Zinc in PDB 5oh4: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidine-2,6-Dione (Glutarimide)

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidine-2,6-Dione (Glutarimide), PDB code: 5oh4 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)	37.10 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.180, 59.661, 88.289, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidine-2,6-Dione (Glutarimide) (pdb code 5oh4). 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 Piperidine-2,6-Dione (Glutarimide), PDB code: 5oh4:
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 Piperidine-2,6-Dione (Glutarimide)


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 Piperidine-2,6-Dione (Glutarimide) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:26.8 occ:1.00 SG A:CYS93 2.2 27.4 1.0 SG A:CYS24 2.3 25.5 1.0 SG A:CYS27 2.3 30.0 1.0 SG A:CYS90 2.4 23.6 1.0 CB A:CYS24 3.1 22.6 1.0 CB A:CYS90 3.2 26.2 1.0 CB A:CYS93 3.3 29.0 1.0 CB A:CYS27 3.5 28.8 1.0 N A:CYS93 3.7 28.3 1.0 N A:CYS27 4.0 28.6 1.0 CA A:CYS93 4.1 28.9 1.0 CA A:CYS27 4.3 28.8 1.0 CB A:GLN26 4.4 38.2 1.0 CA A:CYS24 4.6 22.9 1.0 CB A:SER95 4.6 30.9 1.0 CB A:GLN92 4.6 26.5 1.0 CB A:GLN29 4.6 25.5 0.5 CB A:GLN29 4.6 25.6 0.5 CA A:CYS90 4.6 26.0 1.0 C A:GLN26 4.7 31.8 1.0 C A:CYS93 4.8 28.9 1.0 C A:GLN92 4.8 28.6 1.0 N A:GLN26 4.9 33.3 1.0 N A:GLY28 4.9 26.5 1.0 C A:CYS27 4.9 26.8 1.0 CA A:GLN26 4.9 35.2 1.0 N A:GLY94 5.0 28.8 1.0 N A:SER95 5.0 28.6 1.0 C A:CYS24 5.0 25.2 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidine-2,6-Dione (Glutarimide)


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 Piperidine-2,6-Dione (Glutarimide) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.1 occ:1.00 SG B:CYS93 2.3 31.8 1.0 SG B:CYS27 2.3 33.4 1.0 SG B:CYS90 2.3 36.2 1.0 SG B:CYS24 2.4 31.5 1.0 CB B:CYS90 3.2 33.5 1.0 CB B:CYS24 3.2 32.4 1.0 CB B:CYS93 3.3 33.5 1.0 CB B:CYS27 3.4 36.4 1.0 N B:CYS93 3.7 32.1 1.0 N B:CYS27 3.9 37.2 1.0 CA B:CYS93 4.0 33.9 1.0 CA B:CYS27 4.2 36.7 1.0 CB B:GLN92 4.5 34.9 1.0 CB B:GLN29 4.6 40.9 1.0 CA B:CYS90 4.6 31.8 1.0 CA B:CYS24 4.7 31.2 1.0 CB B:GLN26 4.7 44.2 1.0 C B:GLN92 4.7 33.9 1.0 CB B:SER95 4.7 31.6 1.0 C B:GLN26 4.8 41.1 1.0 C B:CYS27 4.8 36.0 1.0 C B:CYS93 4.8 33.0 1.0 N B:GLY28 4.8 34.3 1.0 OE1 B:GLN26 4.9 57.5 1.0 N B:GLN29 5.0 36.5 1.0 CA B:GLN92 5.0 34.1 1.0 N B:GLY94 5.0 31.7 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidine-2,6-Dione (Glutarimide)


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 Piperidine-2,6-Dione (Glutarimide) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:39.7 occ:1.00 SG C:CYS93 2.2 43.0 1.0 SG C:CYS27 2.3 41.6 1.0 SG C:CYS90 2.4 37.7 1.0 SG C:CYS24 2.4 43.0 1.0 CB C:CYS90 3.2 38.7 1.0 CB C:CYS24 3.2 41.9 1.0 CB C:CYS93 3.3 41.6 1.0 CB C:CYS27 3.3 47.2 1.0 N C:CYS93 3.6 41.0 1.0 N C:CYS27 3.9 50.8 1.0 CA C:CYS93 4.0 41.3 1.0 CA C:CYS27 4.2 49.0 1.0 CB C:GLN92 4.5 39.2 1.0 CB C:GLN26 4.5 53.8 1.0 CB C:GLN29 4.6 40.7 1.0 CB C:SER95 4.6 45.0 1.0 CA C:CYS24 4.7 43.0 1.0 C C:GLN92 4.7 40.4 1.0 CA C:CYS90 4.7 37.7 1.0 C C:GLN26 4.7 53.5 1.0 C C:CYS93 4.7 40.4 1.0 C C:CYS27 4.8 46.5 1.0 N C:GLY28 4.8 45.3 1.0 N C:GLY94 4.9 40.7 1.0 N C:SER95 5.0 43.1 1.0 N C:GLN29 5.0 40.8 1.0 N C:GLN26 5.0 51.3 1.0 CA C:GLN92 5.0 39.3 1.0 CA C:GLN26 5.0 53.2 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