Zinc in PDB 5oh2: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pyrrolidin-2-One (Butyrolactam)

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pyrrolidin-2-One (Butyrolactam), PDB code: 5oh2 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)	37.40 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.911, 59.686, 88.443, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.5

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pyrrolidin-2-One (Butyrolactam) (pdb code 5oh2). 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 Pyrrolidin-2-One (Butyrolactam), PDB code: 5oh2:
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 Pyrrolidin-2-One (Butyrolactam)


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 Pyrrolidin-2-One (Butyrolactam) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:21.9 occ:1.00 SG A:CYS24 2.3 21.1 1.0 SG A:CYS93 2.3 23.9 1.0 SG A:CYS27 2.3 22.6 1.0 SG A:CYS90 2.4 20.9 1.0 CB A:CYS90 3.1 20.6 1.0 CB A:CYS24 3.2 20.3 1.0 CB A:CYS93 3.3 22.3 1.0 CB A:CYS27 3.5 24.4 1.0 N A:CYS93 3.8 22.2 1.0 N A:CYS27 3.9 24.6 1.0 CA A:CYS93 4.1 23.3 1.0 CA A:CYS27 4.2 24.1 1.0 CB A:GLN26 4.5 31.9 1.0 CB A:GLN29 4.5 21.5 0.5 CB A:SER95 4.5 27.1 1.0 CB A:GLN29 4.5 21.8 0.5 CA A:CYS24 4.6 20.4 1.0 CA A:CYS90 4.6 20.0 1.0 C A:GLN26 4.6 27.3 1.0 CB A:GLN92 4.7 21.5 1.0 C A:CYS93 4.7 23.7 1.0 N A:GLY94 4.8 23.2 1.0 N A:SER95 4.9 23.8 1.0 C A:GLN92 4.9 22.7 1.0 N A:GLY28 4.9 22.0 1.0 C A:CYS27 4.9 23.8 1.0 CA A:GLN26 4.9 28.7 1.0 N A:GLN26 4.9 24.8 1.0 N A:GLN29 5.0 21.2 1.0 C A:CYS24 5.0 21.9 1.0

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


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 Pyrrolidin-2-One (Butyrolactam) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:30.5 occ:1.00 SG B:CYS27 2.2 32.2 1.0 SG B:CYS90 2.3 29.1 1.0 SG B:CYS93 2.4 33.9 1.0 SG B:CYS24 2.4 30.3 1.0 CB B:CYS90 3.1 28.4 1.0 CB B:CYS24 3.1 29.9 1.0 CB B:CYS93 3.4 35.0 1.0 CB B:CYS27 3.4 35.6 1.0 N B:CYS93 3.8 31.1 1.0 N B:CYS27 3.8 34.9 1.0 CA B:CYS93 4.1 34.1 1.0 CA B:CYS27 4.1 34.9 1.0 CB B:GLN29 4.4 36.6 1.0 CB B:GLN92 4.5 32.3 1.0 CB B:GLN26 4.6 39.9 1.0 CA B:CYS90 4.6 25.1 1.0 CA B:CYS24 4.6 27.1 1.0 C B:GLN26 4.7 36.6 1.0 CB B:SER95 4.7 30.0 1.0 C B:GLN92 4.8 32.4 1.0 C B:CYS27 4.8 33.4 1.0 C B:CYS93 4.8 32.7 1.0 N B:GLY28 4.8 31.3 1.0 N B:GLN29 4.9 31.2 1.0 N B:GLY94 4.9 30.6 1.0 N B:GLN92 5.0 29.0 1.0 CA B:GLN92 5.0 31.5 1.0

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


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 Pyrrolidin-2-One (Butyrolactam) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.1 occ:1.00 SG C:CYS93 2.2 36.4 1.0 SG C:CYS27 2.3 33.1 1.0 SG C:CYS90 2.3 30.8 1.0 SG C:CYS24 2.4 33.6 1.0 CB C:CYS90 3.1 31.4 1.0 CB C:CYS24 3.2 31.6 1.0 CB C:CYS93 3.3 35.4 1.0 CB C:CYS27 3.4 38.7 1.0 N C:CYS93 3.7 31.3 1.0 N C:CYS27 3.9 41.8 1.0 CA C:CYS93 4.0 33.8 1.0 CA C:CYS27 4.2 40.1 1.0 CB C:GLN29 4.5 29.9 1.0 CB C:GLN26 4.5 46.4 1.0 CB C:SER95 4.5 36.5 1.0 CA C:CYS90 4.6 31.4 1.0 CB C:GLN92 4.6 29.4 1.0 CA C:CYS24 4.7 33.5 1.0 C C:CYS93 4.7 34.6 1.0 C C:GLN26 4.7 44.1 1.0 C C:GLN92 4.8 31.3 1.0 N C:GLY94 4.8 34.3 1.0 N C:SER95 4.9 35.3 1.0 C C:CYS27 4.9 38.9 1.0 N C:GLY28 4.9 35.6 1.0 N C:GLN29 4.9 32.0 1.0 CA C:GLN26 5.0 45.3 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