Zinc in PDB 5ohb: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidin-2-One (Valerolactam)

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidin-2-One (Valerolactam), PDB code: 5ohb 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)	37.20 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.517, 59.630, 88.557, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 21.2

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidin-2-One (Valerolactam) (pdb code 5ohb). 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 Piperidin-2-One (Valerolactam), PDB code: 5ohb:
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 Piperidin-2-One (Valerolactam)


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 Piperidin-2-One (Valerolactam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:21.4 occ:1.00 SG A:CYS24 2.3 20.5 1.0 SG A:CYS93 2.3 23.0 1.0 SG A:CYS27 2.3 21.4 1.0 SG A:CYS90 2.3 20.0 1.0 CB A:CYS24 3.1 19.5 1.0 CB A:CYS90 3.1 20.1 1.0 CB A:CYS93 3.3 22.1 1.0 CB A:CYS27 3.4 22.2 1.0 N A:CYS93 3.8 21.6 1.0 N A:CYS27 3.9 22.5 1.0 CA A:CYS93 4.1 22.6 1.0 CA A:CYS27 4.2 24.7 1.0 CB A:GLN29 4.4 18.5 0.5 CB A:GLN26 4.5 29.0 1.0 CB A:SER95 4.5 28.2 1.0 CA A:CYS24 4.6 19.5 1.0 C A:GLN26 4.6 27.0 1.0 CA A:CYS90 4.6 20.0 1.0 CB A:GLN29 4.7 20.6 0.5 CB A:GLN92 4.7 21.8 1.0 C A:CYS93 4.8 23.8 1.0 N A:GLY94 4.9 22.8 1.0 CA A:GLN26 4.9 25.9 1.0 N A:GLN26 4.9 22.6 1.0 C A:GLN92 4.9 21.7 1.0 C A:CYS27 4.9 23.5 1.0 N A:GLY28 4.9 21.1 1.0 C A:CYS24 5.0 19.3 1.0 N A:SER95 5.0 22.2 1.0 N A:GLN29 5.0 19.7 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidin-2-One (Valerolactam)


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 Piperidin-2-One (Valerolactam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:28.7 occ:1.00 SG B:CYS90 2.3 25.9 1.0 SG B:CYS93 2.3 31.1 1.0 SG B:CYS24 2.4 27.0 1.0 SG B:CYS27 2.4 30.9 1.0 CB B:CYS90 3.1 25.6 1.0 CB B:CYS24 3.2 28.2 1.0 CB B:CYS93 3.3 33.3 1.0 CB B:CYS27 3.3 31.9 1.0 N B:CYS27 3.8 30.1 1.0 N B:CYS93 3.8 28.7 1.0 CA B:CYS27 4.1 30.9 1.0 CA B:CYS93 4.1 32.2 1.0 CA B:CYS90 4.6 23.3 1.0 CB B:GLN92 4.6 28.9 1.0 CA B:CYS24 4.7 24.3 1.0 CB B:GLN26 4.7 36.5 1.0 C B:GLN26 4.7 32.6 1.0 CB B:SER95 4.7 30.7 1.0 C B:CYS27 4.7 30.9 1.0 C B:CYS93 4.8 32.3 1.0 C B:GLN92 4.8 29.5 1.0 CB B:GLN29 4.8 33.5 1.0 N B:GLY28 4.8 28.1 1.0 N B:GLY94 4.9 29.9 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Piperidin-2-One (Valerolactam)


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 Piperidin-2-One (Valerolactam) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:29.3 occ:1.00 SG C:CYS93 2.2 32.8 1.0 SG C:CYS27 2.3 29.1 1.0 SG C:CYS24 2.4 31.2 1.0 SG C:CYS90 2.4 28.2 1.0 CB C:CYS24 3.1 30.4 1.0 CB C:CYS90 3.2 28.4 1.0 CB C:CYS27 3.3 32.9 1.0 CB C:CYS93 3.3 33.0 1.0 N C:CYS93 3.8 28.9 1.0 N C:CYS27 3.8 36.4 1.0 CA C:CYS93 4.1 30.6 1.0 CA C:CYS27 4.1 34.8 1.0 CB C:GLN29 4.4 27.0 1.0 CB C:GLN26 4.5 42.2 1.0 CB C:SER95 4.5 34.9 1.0 CB C:GLN92 4.6 27.2 1.0 CA C:CYS24 4.6 31.2 1.0 CA C:CYS90 4.6 28.5 1.0 N C:GLY28 4.7 31.9 1.0 C C:GLN26 4.7 41.0 1.0 C C:CYS93 4.7 32.8 1.0 C C:CYS27 4.7 34.6 1.0 C C:GLN92 4.8 29.4 1.0 N C:GLN29 4.8 29.2 1.0 N C:SER95 4.8 32.6 1.0 N C:GLY94 4.9 32.2 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