Zinc 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:

Nickel

(Ni)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain, PDB code: 5g0f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain


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 Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2082 b:22.6 occ:0.90 ND1 A:HIS981 2.2 29.0 1.0 SG A:CYS1049 2.2 23.1 1.0 SG A:CYS979 2.4 24.4 1.0 SG A:CYS1052 2.5 33.3 1.0 CG A:HIS981 3.1 26.8 1.0 CE1 A:HIS981 3.1 30.2 1.0 CB A:CYS979 3.3 21.0 1.0 CB A:CYS1049 3.3 17.7 1.0 CB A:HIS981 3.5 21.8 1.0 CB A:CYS1052 3.5 28.3 1.0 N A:CYS1052 3.9 27.0 1.0 N A:HIS981 4.0 22.0 1.0 CD A:PRO980 4.1 26.0 1.0 NE2 A:HIS981 4.2 31.4 1.0 CD2 A:HIS981 4.3 30.6 1.0 CA A:CYS1052 4.3 28.0 1.0 CA A:HIS981 4.3 21.7 1.0 CB A:ALA1051 4.4 25.4 1.0 N A:PRO980 4.4 23.3 1.0 CA A:CYS979 4.5 21.4 1.0 C A:CYS979 4.5 25.1 1.0 C A:ALA1051 4.7 31.0 1.0 CA A:CYS1049 4.7 17.5 1.0 C A:PRO980 4.9 27.0 1.0 CA A:ALA1051 5.0 24.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain


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 Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2083 b:23.2 occ:0.90 NE2 A:HIS1030 2.0 29.6 1.0 ND1 A:HIS1036 2.1 28.4 1.0 SG A:CYS1011 2.3 22.3 1.0 SG A:CYS1014 2.5 27.4 1.0 CE1 A:HIS1030 2.8 30.6 1.0 CE1 A:HIS1036 3.1 28.3 1.0 CG A:HIS1036 3.1 27.2 1.0 CD2 A:HIS1030 3.2 29.0 1.0 CB A:CYS1011 3.2 17.8 1.0 CB A:HIS1036 3.4 23.6 1.0 CB A:CYS1014 3.7 24.7 1.0 N A:CYS1014 3.9 21.6 1.0 ND1 A:HIS1030 4.1 31.2 1.0 OG A:SER1034 4.2 38.1 1.0 CG A:HIS1030 4.2 28.2 1.0 NE2 A:HIS1036 4.2 29.5 1.0 CD2 A:HIS1036 4.3 29.2 1.0 CB A:PHE1013 4.3 22.5 1.0 CA A:CYS1014 4.4 22.9 1.0 O A:HOH3101 4.6 34.9 1.0 CA A:CYS1011 4.7 15.9 1.0 CB A:SER1034 4.7 32.0 1.0 C A:PHE1013 4.9 24.2 1.0 CA A:HIS1036 5.0 24.4 1.0 CA A:PHE1013 5.0 20.7 1.0 N A:PHE1013 5.0 20.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Danio Rerio HDAC6 Znf-Ubp Domain


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 Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2084 b:18.2 occ:1.00 ND1 A:HIS1026 2.0 19.0 1.0 SG A:CYS1019 2.3 18.6 1.0 SG A:CYS999 2.3 19.2 1.0 SG A:CYS1002 2.3 20.9 1.0 CE1 A:HIS1026 2.9 19.0 1.0 CG A:HIS1026 3.1 18.3 1.0 CB A:CYS999 3.2 15.3 1.0 CB A:CYS1019 3.3 15.2 1.0 CB A:HIS1026 3.5 15.5 1.0 CB A:CYS1002 3.5 18.7 1.0 N A:CYS1002 3.7 19.5 1.0 N A:CYS1019 3.9 15.9 1.0 NE2 A:HIS1026 4.1 19.9 1.0 CB A:ASN1024 4.1 16.5 1.0 CD2 A:HIS1026 4.2 20.6 1.0 CA A:CYS1019 4.2 14.9 1.0 CA A:CYS1002 4.2 19.3 1.0 CB A:GLU1001 4.4 24.8 1.0 C A:GLU1001 4.6 26.2 1.0 CA A:CYS999 4.7 16.0 1.0 N A:HIS1026 4.7 16.9 1.0 ND2 A:ASN1024 4.7 22.6 1.0 CA A:HIS1026 4.7 16.6 1.0 CA A:GLU1001 4.8 23.1 1.0 N A:GLU1001 4.8 22.3 1.0 CA A:ASN1024 4.9 17.4 1.0 N A:ASN1024 4.9 16.3 1.0 C A:CYS1002 5.0 23.5 1.0 CG A:ASN1024 5.0 30.3 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