Zinc in PDB 4v30: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Lenalidomide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Lenalidomide, PDB code: 4v30 was solved by M.D.Hartmann, A.N.Lupas, B.Hernandez Alvarez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.682, 59.743, 88.064, 90.00, 90.00, 90.00
R / Rfree (%)	18.521 / 23.875

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Lenalidomide (pdb code 4v30). 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 Lenalidomide, PDB code: 4v30:
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 Lenalidomide


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 Lenalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:20.3 occ:1.00 SG A:CYS27 2.3 20.5 1.0 SG A:CYS93 2.3 20.2 1.0 SG A:CYS24 2.3 19.3 1.0 SG A:CYS90 2.4 19.1 1.0 CB A:CYS24 3.1 18.6 1.0 CB A:CYS90 3.2 18.3 1.0 CB A:CYS93 3.3 21.1 1.0 CB A:CYS27 3.5 21.9 1.0 N A:CYS93 3.9 21.1 1.0 N A:CYS27 3.9 21.6 1.0 CA A:CYS93 4.1 21.9 1.0 CA A:CYS27 4.3 21.8 1.0 CB A:GLN29 4.5 20.1 0.5 CB A:GLN29 4.5 20.4 0.5 CB A:SER95 4.5 20.6 1.0 CA A:CYS24 4.6 18.3 1.0 CB A:GLN26 4.6 26.2 1.0 CA A:CYS90 4.7 18.4 1.0 C A:GLN26 4.7 23.7 1.0 C A:CYS93 4.7 22.3 1.0 N A:GLY94 4.8 21.8 1.0 CB A:GLN92 4.8 21.1 1.0 N A:GLY28 4.9 20.1 1.0 N A:SER95 4.9 20.9 1.0 N A:GLN26 4.9 21.7 1.0 C A:CYS27 4.9 21.5 1.0 N A:GLN29 4.9 20.2 1.0 C A:GLN92 5.0 22.2 1.0 CA A:GLN26 5.0 23.9 1.0

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


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 Lenalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:28.3 occ:1.00 SG B:CYS27 2.2 29.8 1.0 SG B:CYS93 2.3 29.8 1.0 SG B:CYS90 2.3 26.8 1.0 SG B:CYS24 2.4 27.1 1.0 CB B:CYS24 3.2 26.0 1.0 CB B:CYS90 3.2 24.4 1.0 CB B:CYS93 3.4 32.1 1.0 CB B:CYS27 3.4 32.9 1.0 N B:CYS27 3.8 32.0 1.0 N B:CYS93 3.8 30.1 1.0 CA B:CYS27 4.1 33.3 1.0 CA B:CYS93 4.1 31.7 1.0 CB B:GLN92 4.6 29.8 1.0 CA B:CYS24 4.6 25.0 1.0 CA B:CYS90 4.7 23.3 1.0 CB B:SER95 4.7 25.7 1.0 C B:GLN26 4.7 34.1 1.0 C B:CYS27 4.8 33.2 1.0 C B:GLN92 4.8 31.0 1.0 CB B:GLN26 4.8 34.8 1.0 C B:CYS93 4.8 30.9 1.0 CB B:GLN29 4.8 31.1 1.0 N B:GLY28 4.9 31.3 1.0 N B:GLY94 4.9 29.1 1.0 N B:SER95 4.9 26.6 1.0 N B:GLN29 5.0 30.8 1.0

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


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 Lenalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:30.1 occ:1.00 SG C:CYS93 2.3 33.1 1.0 SG C:CYS90 2.3 28.3 1.0 SG C:CYS27 2.3 29.9 1.0 SG C:CYS24 2.4 31.0 1.0 CB C:CYS90 3.1 28.7 1.0 CB C:CYS24 3.2 30.7 1.0 CB C:CYS93 3.4 32.6 1.0 CB C:CYS27 3.5 32.4 1.0 N C:CYS93 3.9 30.7 1.0 N C:CYS27 3.9 35.2 1.0 CA C:CYS27 4.2 34.0 1.0 CA C:CYS93 4.2 32.0 1.0 CB C:GLN29 4.4 29.0 1.0 CA C:CYS90 4.5 28.6 1.0 CB C:SER95 4.6 32.9 1.0 CB C:GLN26 4.6 39.8 1.0 CA C:CYS24 4.7 31.6 1.0 C C:GLN26 4.7 37.4 1.0 N C:GLY28 4.7 32.9 1.0 CB C:GLN92 4.7 28.4 1.0 C C:CYS27 4.8 33.7 1.0 N C:GLY94 4.8 32.1 1.0 C C:CYS93 4.8 32.7 1.0 N C:GLN29 4.8 30.3 1.0 C C:GLN92 4.8 30.1 1.0 N C:SER95 4.9 32.6 1.0

M.D.Hartmann, I.Boichenko, M.Coles, F.Zanini, A.N.Lupas, B.Hernandez Alvarez. Thalidomide Mimics Uridine Binding to An Aromatic Cage in Cereblon. J.Struct.Biol. V. 188 225 2014.
ISSN: ISSN 1047-8477
PubMed: 25448889
DOI: 10.1016/J.JSB.2014.10.010