Atomistry » Zinc » PDB 8b9v-8bru » 8bjk
Atomistry »
  Zinc »
    PDB 8b9v-8bru »
      8bjk »

Zinc in PDB 8bjk: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352

Protein crystallography data

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352, PDB code: 8bjk was solved by C.Barinka, L.Motlova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.64 / 1.35
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.49, 83.78, 94.33, 90, 90, 90
R / Rfree (%) 16.8 / 20.7

Other elements in 8bjk:

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 (pdb code 8bjk). 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 X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352, PDB code: 8bjk:

Zinc binding site 1 out of 1 in 8bjk

Go back to Zinc Binding Sites List in 8bjk
Zinc binding site 1 out of 1 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:13.7
occ:1.00
OD1 A:ASP612 2.0 7.7 1.0
OD2 A:ASP705 2.0 9.2 1.0
ND1 A:HIS614 2.0 8.1 1.0
N4 A:QXF804 2.1 9.0 1.0
O1 A:QXF804 2.6 10.6 1.0
CG A:ASP612 2.7 9.0 1.0
OD2 A:ASP612 2.7 8.3 1.0
N3 A:QXF804 2.9 8.4 1.0
CE1 A:HIS614 2.9 10.6 1.0
CG A:ASP705 3.0 10.0 1.0
C13 A:QXF804 3.1 6.8 1.0
CG A:HIS614 3.1 9.8 1.0
OD1 A:ASP705 3.3 8.6 1.0
CB A:HIS614 3.6 9.2 1.0
N A:HIS614 3.8 8.4 1.0
NE2 A:HIS614 4.1 10.6 1.0
NE2 A:HIS573 4.1 9.6 1.0
CB A:ASP612 4.1 7.6 1.0
CD2 A:HIS614 4.2 10.7 1.0
CG1 A:VAL613 4.2 9.0 1.0
CA A:GLY743 4.3 8.4 1.0
N A:VAL613 4.3 8.3 1.0
CB A:ASP705 4.3 9.4 1.0
CA A:HIS614 4.3 9.1 1.0
C11 A:QXF804 4.4 6.8 1.0
CE1 A:HIS573 4.5 8.4 1.0
OH A:TYR745 4.6 10.4 1.0
N A:GLY743 4.6 7.2 1.0
CE2 A:TYR745 4.8 11.1 1.0
C A:ASP612 4.8 7.8 1.0
NE2 A:HIS574 4.8 9.2 1.0
C A:VAL613 4.8 8.8 1.0
CA A:ASP612 4.8 8.4 1.0
C10 A:QXF804 4.9 8.2 1.0
CA A:VAL613 4.9 8.8 1.0

Reference:

L.Motlova, I.Snajdr, Z.Kutil, E.Andris, J.Ptacek, A.Novotna, Z.Novakova, B.Havlinova, W.Tueckmantel, H.Draberova, P.Majer, M.Schutkowski, A.Kozikowski, L.Rulisek, C.Barinka. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors By Histone Deacetylase 6 (HDAC6). Acs Chem.Biol. V. 18 1594 2023.
ISSN: ESSN 1554-8937
PubMed: 37392419
DOI: 10.1021/ACSCHEMBIO.3C00212
Page generated: Wed Oct 30 18:21:39 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy