Nickel in PDB 5amh: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form, PDB code: 5amh 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)	30.77 / 1.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.720, 51.720, 84.710, 90.00, 90.00, 120.00
R / Rfree (%)	12.565 / 15.737

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	7 atoms

The binding sites of Nickel atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form (pdb code 5amh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form, PDB code: 5amh:

Nickel binding site 1 out of 1 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Thalidomide, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1134 b:31.5 occ:0.50 ND1 A:HIS44 1.8 23.4 1.0 O A:HOH2070 2.2 26.7 0.5 O A:HOH2068 2.3 23.1 1.0 O A:HOH2069 2.3 22.1 1.0 CE1 A:HIS44 2.5 27.8 1.0 CG A:HIS44 2.9 18.3 1.0 CB A:HIS44 3.5 17.8 1.0 O A:HOH2064 3.6 19.4 1.0 NE2 A:HIS44 3.7 23.9 1.0 CD2 A:HIS44 3.9 21.7 1.0 N A:HIS44 4.2 15.3 1.0 CA A:HIS44 4.5 15.8 1.0 CB A:PRO39 4.6 21.2 1.0 CA A:PRO39 5.0 17.5 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