Zinc in PDB 5oh3: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Ethosuximide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Ethosuximide, PDB code: 5oh3 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)	37.33 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.880, 59.790, 88.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.1

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Ethosuximide (pdb code 5oh3). 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 Ethosuximide, PDB code: 5oh3:
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 Ethosuximide


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 Ethosuximide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.6 occ:1.00 SG A:CYS93 2.3 25.5 1.0 SG A:CYS24 2.3 23.2 1.0 SG A:CYS27 2.3 27.4 1.0 SG A:CYS90 2.3 23.8 1.0 CB A:CYS90 3.1 22.9 1.0 CB A:CYS24 3.2 22.4 1.0 CB A:CYS93 3.3 26.9 1.0 CB A:CYS27 3.4 29.0 1.0 N A:CYS93 3.8 26.2 1.0 N A:CYS27 3.8 28.4 1.0 CA A:CYS93 4.0 27.8 1.0 CA A:CYS27 4.2 28.7 1.0 CB A:SER95 4.5 27.8 1.0 CB A:GLN29 4.5 25.8 0.5 CB A:GLN26 4.5 34.7 1.0 CB A:GLN29 4.5 26.6 0.5 CA A:CYS90 4.6 23.0 1.0 CA A:CYS24 4.6 21.7 1.0 C A:GLN26 4.6 30.4 1.0 CB A:GLN92 4.7 25.1 1.0 C A:CYS93 4.7 28.4 1.0 N A:GLY94 4.9 27.4 1.0 N A:SER95 4.9 26.4 1.0 C A:CYS27 4.9 28.1 1.0 C A:GLN92 4.9 26.6 1.0 N A:GLY28 4.9 27.0 1.0 CA A:GLN26 4.9 32.1 1.0 N A:GLN29 4.9 26.4 1.0 N A:GLN26 4.9 28.8 1.0 C A:CYS24 5.0 23.4 1.0

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


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 Ethosuximide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:36.5 occ:1.00 SG B:CYS27 2.3 35.1 1.0 SG B:CYS90 2.3 35.1 1.0 SG B:CYS93 2.3 38.3 1.0 SG B:CYS24 2.4 32.8 1.0 CB B:CYS24 3.1 31.9 1.0 CB B:CYS90 3.2 32.8 1.0 CB B:CYS93 3.3 40.6 1.0 CB B:CYS27 3.4 38.4 1.0 N B:CYS93 3.7 39.4 1.0 N B:CYS27 3.8 37.9 1.0 CA B:CYS93 4.0 40.8 1.0 CA B:CYS27 4.1 38.1 1.0 CB B:GLN29 4.5 38.5 1.0 CB B:GLN92 4.6 40.3 1.0 CA B:CYS90 4.6 31.4 1.0 CB B:GLN26 4.6 45.8 1.0 CA B:CYS24 4.6 30.9 1.0 CB B:SER95 4.6 36.2 1.0 C B:GLN26 4.7 40.8 1.0 C B:GLN92 4.8 41.0 1.0 C B:CYS93 4.8 39.3 1.0 C B:CYS27 4.8 36.9 1.0 N B:GLY28 4.8 34.7 1.0 N B:GLN29 4.9 35.7 1.0 N B:GLY94 4.9 37.6 1.0 CA B:GLN26 5.0 42.2 1.0

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


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 Ethosuximide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:43.8 occ:1.00 SG C:CYS93 2.3 45.9 1.0 SG C:CYS90 2.4 41.4 1.0 SG C:CYS24 2.4 46.4 1.0 SG C:CYS27 2.4 41.3 1.0 CB C:CYS24 3.1 46.5 1.0 CB C:CYS90 3.2 45.4 1.0 CB C:CYS93 3.3 43.9 1.0 CB C:CYS27 3.3 44.6 1.0 N C:CYS93 3.7 42.3 1.0 N C:CYS27 3.8 48.4 1.0 CA C:CYS93 4.1 43.6 1.0 CA C:CYS27 4.1 45.6 1.0 CB C:GLN29 4.4 40.6 1.0 CB C:SER95 4.5 55.6 1.0 CB C:GLN26 4.5 59.4 1.0 CB C:GLN92 4.5 37.6 1.0 CA C:CYS24 4.6 48.2 1.0 CA C:CYS90 4.6 46.5 1.0 N C:GLY28 4.6 44.6 1.0 C C:CYS27 4.7 44.9 1.0 C C:CYS93 4.7 46.6 1.0 C C:GLN26 4.7 52.0 1.0 C C:GLN92 4.8 40.2 1.0 N C:GLY94 4.8 47.0 1.0 N C:GLN29 4.8 40.8 1.0 N C:SER95 4.8 52.8 1.0 N C:GLN26 5.0 55.2 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