Zinc in PDB 5amj: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash II Structure

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash II Structure, PDB code: 5amj 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)	37.24 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.350, 59.430, 86.040, 90.00, 90.00, 90.00
R / Rfree (%)	15.495 / 19.053

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash II Structure (pdb code 5amj). 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, Wash II Structure, PDB code: 5amj:
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, Wash II Structure


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, Wash II Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:18.1 occ:1.00 SG A:CYS27 2.3 19.3 1.0 SG A:CYS24 2.3 16.7 1.0 SG A:CYS90 2.3 17.4 1.0 SG A:CYS93 2.3 19.5 1.0 CB A:CYS24 3.1 14.4 1.0 CB A:CYS90 3.2 16.6 1.0 CB A:CYS93 3.3 19.5 1.0 CB A:CYS27 3.4 22.1 1.0 N A:CYS93 3.7 18.3 1.0 N A:CYS27 3.9 22.2 1.0 CA A:CYS93 4.0 19.2 1.0 CA A:CYS27 4.2 21.8 1.0 CB A:GLN29 4.5 17.5 0.5 CB A:GLN26 4.5 27.8 1.0 CB A:GLN29 4.5 16.9 0.5 CB A:SER95 4.6 24.8 1.0 C A:GLN26 4.6 24.8 1.0 CA A:CYS90 4.6 15.7 1.0 CA A:CYS24 4.6 15.3 1.0 CB A:GLN92 4.8 17.5 1.0 C A:CYS93 4.8 20.0 1.0 C A:CYS27 4.8 21.1 1.0 C A:GLN92 4.8 18.8 1.0 N A:GLY28 4.9 18.0 1.0 N A:GLY94 4.9 19.6 1.0 N A:GLN29 4.9 17.1 1.0 N A:GLN26 4.9 19.8 1.0 CA A:GLN26 4.9 24.9 1.0 N A:SER95 4.9 20.9 1.0

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


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, Wash II Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:25.9 occ:1.00 SG B:CYS27 2.3 28.4 1.0 SG B:CYS93 2.3 27.3 1.0 SG B:CYS90 2.4 22.9 1.0 SG B:CYS24 2.4 22.5 1.0 CB B:CYS90 3.1 21.7 1.0 CB B:CYS24 3.1 21.2 1.0 CB B:CYS27 3.2 30.4 1.0 CB B:CYS93 3.3 30.1 1.0 N B:CYS93 3.7 28.4 1.0 N B:CYS27 3.8 29.2 1.0 CA B:CYS27 4.1 30.2 1.0 CA B:CYS93 4.1 29.6 1.0 CB B:GLN29 4.3 24.1 0.5 CA B:CYS90 4.6 20.8 1.0 CB B:SER95 4.6 27.5 1.0 CB B:GLN26 4.6 36.5 1.0 CA B:CYS24 4.6 20.9 1.0 CB B:GLN92 4.7 27.4 1.0 C B:GLN26 4.7 32.5 1.0 C B:CYS27 4.7 29.0 1.0 CB B:GLN29 4.7 28.0 0.5 C B:CYS93 4.8 29.3 1.0 C B:GLN92 4.8 29.3 1.0 N B:GLY28 4.8 27.4 1.0 N B:GLY94 4.8 26.9 1.0 N B:GLN29 4.9 26.4 1.0 N B:SER95 5.0 26.4 1.0

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


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, Wash II Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:27.2 occ:1.00 SG C:CYS93 2.3 27.8 1.0 SG C:CYS27 2.3 25.4 1.0 SG C:CYS90 2.3 26.1 1.0 SG C:CYS24 2.3 28.1 1.0 CB C:CYS90 3.1 27.5 1.0 CB C:CYS24 3.2 26.9 1.0 CB C:CYS93 3.3 29.0 1.0 CB C:CYS27 3.4 28.0 1.0 N C:CYS93 3.7 27.5 1.0 N C:CYS27 3.8 30.3 1.0 CA C:CYS93 4.0 28.2 1.0 CA C:CYS27 4.1 28.9 1.0 CB C:GLN29 4.4 24.5 1.0 CB C:SER95 4.5 32.9 1.0 CB C:GLN26 4.5 42.0 1.0 CA C:CYS90 4.6 26.4 1.0 CA C:CYS24 4.7 27.3 1.0 C C:GLN26 4.7 33.5 1.0 C C:CYS93 4.7 29.7 1.0 CB C:GLN92 4.7 24.4 1.0 C C:CYS27 4.8 28.8 1.0 C C:GLN92 4.8 25.9 1.0 N C:GLY28 4.8 28.0 1.0 N C:GLY94 4.8 29.4 1.0 N C:GLN29 4.9 26.2 1.0 N C:SER95 4.9 31.2 1.0 CA C:GLN26 5.0 36.2 1.0

M.D.Hartmann, I.Boichenko, M.Coles, A.N.Lupas, B.Hernandez Alvarez. Structural Dynamics of the Cereblon Ligand Binding Domain. Plos One V. 10 28342 2015.
ISSN: ISSN 1932-6203
PubMed: 26024445
DOI: 10.1371/JOURNAL.PONE.0128342