Zinc in PDB 5oh8: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Rolipram

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Rolipram, PDB code: 5oh8 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.339, 59.523, 88.031, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Rolipram (pdb code 5oh8). 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 Rolipram, PDB code: 5oh8:
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 Rolipram


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 Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:34.7 occ:1.00 SG A:CYS24 2.3 31.4 1.0 SG A:CYS93 2.3 35.7 1.0 SG A:CYS90 2.3 33.3 1.0 SG A:CYS27 2.3 36.5 1.0 CB A:CYS24 3.1 29.7 1.0 CB A:CYS90 3.2 31.6 1.0 CB A:CYS93 3.3 37.4 1.0 CB A:CYS27 3.5 38.7 1.0 N A:CYS93 3.8 36.7 1.0 N A:CYS27 3.9 34.1 1.0 CA A:CYS93 4.1 39.4 1.0 CA A:CYS27 4.2 34.9 1.0 CB A:GLN29 4.4 35.1 0.5 CB A:SER95 4.5 40.7 1.0 CB A:GLN29 4.5 35.1 0.5 CB A:GLN26 4.5 46.4 1.0 CA A:CYS24 4.6 29.6 1.0 CA A:CYS90 4.6 31.9 1.0 C A:GLN26 4.6 41.6 1.0 CB A:GLN92 4.7 37.7 1.0 C A:CYS93 4.8 37.4 1.0 C A:CYS27 4.9 36.3 1.0 CA A:GLN26 4.9 42.1 1.0 N A:GLY28 4.9 33.8 1.0 N A:SER95 4.9 34.3 1.0 N A:GLN26 4.9 35.2 1.0 C A:GLN92 4.9 37.3 1.0 N A:GLY94 4.9 36.1 1.0 N A:GLN29 4.9 34.1 1.0

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


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 Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:49.6 occ:1.00 SG B:CYS27 2.2 53.8 1.0 SG B:CYS90 2.3 48.5 1.0 SG B:CYS93 2.4 52.5 1.0 SG B:CYS24 2.4 45.4 1.0 CB B:CYS90 3.0 44.3 1.0 CB B:CYS24 3.2 42.3 1.0 CB B:CYS27 3.3 56.5 1.0 CB B:CYS93 3.5 57.8 1.0 N B:CYS93 3.7 56.8 1.0 N B:CYS27 3.8 50.7 1.0 CA B:CYS27 4.0 54.0 1.0 CA B:CYS93 4.2 58.2 1.0 CA B:CYS90 4.5 40.7 1.0 CB B:GLN29 4.6 50.4 1.0 CB B:GLN92 4.6 58.1 1.0 CB B:GLN26 4.7 52.8 1.0 CA B:CYS24 4.7 40.2 1.0 C B:GLN26 4.7 52.2 1.0 C B:CYS27 4.7 52.3 1.0 CB B:SER95 4.7 48.5 1.0 C B:GLN92 4.7 60.2 1.0 C B:CYS93 4.8 56.2 1.0 N B:GLY28 4.8 49.6 1.0 N B:GLY94 4.9 52.0 1.0 C B:CYS90 4.9 43.6 1.0 N B:GLN92 5.0 54.9 1.0 N B:SER95 5.0 48.2 1.0

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


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 Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:54.1 occ:1.00 SG C:CYS90 2.3 54.9 1.0 SG C:CYS27 2.4 51.5 1.0 SG C:CYS24 2.4 58.9 1.0 SG C:CYS93 2.5 59.5 1.0 CB C:CYS24 3.1 58.2 1.0 CB C:CYS90 3.1 59.4 1.0 CB C:CYS27 3.3 56.9 1.0 CB C:CYS93 3.4 57.3 1.0 N C:CYS27 3.7 59.3 1.0 N C:CYS93 3.8 55.3 1.0 CA C:CYS27 4.1 57.4 1.0 CA C:CYS93 4.2 56.1 1.0 CB C:GLN29 4.4 55.0 1.0 CB C:SER95 4.5 68.3 1.0 CA C:CYS24 4.6 58.1 1.0 CA C:CYS90 4.6 60.1 1.0 CB C:GLN26 4.6 69.7 1.0 C C:GLN26 4.7 64.0 1.0 CB C:GLN92 4.7 47.8 1.0 C C:CYS27 4.7 57.5 1.0 N C:GLY28 4.7 54.8 1.0 C C:GLN92 4.8 50.6 1.0 C C:CYS93 4.8 60.0 1.0 CG C:GLN26 4.8 74.2 1.0 N C:GLN29 4.9 53.4 1.0 N C:GLY94 5.0 61.8 1.0 CA C:GLN26 5.0 65.6 1.0 N C:GLN26 5.0 62.9 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