Zinc in PDB 6v7a: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657, PDB code: 6v7a was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.20 / 2.09
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.461, 64.871, 142.393, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.9

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 (pdb code 6v7a). 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 Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657, PDB code: 6v7a:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657


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 Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:25.5 occ:1.00 OD2 A:ASP705 2.0 22.2 1.0 OD1 A:ASP612 2.0 20.2 1.0 O26 A:QQG804 2.0 26.2 1.0 ND1 A:HIS614 2.1 21.6 1.0 O01 A:QQG804 2.5 30.0 1.0 N25 A:QQG804 2.5 35.8 1.0 CG A:ASP612 2.7 22.6 1.0 OD2 A:ASP612 2.8 24.9 1.0 C02 A:QQG804 2.8 32.1 1.0 CE1 A:HIS614 3.0 25.0 1.0 CG A:ASP705 3.1 23.1 1.0 CG A:HIS614 3.2 23.5 1.0 OD1 A:ASP705 3.5 19.9 1.0 CB A:HIS614 3.7 22.4 1.0 N A:HIS614 4.0 20.2 1.0 NE2 A:HIS614 4.2 23.4 1.0 CB A:ASP612 4.2 20.0 1.0 NE2 A:HIS573 4.2 25.8 1.0 C03 A:QQG804 4.2 29.9 1.0 CD2 A:HIS614 4.3 22.3 1.0 CB A:ASP705 4.3 22.1 1.0 CA A:GLY743 4.3 24.1 1.0 CG1 A:VAL613 4.4 18.0 1.0 N A:VAL613 4.4 20.8 1.0 CA A:HIS614 4.4 20.3 1.0 OH A:TYR745 4.5 24.9 1.0 CE1 A:HIS573 4.6 23.2 1.0 CE2 A:TYR745 4.6 23.2 1.0 NE2 A:HIS574 4.7 24.8 1.0 N A:GLY743 4.8 22.7 1.0 C A:VAL613 4.9 19.9 1.0 C A:ASP612 5.0 20.2 1.0 CA A:ASP612 5.0 20.1 1.0 C04 A:QQG804 5.0 33.0 1.0

A.P.Saraswati, N.Relitti, M.Brindisi, J.D.Osko, G.Chemi, S.Federico, A.Grillo, S.Brogi, N.H.Mccabe, R.C.Turkington, O.Ibrahim, J.O'sullivan, S.Lamponi, M.Ghanim, V.P.Kelly, D.Zisterer, R.Amet, P.Hannon Barroeta, F.Vanni, C.Ulivieri, D.Herp, F.Sarno, A.Di Costanzo, F.Saccoccia, G.Ruberti, M.Jung, L.Altucci, S.Gemma, S.Butini, D.W.Christianson, G.Campiani. Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation. Acs Med.Chem.Lett. V. 11 2268 2020.
ISSN: ISSN 1948-5875
PubMed: 33214839
DOI: 10.1021/ACSMEDCHEMLETT.0C00395