39.0 1.0 N C:GLN26 4.9 48.0 1.0 CA C:GLN26 4.9 49.5 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