Zinc in PDB 6r1c: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 12A

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 12A, PDB code: 6r1c 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)	49.12 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.656, 59.020, 88.593, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.5

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 12A 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 12A (pdb code 6r1c). 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 12A, PDB code: 6r1c:
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 12A


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 12A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:11.2 occ:1.00 SG A:CYS27 2.3 11.3 1.0 SG A:CYS24 2.3 11.0 1.0 SG A:CYS93 2.3 11.6 1.0 SG A:CYS90 2.4 10.4 1.0 CB A:CYS24 3.1 10.8 1.0 CB A:CYS90 3.2 10.4 1.0 CB A:CYS93 3.3 11.9 1.0 CB A:CYS27 3.4 12.4 1.0 N A:CYS93 3.8 12.0 1.0 N A:CYS27 3.8 13.0 1.0 CA A:CYS93 4.1 12.3 1.0 CA A:CYS27 4.2 12.8 1.0 CB A:SER95 4.5 12.8 1.0 CB A:GLN26 4.5 15.8 1.0 CA A:CYS24 4.5 10.6 1.0 CB A:GLN29 4.5 12.3 0.5 CB A:GLN29 4.6 12.8 0.5 CA A:CYS90 4.6 10.6 1.0 C A:GLN26 4.7 14.5 1.0 CB A:GLN92 4.7 12.3 1.0 C A:CYS93 4.8 12.4 1.0 C A:CYS27 4.8 13.0 1.0 N A:GLY94 4.9 12.1 1.0 N A:GLY28 4.9 12.5 1.0 C A:GLN92 4.9 12.4 1.0 N A:SER95 4.9 12.3 1.0 CA A:GLN26 4.9 14.4 1.0 N A:GLN26 4.9 13.0 1.0 C A:CYS24 4.9 10.8 1.0 N A:GLN29 5.0 12.4 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 12A


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 12A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:16.5 occ:1.00 SG B:CYS90 2.3 15.0 1.0 SG B:CYS93 2.3 18.5 1.0 SG B:CYS27 2.3 17.6 1.0 SG B:CYS24 2.4 15.5 1.0 CB B:CYS90 3.2 14.6 1.0 CB B:CYS24 3.2 15.6 1.0 CB B:CYS93 3.3 18.7 1.0 CB B:CYS27 3.4 19.1 1.0 N B:CYS93 3.7 17.8 1.0 N B:CYS27 3.8 20.1 1.0 CA B:CYS93 4.1 18.4 1.0 CA B:CYS27 4.1 19.5 1.0 CB B:GLN92 4.6 17.8 1.0 CA B:CYS90 4.6 14.2 1.0 CA B:CYS24 4.6 15.2 1.0 CB B:SER95 4.7 17.2 1.0 C B:GLN26 4.7 22.5 1.0 CB B:GLN26 4.7 24.4 1.0 CB B:GLN29 4.7 19.5 1.0 C B:GLN92 4.7 17.9 1.0 C B:CYS27 4.7 19.1 1.0 C B:CYS93 4.8 18.3 1.0 N B:GLY28 4.8 17.7 1.0 N B:GLY94 4.9 17.4 1.0 N B:GLN29 4.9 17.5 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 12A


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 12A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:17.8 occ:1.00 SG C:CYS24 2.3 20.1 1.0 SG C:CYS93 2.3 18.5 1.0 SG C:CYS27 2.3 17.4 1.0 SG C:CYS90 2.3 17.1 1.0 CB C:CYS90 3.1 17.6 1.0 CB C:CYS24 3.2 21.0 1.0 CB C:CYS93 3.3 18.0 1.0 CB C:CYS27 3.4 19.8 1.0 N C:CYS93 3.8 16.5 1.0 N C:CYS27 3.8 23.7 1.0 CA C:CYS93 4.1 17.8 1.0 CA C:CYS27 4.2 22.1 1.0 CB C:SER95 4.4 23.6 1.0 CB C:GLN29 4.5 18.6 1.0 CA C:CYS90 4.6 17.3 1.0 CB C:GLN26 4.6 31.1 1.0 CA C:CYS24 4.6 22.6 1.0 CB C:GLN92 4.7 15.2 1.0 C C:GLN26 4.7 27.2 1.0 C C:CYS93 4.7 18.4 1.0 C C:GLN92 4.8 16.3 1.0 N C:GLY94 4.8 18.9 1.0 C C:CYS27 4.8 22.0 1.0 N C:SER95 4.8 21.4 1.0 N C:GLY28 4.8 21.8 1.0 N C:GLN29 4.9 19.9 1.0 N C:GLN26 5.0 28.6 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