Zinc in PDB 4v2z: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pomalidomide

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pomalidomide, PDB code: 4v2z 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)	37.35 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.469, 60.144, 88.460, 90.00, 90.00, 90.00
R / Rfree (%)	16.789 / 20.254

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Pomalidomide (pdb code 4v2z). 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 Pomalidomide, PDB code: 4v2z:
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 Pomalidomide


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 Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:13.7 occ:1.00 SG A:CYS27 2.3 14.7 1.0 SG A:CYS93 2.3 15.4 1.0 SG A:CYS24 2.3 13.6 1.0 SG A:CYS90 2.4 13.7 1.0 CB A:CYS24 3.2 12.4 1.0 CB A:CYS90 3.2 12.6 1.0 CB A:CYS93 3.3 14.6 1.0 CB A:CYS27 3.5 17.1 1.0 N A:CYS93 3.7 13.8 1.0 N A:CYS27 4.0 15.4 1.0 CA A:CYS93 4.0 15.0 1.0 CA A:CYS27 4.2 16.1 1.0 CB A:SER95 4.5 16.6 1.0 CB A:GLN29 4.5 14.3 0.5 CB A:GLN26 4.5 18.0 1.0 CB A:GLN29 4.6 14.0 0.5 CA A:CYS24 4.6 12.3 1.0 CA A:CYS90 4.6 13.0 1.0 C A:GLN26 4.6 17.6 1.0 C A:CYS93 4.7 15.4 1.0 CB A:GLN92 4.8 16.3 1.0 N A:GLY94 4.8 14.4 1.0 N A:GLN26 4.9 14.5 1.0 C A:GLN92 4.9 15.1 1.0 CA A:GLN26 4.9 16.2 1.0 C A:CYS27 4.9 17.0 1.0 N A:SER95 4.9 14.8 1.0 N A:GLN29 4.9 13.3 1.0 C A:CYS24 5.0 12.8 1.0 N A:GLY28 5.0 14.2 1.0

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


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 Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:18.3 occ:1.00 SG B:CYS93 2.3 20.6 1.0 SG B:CYS90 2.3 17.5 1.0 SG B:CYS24 2.4 18.1 1.0 SG B:CYS27 2.4 19.5 1.0 CB B:CYS90 3.1 18.0 1.0 CB B:CYS24 3.2 17.3 1.0 CB B:CYS93 3.3 21.9 1.0 CB B:CYS27 3.4 20.2 1.0 N B:CYS27 3.7 19.5 1.0 N B:CYS93 3.8 18.7 1.0 CA B:CYS93 4.1 19.4 1.0 CA B:CYS27 4.1 19.7 1.0 CB B:GLN29 4.4 18.7 0.5 CA B:CYS90 4.6 16.6 1.0 CB B:GLN92 4.7 19.5 1.0 CB B:SER95 4.7 19.5 1.0 CA B:CYS24 4.7 13.6 1.0 C B:GLN26 4.7 22.0 1.0 CB B:GLN26 4.7 24.9 1.0 C B:CYS27 4.8 19.7 1.0 C B:GLN92 4.8 18.1 1.0 C B:CYS93 4.8 21.5 1.0 N B:GLY28 4.9 17.9 1.0 CB B:GLN29 4.9 16.5 0.5 N B:GLY94 4.9 19.4 1.0 N B:GLN29 4.9 17.9 1.0 N B:SER95 5.0 18.1 1.0

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


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 Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:17.4 occ:1.00 SG C:CYS93 2.3 18.9 1.0 SG C:CYS27 2.3 18.6 1.0 SG C:CYS24 2.3 18.1 1.0 SG C:CYS90 2.4 16.9 1.0 CB C:CYS24 3.1 18.8 1.0 CB C:CYS90 3.2 15.8 1.0 CB C:CYS93 3.4 20.1 1.0 CB C:CYS27 3.4 20.1 1.0 N C:CYS93 3.8 17.8 1.0 N C:CYS27 3.8 19.4 1.0 CA C:CYS93 4.1 19.3 1.0 CA C:CYS27 4.2 21.7 1.0 CB C:GLN29 4.4 17.1 1.0 CB C:SER95 4.5 19.8 1.0 CB C:GLN26 4.5 22.6 1.0 CA C:CYS90 4.6 16.4 1.0 CA C:CYS24 4.6 20.2 1.0 CB C:GLN92 4.7 16.4 1.0 C C:GLN26 4.7 23.5 1.0 C C:CYS93 4.7 18.8 1.0 C C:CYS27 4.7 24.6 1.0 N C:GLY28 4.8 19.9 1.0 C C:GLN92 4.8 18.5 1.0 N C:GLY94 4.9 17.5 1.0 N C:GLN29 4.9 18.8 1.0 N C:SER95 4.9 18.2 1.0 CA C:GLN26 5.0 21.1 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