Zinc in PDB 5oh9: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thiazolidine-2,4-Dione

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thiazolidine-2,4-Dione, PDB code: 5oh9 was solved by I.Boichenko, R.Albrecht, A.N.Lupas, B.Hernandez Alvarez, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.30 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.548, 59.914, 88.562, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thiazolidine-2,4-Dione (pdb code 5oh9). 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 Thiazolidine-2,4-Dione, PDB code: 5oh9:
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 Thiazolidine-2,4-Dione


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 Thiazolidine-2,4-Dione within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.6 occ:1.00 SG A:CYS24 2.3 17.9 1.0 SG A:CYS93 2.3 20.4 1.0 SG A:CYS27 2.3 19.1 1.0 SG A:CYS90 2.4 17.8 1.0 CB A:CYS24 3.1 18.3 1.0 CB A:CYS90 3.1 17.1 1.0 CB A:CYS93 3.3 19.7 1.0 CB A:CYS27 3.4 19.6 1.0 N A:CYS93 3.8 18.9 1.0 N A:CYS27 3.9 19.3 1.0 CA A:CYS93 4.1 19.8 1.0 CA A:CYS27 4.3 21.3 1.0 CB A:GLN29 4.4 17.1 0.5 CB A:SER95 4.5 22.7 1.0 CB A:GLN26 4.5 26.8 1.0 CA A:CYS24 4.6 16.6 1.0 CA A:CYS90 4.6 17.0 1.0 C A:GLN26 4.6 23.6 1.0 CB A:GLN29 4.6 18.7 0.5 CB A:GLN92 4.7 19.2 1.0 C A:CYS93 4.7 21.1 1.0 N A:GLY94 4.9 19.7 1.0 C A:GLN92 4.9 19.4 1.0 CA A:GLN26 4.9 23.8 1.0 N A:SER95 4.9 19.4 1.0 N A:GLN26 4.9 21.7 1.0 N A:GLY28 4.9 18.6 1.0 C A:CYS27 4.9 21.0 1.0 N A:GLN29 5.0 18.5 1.0 C A:CYS24 5.0 16.3 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thiazolidine-2,4-Dione


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 Thiazolidine-2,4-Dione within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:25.1 occ:1.00 SG B:CYS27 2.3 26.2 1.0 SG B:CYS90 2.3 22.8 1.0 SG B:CYS93 2.3 27.1 1.0 SG B:CYS24 2.4 24.7 1.0 CB B:CYS90 3.1 22.1 1.0 CB B:CYS24 3.2 24.1 1.0 CB B:CYS93 3.3 29.1 1.0 CB B:CYS27 3.3 28.7 1.0 N B:CYS27 3.7 28.4 1.0 N B:CYS93 3.8 26.1 1.0 CA B:CYS27 4.1 28.3 1.0 CA B:CYS93 4.1 28.3 1.0 CB B:GLN92 4.6 25.4 1.0 CA B:CYS90 4.6 21.1 1.0 CB B:GLN26 4.6 33.2 1.0 CA B:CYS24 4.7 21.7 1.0 CB B:SER95 4.7 24.2 1.0 C B:GLN26 4.7 30.6 1.0 C B:CYS27 4.7 27.9 1.0 CB B:GLN29 4.8 29.3 1.0 C B:CYS93 4.8 27.9 1.0 C B:GLN92 4.8 26.8 1.0 N B:GLY28 4.8 25.8 1.0 N B:GLY94 4.9 25.9 1.0 N B:GLN29 5.0 26.6 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thiazolidine-2,4-Dione


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 Thiazolidine-2,4-Dione within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:25.0 occ:1.00 SG C:CYS27 2.3 24.6 1.0 SG C:CYS93 2.3 29.4 1.0 SG C:CYS24 2.3 25.7 1.0 SG C:CYS90 2.4 23.6 1.0 CB C:CYS24 3.1 25.7 1.0 CB C:CYS90 3.2 23.4 1.0 CB C:CYS93 3.3 27.9 1.0 CB C:CYS27 3.4 28.3 1.0 N C:CYS93 3.8 25.2 1.0 N C:CYS27 3.8 30.6 1.0 CA C:CYS93 4.1 27.1 1.0 CA C:CYS27 4.1 30.2 1.0 CB C:GLN29 4.4 23.4 1.0 CB C:SER95 4.5 29.8 1.0 CB C:GLN26 4.6 35.1 1.0 CA C:CYS24 4.6 26.2 1.0 CA C:CYS90 4.6 23.8 1.0 CB C:GLN92 4.6 23.5 1.0 C C:GLN26 4.7 33.3 1.0 C C:CYS27 4.7 31.1 1.0 C C:CYS93 4.7 28.1 1.0 N C:GLY28 4.8 28.5 1.0 C C:GLN92 4.8 25.4 1.0 N C:GLN29 4.8 25.8 1.0 N C:GLY94 4.8 27.6 1.0 N C:SER95 4.9 28.1 1.0

I.Boichenko, K.Bar, S.Deiss, C.Heim, R.Albrecht, A.N.Lupas, B.Hernandez Alvarez, M.D.Hartmann. Chemical Ligand Space of Cereblon. Acs Omega V. 3 11163 2018.
ISSN: ESSN 2470-1343
PubMed: 31459225
DOI: 10.1021/ACSOMEGA.8B00959