Zinc in PDB 4v2y: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, PDB code: 4v2y 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)	37.33 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.490, 60.040, 88.470, 90.00, 90.00, 90.00
R / Rfree (%)	16.201 / 19.457

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide (pdb code 4v2y). 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 Thalidomide, PDB code: 4v2y:
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 Thalidomide


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 Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:12.2 occ:1.00 SG A:CYS93 2.3 13.6 1.0 SG A:CYS27 2.3 13.2 1.0 SG A:CYS24 2.3 12.3 1.0 SG A:CYS90 2.4 12.5 1.0 CB A:CYS24 3.1 10.6 1.0 CB A:CYS90 3.2 11.1 1.0 CB A:CYS93 3.3 13.7 1.0 CB A:CYS27 3.4 15.4 1.0 N A:CYS93 3.8 12.4 1.0 N A:CYS27 4.0 14.3 1.0 CA A:CYS93 4.1 13.0 1.0 CA A:CYS27 4.2 14.3 1.0 CB A:GLN29 4.5 11.7 0.5 CB A:SER95 4.5 15.4 1.0 CA A:CYS24 4.5 11.0 1.0 CB A:GLN26 4.6 17.5 1.0 C A:GLN26 4.6 17.0 1.0 CA A:CYS90 4.6 10.8 1.0 CB A:GLN29 4.6 12.6 0.5 C A:CYS93 4.7 14.4 1.0 CB A:GLN92 4.8 14.1 1.0 N A:GLY94 4.8 13.8 1.0 N A:GLN26 4.9 13.3 1.0 C A:GLN92 4.9 13.0 1.0 CA A:GLN26 4.9 14.8 1.0 N A:SER95 4.9 12.6 1.0 C A:CYS27 4.9 16.0 1.0 C A:CYS24 4.9 12.5 1.0 N A:GLN29 4.9 12.7 1.0 N A:GLY28 5.0 13.3 1.0

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


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 Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:15.2 occ:1.00 SG B:CYS90 2.3 15.0 1.0 SG B:CYS27 2.3 16.1 1.0 SG B:CYS24 2.3 15.0 1.0 SG B:CYS93 2.4 17.2 1.0 CB B:CYS90 3.2 15.3 1.0 CB B:CYS24 3.2 15.7 1.0 CB B:CYS27 3.3 16.8 1.0 CB B:CYS93 3.4 18.5 1.0 N B:CYS27 3.7 16.5 1.0 N B:CYS93 3.8 15.5 1.0 CA B:CYS27 4.1 16.5 1.0 CA B:CYS93 4.1 14.1 1.0 CB B:GLN29 4.5 16.6 0.5 CA B:CYS90 4.6 13.8 1.0 CB B:GLN92 4.6 16.7 1.0 C B:GLN26 4.7 19.0 1.0 CA B:CYS24 4.7 13.0 1.0 CB B:SER95 4.7 16.4 1.0 CB B:GLN26 4.7 20.8 1.0 C B:CYS27 4.8 15.2 1.0 C B:GLN92 4.8 16.4 1.0 C B:CYS93 4.8 18.7 1.0 N B:GLY28 4.9 14.6 1.0 CB B:GLN29 4.9 15.9 0.5 N B:GLY94 4.9 15.9 1.0 N B:GLN29 5.0 15.5 1.0 N B:SER95 5.0 14.4 1.0

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


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 Thalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:15.1 occ:1.00 SG C:CYS93 2.3 16.4 1.0 SG C:CYS24 2.3 15.6 1.0 SG C:CYS27 2.3 16.5 1.0 SG C:CYS90 2.4 14.6 1.0 CB C:CYS24 3.1 16.4 1.0 CB C:CYS90 3.1 14.5 1.0 CB C:CYS93 3.3 16.1 1.0 CB C:CYS27 3.4 19.0 1.0 N C:CYS93 3.8 14.6 1.0 N C:CYS27 3.8 17.4 1.0 CA C:CYS93 4.1 16.4 1.0 CA C:CYS27 4.1 18.9 1.0 CB C:GLN29 4.4 15.7 1.0 CB C:GLN26 4.5 21.0 1.0 CB C:SER95 4.5 16.9 1.0 CA C:CYS24 4.6 17.0 1.0 CA C:CYS90 4.6 13.7 1.0 CB C:GLN92 4.7 14.0 1.0 C C:GLN26 4.7 20.6 1.0 C C:CYS93 4.7 16.6 1.0 C C:CYS27 4.7 21.8 1.0 C C:GLN92 4.8 15.5 1.0 N C:GLY28 4.8 17.9 1.0 N C:GLY94 4.8 15.8 1.0 N C:GLN29 4.9 17.5 1.0 N C:SER95 4.9 17.0 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