Zinc in PDB 4v31: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Deoxyuridine

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Deoxyuridine, PDB code: 4v31 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)	37.41 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.809, 59.993, 88.370, 90.00, 90.00, 90.00
R / Rfree (%)	16.386 / 21.855

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Deoxyuridine (pdb code 4v31). 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 Deoxyuridine, PDB code: 4v31:
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 Deoxyuridine


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 Deoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:14.7 occ:1.00 SG A:CYS24 2.3 14.3 1.0 SG A:CYS27 2.3 15.4 1.0 SG A:CYS93 2.3 14.7 1.0 SG A:CYS90 2.4 14.4 1.0 CB A:CYS24 3.1 14.5 1.0 CB A:CYS90 3.2 15.5 1.0 CB A:CYS93 3.3 15.0 1.0 CB A:CYS27 3.5 15.6 1.0 N A:CYS93 3.7 14.9 1.0 N A:CYS27 3.9 14.9 1.0 CA A:CYS93 4.1 16.4 1.0 CA A:CYS27 4.3 15.9 1.0 CB A:SER95 4.5 20.8 1.0 CB A:GLN29 4.5 14.8 1.0 C A:GLN26 4.5 20.2 1.0 CA A:CYS24 4.6 14.3 1.0 CB A:GLN26 4.6 20.5 1.0 CA A:CYS90 4.7 14.3 1.0 CB A:GLN92 4.7 15.1 1.0 C A:CYS93 4.8 16.7 1.0 N A:GLY94 4.8 17.0 1.0 N A:GLN26 4.9 15.8 1.0 C A:GLN92 4.9 15.0 1.0 CA A:GLN26 4.9 18.5 1.0 N A:SER95 4.9 14.9 1.0 C A:CYS27 4.9 16.9 1.0 C A:CYS24 5.0 13.6 1.0

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


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 Deoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:19.6 occ:1.00 SG B:CYS90 2.3 17.1 1.0 SG B:CYS27 2.3 19.0 1.0 SG B:CYS24 2.3 19.3 1.0 SG B:CYS93 2.3 20.1 1.0 CB B:CYS90 3.1 16.5 1.0 CB B:CYS24 3.2 19.8 1.0 CB B:CYS93 3.3 20.8 1.0 CB B:CYS27 3.4 20.5 1.0 N B:CYS93 3.8 17.8 1.0 N B:CYS27 3.8 21.4 1.0 CA B:CYS93 4.1 20.0 1.0 CA B:CYS27 4.1 21.2 1.0 CA B:CYS90 4.6 15.3 1.0 CB B:GLN26 4.6 27.7 1.0 CB B:SER95 4.6 21.0 1.0 CB B:GLN92 4.6 19.4 1.0 CB B:GLN29 4.6 24.3 1.0 CA B:CYS24 4.6 17.6 1.0 C B:GLN26 4.7 24.4 1.0 C B:GLN92 4.8 19.0 1.0 C B:CYS93 4.8 20.1 1.0 C B:CYS27 4.8 21.3 1.0 N B:GLY28 4.8 19.6 1.0 N B:GLY94 4.9 19.0 1.0 N B:GLN29 4.9 19.4 1.0 N B:SER95 5.0 20.3 1.0

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


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 Deoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:19.7 occ:1.00 SG C:CYS27 2.3 20.5 1.0 SG C:CYS93 2.3 20.9 1.0 SG C:CYS90 2.3 19.9 1.0 SG C:CYS24 2.3 21.0 1.0 CB C:CYS24 3.1 21.6 1.0 CB C:CYS90 3.2 17.9 1.0 CB C:CYS93 3.3 20.1 1.0 CB C:CYS27 3.4 28.1 1.0 N C:CYS27 3.8 27.2 1.0 N C:CYS93 3.8 19.5 1.0 CA C:CYS93 4.1 20.3 1.0 CA C:CYS27 4.1 29.3 1.0 CB C:GLN29 4.4 17.7 1.0 CB C:GLN26 4.5 32.6 1.0 CB C:SER95 4.5 22.7 1.0 CA C:CYS24 4.5 22.4 1.0 CA C:CYS90 4.7 18.4 1.0 CB C:GLN92 4.7 17.6 1.0 C C:GLN26 4.7 28.2 1.0 C C:CYS93 4.7 20.6 1.0 C C:CYS27 4.8 27.1 1.0 C C:GLN92 4.8 19.9 1.0 N C:GLY28 4.8 23.0 1.0 N C:GLY94 4.8 21.2 1.0 N C:SER95 4.9 22.1 1.0 N C:GLN29 4.9 19.2 1.0 CA C:GLN26 5.0 29.3 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