Zinc in PDB 5g0j: Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A, PDB code: 5g0j 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)	50.00 / 2.88
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	187.224, 187.224, 102.718, 90.00, 90.00, 120.00
R / Rfree (%)	17.56 / 21.41

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A (pdb code 5g0j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A, PDB code: 5g0j:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1811 b:0.9 occ:1.00 O A:HOH2141 1.9 0.5 1.0 O A:N4R1817 2.0 0.4 1.0 OD1 A:ASP612 2.0 0.7 1.0 OD2 A:ASP705 2.1 0.9 1.0 ND1 A:HIS614 2.5 0.1 1.0 CG A:ASP612 2.8 0.6 1.0 OD2 A:ASP612 2.8 0.4 1.0 C11 A:N4R1817 2.9 0.9 1.0 CG A:ASP705 3.0 0.7 1.0 O1 A:N4R1817 3.3 0.5 1.0 CE1 A:HIS614 3.4 0.7 1.0 OD1 A:ASP705 3.5 0.1 1.0 CG A:HIS614 3.5 1.0 1.0 N1 A:N4R1817 3.5 0.4 1.0 CB A:HIS614 3.8 0.5 1.0 N A:HIS614 4.0 95.8 1.0 NE2 A:HIS573 4.0 92.7 1.0 C8 A:N4R1817 4.1 0.9 1.0 CB A:ASP705 4.1 87.4 1.0 CA A:GLY743 4.2 94.4 1.0 CB A:ASP612 4.2 89.8 1.0 CE1 A:HIS573 4.3 92.2 1.0 N A:VAL613 4.4 91.9 1.0 CA A:HIS614 4.5 98.2 1.0 C7 A:N4R1817 4.5 0.5 1.0 NE2 A:HIS614 4.6 0.0 1.0 NE2 A:HIS574 4.6 97.5 1.0 CD2 A:HIS614 4.6 0.2 1.0 N A:GLY743 4.7 94.4 1.0 CE2 A:TYR745 4.7 97.7 1.0 CG1 A:VAL613 4.7 94.5 1.0 C A:ASP612 4.8 94.0 1.0 OH A:TYR745 4.9 0.7 1.0 CA A:ASP612 4.9 88.9 1.0 C A:VAL613 4.9 96.6 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