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Zinc in PDB 5icn: HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4

Enzymatic activity of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4

All present enzymatic activity of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4:
3.5.1.98;

Protein crystallography data

The structure of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4, PDB code: 5icn was solved by C.J.Millard, N.S.Robertson, P.J.Watson, A.G.Jameson, J.W.R.Schwabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.40 / 3.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.815, 107.815, 134.161, 90.00, 90.00, 120.00
R / Rfree (%) 25.5 / 29.9

Other elements in 5icn:

The structure of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 (pdb code 5icn). 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 HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4, PDB code: 5icn:

Zinc binding site 1 out of 1 in 5icn

Go back to Zinc Binding Sites List in 5icn
Zinc binding site 1 out of 1 in the HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC1:MTA1 in Complex with Inositol-6-Phosphate and A Novel Peptide Inhibitor Based on Histone H4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:24.9
occ:1.00
 OD2 B:ASP264 1.9 14.5 1.0
OD1 B:ASP176 2.0 26.2 1.0
ND1 B:HIS178 2.1 27.8 1.0
O2 C:6A016 2.4 37.4 1.0
C1 C:6A016 2.8 38.9 1.0
CG B:ASP176 2.8 26.6 1.0
CG B:ASP264 2.8 14.8 1.0
O1 C:6A016 2.9 39.1 1.0
OD2 B:ASP176 3.0 27.2 1.0
CG B:HIS178 3.0 27.9 1.0
N1 C:6A016 3.1 38.1 1.0
OD1 B:ASP264 3.1 15.0 1.0
CE1 B:HIS178 3.1 27.9 1.0
CB B:HIS178 3.3 28.0 1.0
N B:HIS178 3.6 27.4 1.0
CG2 B:ILE177 3.9 25.1 1.0
CA B:HIS178 4.1 27.9 1.0
C2 C:6A016 4.1 41.8 1.0
CA B:GLY301 4.2 21.8 1.0
CD2 B:HIS178 4.2 27.7 1.0
CB B:ASP176 4.2 26.9 1.0
NE2 B:HIS178 4.2 27.5 1.0
CB B:ASP264 4.2 14.9 1.0
N B:ILE177 4.4 26.2 1.0
NE2 B:HIS140 4.4 38.2 1.0
C3 C:6A016 4.5 43.9 1.0
NE2 B:HIS141 4.6 44.2 1.0
C B:ILE177 4.6 26.4 1.0
N B:GLY301 4.6 21.9 1.0
CE2 B:TYR303 4.8 23.0 1.0
CA B:ILE177 4.8 25.7 1.0
C B:ASP176 4.8 26.8 1.0
CA B:ASP176 4.9 27.4 1.0
OH B:TYR303 4.9 25.2 1.0
O B:HIS178 4.9 28.5 1.0
CB B:ILE177 5.0 25.0 1.0

Reference:

P.J.Watson, C.J.Millard, A.M.Riley, N.S.Robertson, L.C.Wright, H.Y.Godage, S.M.Cowley, A.G.Jamieson, B.V.Potter, J.W.Schwabe. Insights Into the Activation Mechanism of Class I Hdac Complexes By Inositol Phosphates. Nat Commun V. 7 11262 2016.
ISSN: ESSN 2041-1723
PubMed: 27109927
DOI: 10.1038/NCOMMS11262
Page generated: Sun Oct 27 18:02:52 2024

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