Zinc in PDB 5oha: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with 2-Thiohydantoin

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with 2-Thiohydantoin, PDB code: 5oha 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 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.595, 59.851, 88.251, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.7

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


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 2-Thiohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:16.5 occ:1.00 SG A:CYS27 2.3 17.0 1.0 SG A:CYS24 2.3 16.6 1.0 SG A:CYS93 2.3 18.3 1.0 SG A:CYS90 2.4 16.2 1.0 CB A:CYS24 3.1 14.8 1.0 CB A:CYS90 3.2 15.8 1.0 CB A:CYS93 3.3 18.5 1.0 CB A:CYS27 3.4 18.1 1.0 N A:CYS93 3.8 15.6 1.0 N A:CYS27 3.9 16.1 1.0 CA A:CYS93 4.1 17.0 1.0 CA A:CYS27 4.2 18.0 1.0 CB A:GLN29 4.4 17.0 0.5 CB A:SER95 4.5 22.5 1.0 CA A:CYS24 4.5 15.1 1.0 CB A:GLN26 4.5 22.3 1.0 C A:GLN26 4.6 23.3 1.0 CA A:CYS90 4.6 16.8 1.0 CB A:GLN29 4.6 17.9 0.5 CB A:GLN92 4.7 18.4 1.0 C A:CYS93 4.8 19.0 1.0 N A:GLY94 4.9 17.0 1.0 C A:CYS27 4.9 19.4 1.0 N A:GLN26 4.9 17.6 1.0 C A:GLN92 4.9 16.3 1.0 CA A:GLN26 4.9 21.8 1.0 N A:GLY28 4.9 16.9 1.0 N A:GLN29 4.9 15.9 1.0 N A:SER95 5.0 17.2 1.0 C A:CYS24 5.0 16.4 1.0

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


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 2-Thiohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:21.2 occ:1.00 SG B:CYS93 2.3 24.3 1.0 SG B:CYS90 2.3 21.0 1.0 SG B:CYS24 2.4 20.6 1.0 SG B:CYS27 2.4 23.0 1.0 CB B:CYS90 3.1 22.0 1.0 CB B:CYS24 3.2 20.5 1.0 CB B:CYS93 3.3 26.9 1.0 CB B:CYS27 3.3 24.5 1.0 N B:CYS27 3.8 20.9 1.0 N B:CYS93 3.8 20.5 1.0 CA B:CYS27 4.1 23.1 1.0 CA B:CYS93 4.1 22.9 1.0 CA B:CYS90 4.6 18.3 1.0 CB B:GLN92 4.6 21.6 1.0 CB B:SER95 4.7 24.2 1.0 CB B:GLN26 4.7 28.2 1.0 CA B:CYS24 4.7 17.1 1.0 C B:GLN26 4.7 25.6 1.0 C B:CYS27 4.7 24.4 1.0 C B:CYS93 4.8 26.9 1.0 C B:GLN92 4.8 21.4 1.0 CB B:GLN29 4.8 24.9 1.0 N B:GLY28 4.8 20.8 1.0 N B:GLY94 4.9 23.3 1.0 N B:GLN29 5.0 23.4 1.0

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


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 2-Thiohydantoin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:22.6 occ:1.00 SG C:CYS93 2.3 24.6 1.0 SG C:CYS27 2.3 22.6 1.0 SG C:CYS24 2.3 23.9 1.0 SG C:CYS90 2.4 21.8 1.0 CB C:CYS24 3.1 22.2 1.0 CB C:CYS90 3.2 21.2 1.0 CB C:CYS93 3.3 24.4 1.0 CB C:CYS27 3.4 24.9 1.0 N C:CYS93 3.8 20.9 1.0 N C:CYS27 3.8 28.7 1.0 CA C:CYS93 4.1 22.2 1.0 CA C:CYS27 4.1 27.0 1.0 CB C:GLN29 4.4 20.7 1.0 CB C:SER95 4.5 30.5 1.0 CB C:GLN26 4.6 29.1 1.0 CA C:CYS90 4.6 21.0 1.0 CA C:CYS24 4.6 23.1 1.0 CB C:GLN92 4.7 20.3 1.0 C C:GLN26 4.7 35.5 1.0 C C:CYS93 4.7 25.5 1.0 N C:GLY28 4.7 25.1 1.0 C C:CYS27 4.7 32.6 1.0 C C:GLN92 4.8 23.2 1.0 N C:GLY94 4.8 23.3 1.0 N C:GLN29 4.8 24.4 1.0 N C:SER95 4.9 24.4 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