Zinc in PDB 6r1w: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 16B

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 16B, PDB code: 6r1w 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)	47.62 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.534, 59.441, 88.359, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.8

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 16B (pdb code 6r1w). 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 16B, PDB code: 6r1w:
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 16B


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 16B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:11.8 occ:1.00 SG A:CYS24 2.3 11.6 1.0 SG A:CYS27 2.3 12.7 1.0 SG A:CYS93 2.3 12.4 1.0 SG A:CYS90 2.4 11.2 1.0 CB A:CYS24 3.1 10.3 1.0 CB A:CYS90 3.2 10.0 1.0 CB A:CYS93 3.3 11.9 1.0 CB A:CYS27 3.4 13.0 1.0 N A:CYS93 3.8 12.2 1.0 N A:CYS27 3.9 14.0 1.0 CA A:CYS93 4.0 12.2 1.0 CA A:CYS27 4.2 14.2 1.0 CB A:SER95 4.5 13.8 1.0 CB A:GLN26 4.5 17.1 1.0 CB A:GLN29 4.5 10.9 0.5 CA A:CYS24 4.5 10.4 1.0 C A:GLN26 4.6 16.5 1.0 CA A:CYS90 4.6 10.8 1.0 CB A:GLN29 4.6 12.3 0.5 C A:CYS93 4.7 12.7 1.0 CB A:GLN92 4.8 12.3 1.0 N A:GLY94 4.8 12.1 1.0 C A:CYS27 4.8 14.5 1.0 N A:GLN26 4.9 13.2 1.0 C A:GLN92 4.9 12.4 1.0 CA A:GLN26 4.9 15.0 1.0 N A:SER95 4.9 12.4 1.0 N A:GLY28 4.9 12.9 1.0 C A:CYS24 4.9 11.0 1.0 N A:GLN29 5.0 12.2 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 16B


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 16B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.4 occ:1.00 SG B:CYS90 2.3 14.4 1.0 SG B:CYS27 2.3 16.5 1.0 SG B:CYS24 2.3 14.8 1.0 SG B:CYS93 2.4 17.1 1.0 CB B:CYS90 3.2 14.3 1.0 CB B:CYS24 3.2 13.3 1.0 CB B:CYS93 3.3 17.4 1.0 CB B:CYS27 3.4 16.8 1.0 N B:CYS27 3.7 16.2 1.0 N B:CYS93 3.8 16.0 1.0 CA B:CYS27 4.0 16.6 1.0 CA B:CYS93 4.1 16.3 1.0 CA B:CYS90 4.6 13.2 1.0 C B:GLN26 4.7 19.2 1.0 CA B:CYS24 4.7 12.4 1.0 CB B:GLN92 4.7 15.7 1.0 CB B:SER95 4.7 16.9 1.0 CB B:GLN26 4.7 20.8 1.0 C B:CYS27 4.7 16.1 1.0 C B:GLN92 4.8 15.8 1.0 CB B:GLN29 4.8 18.3 1.0 C B:CYS93 4.8 16.3 1.0 N B:GLY28 4.8 14.8 1.0 N B:GLY94 4.9 15.6 1.0 N B:GLN29 5.0 15.9 1.0 N B:SER95 5.0 15.5 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 16B


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 16B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:15.7 occ:1.00 SG C:CYS93 2.3 16.4 1.0 SG C:CYS27 2.3 16.6 1.0 SG C:CYS24 2.3 15.8 1.0 SG C:CYS90 2.3 14.7 1.0 CB C:CYS24 3.1 14.7 1.0 CB C:CYS90 3.2 15.2 1.0 CB C:CYS93 3.3 15.1 1.0 CB C:CYS27 3.4 18.8 1.0 N C:CYS93 3.8 14.1 1.0 N C:CYS27 3.8 20.0 1.0 CA C:CYS93 4.1 15.7 1.0 CA C:CYS27 4.1 20.1 1.0 CB C:GLN29 4.4 16.1 1.0 CB C:SER95 4.5 18.0 1.0 CB C:GLN26 4.5 26.0 1.0 CA C:CYS24 4.6 16.1 1.0 CA C:CYS90 4.6 14.1 1.0 CB C:GLN92 4.7 14.0 1.0 C C:CYS93 4.7 15.5 1.0 C C:GLN26 4.7 25.5 1.0 C C:GLN92 4.8 15.2 1.0 C C:CYS27 4.8 21.4 1.0 N C:GLY94 4.8 16.2 1.0 N C:GLY28 4.8 19.2 1.0 N C:SER95 4.9 17.1 1.0 N C:GLN29 4.9 16.4 1.0 CA C:GLN26 5.0 24.1 1.0 N C:GLN26 5.0 22.9 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