Zinc in PDB 7qno: Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2

The structure of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2, PDB code: 7qno was solved by G.Kempf, G.Langousis, J.Sanchez, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.34 / 2.38
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	186.134, 186.134, 102.442, 90, 90, 120
R / Rfree (%)	21.2 / 22.8

The structure of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 (pdb code 7qno). 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 Ligand-Free Danio Rerio HDAC6 CD1 CD2, PDB code: 7qno:

Zinc binding site 1 out of 1 in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2


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 Ligand-Free Danio Rerio HDAC6 CD1 CD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:100.0 occ:1.00 ND1 A:HIS614 1.9 102.4 1.0 OD2 A:ASP705 2.0 108.8 1.0 O A:HOH1001 2.0 105.0 1.0 OD2 A:ASP612 2.0 106.3 1.0 OD1 A:ASP612 2.0 105.4 1.0 CG A:ASP612 2.3 102.4 1.0 CE1 A:HIS614 2.5 103.8 1.0 HE1 A:HIS614 2.6 126.1 0.0 HA3 A:GLY743 2.7 116.5 0.0 CG A:HIS614 3.0 106.5 1.0 CG A:ASP705 3.1 108.7 1.0 H A:HIS614 3.1 122.6 0.0 HB2 A:HIS614 3.3 125.1 0.0 HE1 A:HIS573 3.4 115.3 0.0 HG12 A:VAL613 3.5 122.9 0.0 OD1 A:ASP705 3.5 117.6 1.0 NE2 A:HIS614 3.5 103.8 1.0 CB A:HIS614 3.6 103.0 1.0 H A:GLY743 3.7 111.0 0.0 OH A:TYR745 3.7 100.5 1.0 CA A:GLY743 3.7 95.8 1.0 CD2 A:HIS614 3.8 99.8 1.0 CB A:ASP612 3.8 91.1 1.0 N A:HIS614 3.9 100.8 1.0 HE2 A:TYR745 3.9 118.3 0.0 H A:VAL613 3.9 123.2 0.0 CE1 A:HIS573 4.0 94.8 1.0 HH A:TYR745 4.0 122.2 0.0 N A:GLY743 4.1 91.2 1.0 HA2 A:GLY743 4.1 116.5 0.0 H A:GLY744 4.2 114.3 0.0 HE2 A:HIS614 4.2 126.2 0.0 HB2 A:ASP612 4.2 110.8 0.0 HB3 A:ASP612 4.2 110.8 0.0 NE2 A:HIS573 4.3 93.6 1.0 CB A:ASP705 4.3 100.2 1.0 N A:VAL613 4.4 101.4 1.0 HA3 A:GLY703 4.4 113.9 0.0 CA A:HIS614 4.4 102.2 1.0 HB3 A:ASP705 4.4 121.8 0.0 CG1 A:VAL613 4.4 101.1 1.0 HB3 A:HIS614 4.5 125.1 0.0 CZ A:TYR745 4.5 95.8 1.0 CE2 A:TYR745 4.5 97.3 1.0 HA A:ASP612 4.6 107.6 0.0 HB2 A:ASP705 4.6 121.8 0.0 C A:GLY743 4.6 91.0 1.0 NE2 A:HIS574 4.6 94.5 1.0 HD2 A:HIS614 4.6 121.3 0.0 CA A:ASP612 4.7 88.3 1.0 N A:GLY744 4.7 94.0 1.0 HG13 A:VAL613 4.8 122.9 0.0 C A:ASP612 4.8 94.6 1.0 HG11 A:VAL613 4.8 122.9 0.0 HB3 A:GLU742 4.9 104.5 0.0 C A:VAL613 4.9 99.2 1.0 H A:ASP705 4.9 123.5 0.0

G.Langousis, J.Sanchez, G.Kempf, P.Matthias. Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol.Biol. V.2589 467 2023.
ISSN: ISSN 1064-3745
PubMed: 36255643
DOI: 10.1007/978-1-0716-2788-4_30