Zinc in PDB 5g0i: Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A, PDB code: 5g0i 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)	45.58 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.560, 52.830, 186.420, 90.00, 108.92, 90.00
R / Rfree (%)	17.39 / 20.03

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

Potassium	(K)	8 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A (pdb code 5g0i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A, PDB code: 5g0i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) 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 Cleaved) in Complex with Nexturastat A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:41.5 occ:0.84 OD2 A:ASP705 1.9 43.6 1.0 OD1 A:ASP612 2.1 39.2 1.0 O A:HOH2316 2.1 42.5 1.0 ND1 A:HIS614 2.2 36.5 1.0 O A:N4R1808 2.6 51.3 1.0 OD2 A:ASP612 2.7 35.0 1.0 CG A:ASP612 2.7 37.7 1.0 CG A:ASP705 3.0 36.8 1.0 CE1 A:HIS614 3.2 36.5 1.0 CG A:HIS614 3.3 34.9 1.0 OD1 A:ASP705 3.4 36.4 1.0 C11 A:N4R1808 3.5 52.0 1.0 CB A:HIS614 3.6 30.5 1.0 O1 A:N4R1808 4.0 63.8 1.0 N A:HIS614 4.0 27.9 1.0 N1 A:N4R1808 4.1 56.2 1.0 NE2 A:HIS573 4.1 39.9 1.0 CB A:ASP612 4.2 33.5 1.0 CA A:GLY743 4.3 42.5 1.0 CB A:ASP705 4.3 33.8 1.0 NE2 A:HIS614 4.3 37.5 1.0 CD2 A:HIS614 4.4 37.4 1.0 CG1 A:VAL613 4.4 33.5 1.0 CA A:HIS614 4.4 28.6 1.0 NE2 A:HIS574 4.5 41.6 1.0 N A:VAL613 4.5 31.0 1.0 C8 A:N4R1808 4.6 49.4 1.0 CE1 A:HIS573 4.6 38.6 1.0 OH A:TYR745 4.6 47.2 1.0 N A:GLY743 4.7 41.8 1.0 CE2 A:TYR745 4.8 41.4 1.0 C A:ASP612 4.9 33.2 1.0 C A:VAL613 5.0 32.0 1.0 CA A:ASP612 5.0 32.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) 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 2 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:39.6 occ:0.80 O A:HOH2111 2.1 38.5 1.0 OD2 A:ASP323 2.1 40.3 1.0 OD1 A:ASP230 2.2 39.9 1.0 ND1 A:HIS232 2.3 37.7 1.0 O A:N4R1809 2.4 49.9 1.0 OD2 A:ASP230 2.7 39.0 1.0 CG A:ASP230 2.8 39.3 1.0 CG A:ASP323 3.1 41.1 1.0 CE1 A:HIS232 3.2 37.3 1.0 C11 A:N4R1809 3.3 52.3 1.0 OD1 A:ASP323 3.4 39.6 1.0 CG A:HIS232 3.4 36.3 1.0 CB A:HIS232 3.7 32.8 1.0 O1 A:N4R1809 3.9 62.3 1.0 N1 A:N4R1809 3.9 57.6 1.0 CA A:GLY361 4.0 35.6 1.0 N A:HIS232 4.0 33.3 1.0 NE2 A:HIS192 4.2 39.9 1.0 C8 A:N4R1809 4.2 51.3 1.0 CB A:ASP230 4.3 34.4 1.0 NE2 A:HIS232 4.4 38.6 1.0 N A:GLY361 4.4 35.6 1.0 CB A:ASP323 4.4 34.8 1.0 CG1 A:VAL231 4.5 35.4 1.0 CD2 A:HIS232 4.5 38.7 1.0 N A:VAL231 4.5 32.0 1.0 CA A:HIS232 4.5 32.6 1.0 CE2 A:TYR363 4.6 38.8 1.0 NE2 A:HIS193 4.6 39.6 1.0 CE1 A:HIS192 4.6 39.5 1.0 OH A:TYR363 4.7 48.1 1.0 C9 A:N4R1809 4.8 52.6 1.0 C A:ASP230 5.0 34.4 1.0 C A:VAL231 5.0 36.6 1.0 C A:GLY361 5.0 42.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) 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 3 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1802 b:44.2 occ:0.66 O B:HOH2058 1.9 42.6 1.0 OD2 B:ASP323 2.0 57.0 1.0 OD1 B:ASP230 2.2 58.7 1.0 ND1 B:HIS232 2.2 55.2 1.0 O B:N4R1809 2.6 57.1 1.0 OD2 B:ASP230 2.8 53.1 1.0 CG B:ASP230 2.8 55.2 1.0 CG B:ASP323 3.0 51.2 1.0 CE1 B:HIS232 3.1 53.5 1.0 OD1 B:ASP323 3.3 49.2 1.0 CG B:HIS232 3.3 56.0 1.0 C11 B:N4R1809 3.5 59.3 1.0 CB B:HIS232 3.7 54.8 1.0 N B:HIS232 4.0 54.3 1.0 O1 B:N4R1809 4.1 69.3 1.0 CA B:GLY361 4.1 50.6 1.0 N1 B:N4R1809 4.2 63.5 1.0 NE2 B:HIS232 4.3 55.2 1.0 CB B:ASP323 4.3 45.5 1.0 CB B:ASP230 4.3 51.1 1.0 CG1 B:VAL231 4.3 54.0 1.0 NE2 B:HIS192 4.4 59.6 1.0 CD2 B:HIS232 4.4 57.8 1.0 N B:VAL231 4.4 51.2 1.0 CA B:HIS232 4.5 55.3 1.0 CE2 B:TYR363 4.5 47.9 1.0 N B:GLY361 4.5 52.7 1.0 C8 B:N4R1809 4.5 59.5 1.0 NE2 B:HIS193 4.7 60.5 1.0 OH B:TYR363 4.7 57.2 1.0 CE1 B:HIS192 4.8 60.6 1.0 C7 B:N4R1809 4.8 60.2 1.0 C B:VAL231 4.9 57.1 1.0 C B:ASP230 4.9 53.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) 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 4 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1803 b:45.1 occ:0.63 O B:HOH2171 1.9 40.5 1.0 OD2 B:ASP705 1.9 50.6 1.0 OD1 B:ASP612 2.2 54.9 1.0 ND1 B:HIS614 2.3 59.3 1.0 O B:N4R1808 2.6 67.0 1.0 OD2 B:ASP612 2.7 45.8 1.0 CG B:ASP612 2.8 51.0 1.0 CG B:ASP705 2.9 59.0 1.0 CE1 B:HIS614 3.2 59.3 1.0 CG B:HIS614 3.3 58.3 1.0 OD1 B:ASP705 3.4 59.2 1.0 C11 B:N4R1808 3.4 68.8 1.0 CB B:HIS614 3.7 53.7 1.0 O1 B:N4R1808 3.7 79.8 1.0 N1 B:N4R1808 3.9 74.7 1.0 N B:HIS614 4.1 54.7 1.0 NE2 B:HIS573 4.1 54.5 1.0 CA B:GLY743 4.2 55.0 1.0 CB B:ASP705 4.2 55.5 1.0 CB B:ASP612 4.3 47.5 1.0 NE2 B:HIS614 4.4 61.5 1.0 CG1 B:VAL613 4.4 60.8 1.0 CD2 B:HIS614 4.5 61.6 1.0 NE2 B:HIS574 4.5 54.7 1.0 C8 B:N4R1808 4.5 66.2 1.0 CA B:HIS614 4.5 54.1 1.0 OH B:TYR745 4.6 60.1 1.0 N B:VAL613 4.6 54.4 1.0 N B:GLY743 4.6 53.7 1.0 CE1 B:HIS573 4.7 54.5 1.0 CE2 B:TYR745 4.7 59.6 1.0 C B:ASP612 5.0 55.7 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