Nickel in PDB 5g0f: Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain

The structure of Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain, PDB code: 5g0f was solved by Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.13 / 1.90
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	100.740, 100.740, 100.740, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.5

The structure of Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Nickel atom in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain (pdb code 5g0f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain, PDB code: 5g0f:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2085 b:25.7 occ:1.00 NE2 A:HIS1069 2.1 21.1 1.0 O A:HOH3146 2.2 22.5 1.0 O A:HOH3158 2.3 40.5 1.0 O A:HOH3147 2.3 28.1 1.0 CD2 A:HIS1069 3.0 20.6 1.0 CE1 A:HIS1069 3.2 21.1 1.0 CG A:HIS1069 4.2 19.0 1.0 O A:HOH3027 4.3 65.8 1.0 ND1 A:HIS1069 4.3 20.6 1.0 O A:HOH3152 4.3 29.2 1.0 CD2 A:PHE1073 4.9 22.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2086 b:27.3 occ:1.00 NE2 A:HIS1057 1.9 32.4 1.0 NE2 A:HIS1062 2.1 19.9 1.0 O A:HOH3132 2.2 46.2 1.0 O A:HOH3138 2.3 33.6 1.0 O A:HOH3130 2.7 37.8 1.0 O A:HOH3131 2.7 44.1 1.0 CE1 A:HIS1057 2.8 32.2 1.0 CE1 A:HIS1062 2.9 20.8 1.0 CD2 A:HIS1057 3.1 32.2 1.0 O A:HOH3159 3.2 46.7 1.0 CD2 A:HIS1062 3.3 19.8 1.0 ND1 A:HIS1057 4.0 32.5 1.0 CG A:HIS1057 4.1 29.9 1.0 ND1 A:HIS1062 4.1 22.8 1.0 CG A:HIS1062 4.3 19.8 1.0 O A:HOH3026 4.4 31.1 1.0

Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias. Structural Insights Into HDAC6 Tubulin Deacetylation and Its Selective Inhibition Nat.Chem.Biol. V. 12 748 2016.
ISSN: ISSN 1552-4450
PubMed: 27454931
DOI: 10.1038/NCHEMBIO.2140