Zinc in PDB 4v32: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Y101F Mutant

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Y101F Mutant, PDB code: 4v32 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)	37.39 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.753, 59.959, 88.414, 90.00, 90.00, 90.00
R / Rfree (%)	18.212 / 23.987

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Y101F Mutant (pdb code 4v32). 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, Y101F Mutant, PDB code: 4v32:
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, Y101F Mutant


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, Y101F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:19.5 occ:1.00 SG A:CYS27 2.3 21.8 1.0 SG A:CYS24 2.3 17.2 1.0 SG A:CYS90 2.3 19.0 1.0 SG A:CYS93 2.4 19.9 1.0 CB A:CYS24 3.0 17.4 1.0 CB A:CYS90 3.2 18.3 1.0 CB A:CYS93 3.3 21.0 1.0 CB A:CYS27 3.5 22.7 1.0 N A:CYS27 3.8 22.8 1.0 N A:CYS93 3.9 21.0 1.0 CA A:CYS93 4.1 21.6 1.0 CA A:CYS27 4.2 22.9 1.0 CB A:GLN29 4.5 20.6 0.5 CB A:SER95 4.5 21.4 1.0 CB A:GLN26 4.5 26.9 1.0 CA A:CYS24 4.5 17.5 1.0 CB A:GLN29 4.6 20.6 0.5 C A:GLN26 4.6 24.7 1.0 CA A:CYS90 4.6 18.3 1.0 CB A:GLN92 4.8 20.6 1.0 C A:CYS93 4.8 21.9 1.0 C A:CYS27 4.9 22.4 1.0 N A:GLN26 4.9 22.9 1.0 CA A:GLN26 4.9 24.8 1.0 N A:GLY94 4.9 21.6 1.0 N A:SER95 4.9 21.5 1.0 N A:GLN29 4.9 20.8 1.0 N A:GLY28 4.9 21.3 1.0 C A:CYS24 5.0 18.2 1.0 C A:GLN92 5.0 21.7 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Y101F Mutant


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, Y101F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:27.9 occ:1.00 SG B:CYS93 2.3 27.8 1.0 SG B:CYS27 2.3 28.3 1.0 SG B:CYS24 2.3 26.2 1.0 SG B:CYS90 2.3 24.9 1.0 CB B:CYS90 3.1 24.3 1.0 CB B:CYS93 3.2 29.9 1.0 CB B:CYS24 3.3 25.2 1.0 CB B:CYS27 3.3 30.6 1.0 N B:CYS27 3.7 30.0 1.0 N B:CYS93 3.7 29.1 1.0 CA B:CYS93 4.0 30.2 1.0 CA B:CYS27 4.1 30.7 1.0 CA B:CYS90 4.6 23.8 1.0 CB B:GLN92 4.6 29.0 1.0 C B:GLN26 4.6 32.1 1.0 CA B:CYS24 4.7 24.9 1.0 CB B:SER95 4.7 26.6 1.0 C B:CYS27 4.7 30.3 1.0 C B:CYS93 4.8 29.9 1.0 C B:GLN92 4.8 30.2 1.0 CB B:GLN29 4.8 29.8 1.0 CB B:GLN26 4.9 33.0 1.0 N B:GLY28 4.9 28.7 1.0 N B:GLY94 4.9 28.8 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Y101F Mutant


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, Y101F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:28.6 occ:1.00 SG C:CYS93 2.2 30.7 1.0 SG C:CYS90 2.3 28.1 1.0 SG C:CYS27 2.3 30.7 1.0 SG C:CYS24 2.4 31.9 1.0 CB C:CYS90 3.2 28.9 1.0 CB C:CYS24 3.2 31.7 1.0 CB C:CYS93 3.3 30.2 1.0 CB C:CYS27 3.4 32.5 1.0 N C:CYS93 3.8 28.8 1.0 N C:CYS27 3.9 35.3 1.0 CA C:CYS93 4.1 29.9 1.0 CA C:CYS27 4.2 33.7 1.0 CB C:GLN29 4.3 28.8 1.0 CB C:GLN26 4.5 40.1 1.0 CA C:CYS90 4.6 28.9 1.0 C C:CYS93 4.6 30.6 1.0 CB C:GLN92 4.7 26.9 1.0 CB C:SER95 4.7 33.1 1.0 CA C:CYS24 4.7 32.7 1.0 N C:GLY94 4.7 30.5 1.0 N C:GLY28 4.7 31.9 1.0 C C:CYS27 4.7 32.7 1.0 C C:GLN26 4.8 37.4 1.0 N C:GLN29 4.8 29.6 1.0 C C:GLN92 4.8 28.1 1.0 N C:SER95 4.9 32.0 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