Zinc in PDB 5amk: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form, PDB code: 5amk 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)	38.98 / 2.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	137.860, 137.860, 154.390, 90.00, 90.00, 120.00
R / Rfree (%)	17.452 / 21.688

The binding sites of Zinc atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form (pdb code 5amk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form, PDB code: 5amk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form


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 Multiple Conformations, Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:34.1 occ:1.00 SG A:CYS27 2.1 27.5 1.0 SG A:CYS24 2.2 29.5 1.0 SG A:CYS93 2.2 31.3 1.0 SG A:CYS90 2.4 32.5 1.0 CB A:CYS90 3.1 33.1 1.0 CB A:CYS24 3.1 29.4 1.0 CB A:CYS27 3.2 30.8 1.0 CB A:CYS93 3.3 33.0 1.0 N A:CYS93 3.8 33.3 1.0 N A:CYS27 3.8 32.6 1.0 CA A:CYS93 4.1 34.2 1.0 CA A:CYS27 4.1 31.3 1.0 CB A:GLN29 4.3 40.0 1.0 CA A:CYS90 4.6 32.5 1.0 OE1 A:GLN92 4.6 41.9 1.0 CA A:CYS24 4.6 29.1 1.0 CB A:GLN26 4.6 40.0 1.0 C A:GLN26 4.6 35.2 1.0 CB A:GLN92 4.6 34.5 1.0 CB A:SER95 4.7 35.5 1.0 C A:CYS27 4.8 31.5 1.0 C A:GLN92 4.8 34.3 1.0 C A:CYS93 4.8 34.8 1.0 N A:GLY94 4.9 34.9 1.0 N A:GLN29 4.9 35.3 1.0 N A:GLN92 5.0 36.5 1.0

Zinc binding site 2 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form


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 Multiple Conformations, Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn150 b:31.4 occ:1.00 SG B:CYS27 2.2 28.1 1.0 SG B:CYS90 2.2 26.9 1.0 SG B:CYS24 2.3 33.8 1.0 SG B:CYS93 2.4 27.1 1.0 CB B:CYS90 3.1 26.9 1.0 CB B:CYS24 3.1 36.2 1.0 CB B:CYS93 3.1 29.1 1.0 CB B:CYS27 3.1 31.4 1.0 N B:CYS27 3.6 31.9 1.0 CA B:CYS27 3.9 32.7 1.0 N B:CYS93 4.1 29.0 1.0 CA B:CYS93 4.2 29.3 1.0 CB B:GLN26 4.5 32.9 1.0 CA B:CYS90 4.5 27.8 1.0 CA B:CYS24 4.6 36.4 1.0 N B:GLY28 4.7 34.5 1.0 C B:CYS27 4.7 34.4 1.0 CB B:GLN92 4.7 43.6 1.0 C B:GLN26 4.7 34.2 1.0 OG B:SER95 4.8 28.1 1.0 CB B:GLN29 4.8 36.7 1.0 C B:CYS93 4.8 30.4 1.0 CB B:SER95 4.9 27.4 1.0 N B:GLN29 5.0 34.7 1.0 C B:GLN92 5.0 32.7 1.0 C B:CYS90 5.0 28.3 1.0

Zinc binding site 3 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form


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 Multiple Conformations, Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn150 b:78.5 occ:1.00 SG C:CYS90 2.2 68.9 1.0 SG C:CYS27 2.3 83.7 1.0 SG C:CYS93 2.3 78.4 1.0 SG C:CYS24 2.5 68.6 1.0 CB C:CYS90 2.9 66.2 1.0 CB C:CYS93 3.4 83.4 1.0 CB C:CYS27 3.4 85.7 1.0 CB C:CYS24 3.4 69.1 1.0 N C:CYS93 3.6 84.5 1.0 N C:CYS27 3.9 81.5 1.0 CA C:CYS93 4.0 83.9 1.0 CA C:CYS27 4.2 84.8 1.0 CB C:GLN26 4.3 82.0 1.0 CA C:CYS90 4.3 65.7 1.0 CB C:SER95 4.5 65.7 1.0 C C:CYS93 4.6 79.9 1.0 N C:GLY94 4.6 76.1 1.0 CB C:GLN92 4.7 92.0 1.0 O C:CYS90 4.7 70.2 1.0 C C:GLN92 4.7 88.1 1.0 C C:CYS90 4.7 69.8 1.0 N C:SER95 4.8 68.4 1.0 C C:GLN26 4.8 83.1 1.0 N C:GLY28 4.8 78.6 1.0 CG C:GLN26 4.9 87.7 1.0 CA C:CYS24 4.9 68.2 1.0 CB C:GLN29 4.9 79.8 1.0 N C:GLN92 5.0 84.7 1.0

Zinc binding site 4 out of 4 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Multiple Conformations, Hexagonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn150 b:36.0 occ:1.00 SG D:CYS90 2.2 35.1 1.0 SG D:CYS27 2.2 36.7 1.0 SG D:CYS24 2.3 31.8 1.0 SG D:CYS93 2.4 34.7 1.0 CB D:CYS90 3.1 33.8 1.0 CB D:CYS93 3.2 35.8 1.0 CB D:CYS24 3.2 30.8 1.0 CB D:CYS27 3.3 38.5 1.0 N D:CYS27 3.8 39.7 1.0 N D:CYS93 3.9 37.8 1.0 CA D:CYS93 4.1 36.7 1.0 CA D:CYS27 4.1 39.0 1.0 CB D:GLN26 4.4 43.8 1.0 CA D:CYS90 4.6 32.7 1.0 CB D:GLN29 4.6 44.6 1.0 CA D:CYS24 4.7 30.0 1.0 N D:GLY28 4.7 37.9 1.0 CB D:GLN92 4.7 47.8 1.0 C D:GLN26 4.7 41.5 1.0 C D:CYS27 4.7 38.8 1.0 CB D:SER95 4.8 34.1 1.0 C D:GLN92 4.8 41.8 1.0 C D:CYS93 4.8 35.4 1.0 N D:GLN92 4.9 41.6 1.0 N D:GLN29 5.0 39.5 1.0 CA D:GLN26 5.0 42.0 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