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

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash I Structure, PDB code: 5ami 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)	37.29 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.250, 59.656, 86.728, 90.00, 90.00, 90.00
R / Rfree (%)	16.508 / 20.942

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash I Structure (pdb code 5ami). 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 I Structure, PDB code: 5ami:
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 I 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 I Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:23.5 occ:1.00 SG A:CYS90 2.3 23.2 1.0 SG A:CYS24 2.3 22.0 1.0 SG A:CYS93 2.3 26.3 1.0 SG A:CYS27 2.4 24.6 1.0 CB A:CYS90 3.1 21.1 1.0 CB A:CYS24 3.1 18.8 1.0 CB A:CYS93 3.4 25.3 1.0 CB A:CYS27 3.5 25.4 1.0 N A:CYS93 3.7 24.4 1.0 N A:CYS27 3.9 25.2 1.0 CA A:CYS93 4.1 26.2 1.0 CA A:CYS27 4.2 26.1 1.0 CB A:GLN29 4.4 22.7 0.5 CB A:SER95 4.5 28.4 1.0 CB A:GLN26 4.5 32.6 1.0 C A:GLN26 4.6 28.3 1.0 CA A:CYS90 4.6 22.0 1.0 CA A:CYS24 4.6 19.1 1.0 CB A:GLN29 4.6 23.8 0.5 CB A:GLN92 4.7 25.1 1.0 C A:CYS93 4.8 26.3 1.0 C A:GLN92 4.8 25.8 1.0 C A:CYS27 4.9 25.9 1.0 CA A:GLN26 4.9 29.6 1.0 N A:GLY28 4.9 22.7 1.0 N A:SER95 4.9 24.9 1.0 N A:GLN29 4.9 23.5 1.0 N A:GLY94 4.9 26.3 1.0 N A:GLN26 4.9 24.9 1.0

Zinc binding site 2 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash I 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 I Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:35.4 occ:1.00 SG B:CYS27 2.3 37.8 1.0 SG B:CYS93 2.3 38.7 1.0 SG B:CYS90 2.3 32.1 1.0 SG B:CYS24 2.4 31.1 1.0 CB B:CYS90 3.1 31.7 1.0 CB B:CYS24 3.1 28.6 1.0 CB B:CYS27 3.3 40.3 1.0 CB B:CYS93 3.4 43.1 1.0 N B:CYS27 3.7 38.4 1.0 N B:CYS93 3.7 40.0 1.0 CA B:CYS27 4.1 39.7 1.0 CA B:CYS93 4.1 41.8 1.0 CB B:GLN29 4.4 30.7 0.5 CA B:CYS90 4.5 30.1 1.0 CA B:CYS24 4.7 26.8 1.0 C B:GLN26 4.7 39.4 1.0 CB B:GLN92 4.7 39.5 1.0 CB B:SER95 4.7 37.9 1.0 C B:CYS27 4.7 38.9 1.0 CB B:GLN26 4.7 42.2 1.0 C B:GLN92 4.8 42.3 1.0 N B:GLY28 4.8 35.7 1.0 C B:CYS93 4.8 41.0 1.0 N B:GLY94 4.9 38.4 1.0 CB B:GLN29 4.9 34.3 0.5 C B:CYS90 5.0 31.0 1.0 N B:GLN29 5.0 33.3 1.0

Zinc binding site 3 out of 3 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Wash I 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 I Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:32.7 occ:1.00 SG C:CYS27 2.3 32.6 1.0 SG C:CYS90 2.3 33.1 1.0 SG C:CYS24 2.4 32.8 1.0 SG C:CYS93 2.4 35.8 1.0 CB C:CYS90 3.1 32.7 1.0 CB C:CYS24 3.2 33.0 1.0 CB C:CYS93 3.3 36.3 1.0 CB C:CYS27 3.4 35.2 1.0 N C:CYS93 3.7 34.5 1.0 N C:CYS27 3.8 37.4 1.0 CA C:CYS93 4.1 34.9 1.0 CA C:CYS27 4.2 36.2 1.0 CB C:GLN29 4.4 32.8 1.0 CB C:SER95 4.5 42.1 1.0 CA C:CYS90 4.6 33.2 1.0 CB C:GLN26 4.6 47.5 1.0 CA C:CYS24 4.6 33.2 1.0 CB C:GLN92 4.7 32.3 1.0 C C:GLN26 4.7 41.4 1.0 C C:GLN92 4.7 33.7 1.0 N C:GLY28 4.8 34.4 1.0 C C:CYS27 4.8 36.8 1.0 C C:CYS93 4.8 36.9 1.0 N C:GLN29 4.8 32.5 1.0 N C:GLY94 4.9 37.7 1.0 N C:SER95 4.9 39.1 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