Zinc in PDB 6z2j: The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex

All present enzymatic activity of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex:
3.5.1.98;

The structure of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex (pdb code 6z2j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex, PDB code: 6z2j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:0.0 occ:1.00 OD2 C:ASP176 2.0 77.0 1.0 OD1 C:ASP176 2.0 77.0 1.0 OD2 C:ASP264 2.0 87.3 1.0 ND1 C:HIS178 2.0 81.1 1.0 CG C:ASP176 2.2 77.0 1.0 HA3 C:GLY301 2.5 81.5 1.0 CE1 C:HIS178 2.7 81.1 1.0 HE1 C:HIS178 2.7 81.1 1.0 CG C:ASP264 3.1 87.3 1.0 CG C:HIS178 3.2 81.1 1.0 HB2 C:HIS178 3.4 81.1 1.0 H C:GLY301 3.4 81.5 1.0 H C:HIS178 3.4 81.1 1.0 CA C:GLY301 3.5 81.5 1.0 CB C:ASP176 3.7 77.0 1.0 OD1 C:ASP264 3.7 87.3 1.0 HG22 C:ILE177 3.8 84.0 1.0 CB C:HIS178 3.8 81.1 1.0 N C:GLY301 3.9 81.5 1.0 HA2 C:GLY301 3.9 81.5 1.0 NE2 C:HIS178 3.9 81.1 1.0 HB3 C:ASP176 3.9 77.0 1.0 HB2 C:ASP176 4.0 77.0 1.0 HB3 C:ASP264 4.1 87.3 1.0 CD2 C:HIS178 4.2 81.1 1.0 HE2 C:HIS140 4.2 69.6 1.0 N C:HIS178 4.2 81.1 1.0 HE1 C:HIS140 4.3 69.6 1.0 CB C:ASP264 4.3 87.3 1.0 C C:GLY301 4.4 81.5 1.0 H C:ILE177 4.5 84.0 1.0 HE22 C:GLN260 4.6 63.8 1.0 OH C:TYR303 4.6 87.6 1.0 HB3 C:HIS178 4.6 81.1 1.0 H C:GLY302 4.6 85.9 1.0 HE2 C:HIS178 4.6 81.1 1.0 HB2 C:ASP264 4.6 87.3 1.0 HA C:ASP176 4.6 77.0 1.0 CA C:HIS178 4.7 81.1 1.0 CA C:ASP176 4.7 77.0 1.0 CG2 C:ILE177 4.7 84.0 1.0 HA3 C:GLY262 4.7 74.6 1.0 NE2 C:HIS140 4.8 69.6 1.0 N C:ILE177 4.8 84.0 1.0 H C:ASP264 4.8 87.3 1.0 CE1 C:HIS140 4.8 69.6 1.0 N C:GLY302 4.8 85.9 1.0 HH C:TYR303 4.9 87.6 1.0 C C:ASP176 5.0 77.0 1.0 HE2 C:TYR303 5.0 87.6 1.0 HG23 C:ILE177 5.0 84.0 1.0

Zinc binding site 2 out of 2 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:98.8 occ:1.00 OD2 E:ASP176 2.0 75.7 1.0 OD1 E:ASP176 2.0 75.7 1.0 OD2 E:ASP264 2.0 83.5 1.0 ND1 E:HIS178 2.0 80.2 1.0 CG E:ASP176 2.2 75.7 1.0 HA3 E:GLY301 2.5 80.9 1.0 CE1 E:HIS178 2.7 80.2 1.0 HE1 E:HIS178 2.7 80.2 1.0 CG E:ASP264 3.1 83.5 1.0 CG E:HIS178 3.2 80.2 1.0 HB2 E:HIS178 3.4 80.2 1.0 H E:GLY301 3.4 80.9 1.0 H E:HIS178 3.4 80.2 1.0 CA E:GLY301 3.5 80.9 1.0 CB E:ASP176 3.7 75.7 1.0 OD1 E:ASP264 3.7 83.5 1.0 HG23 E:ILE177 3.8 82.3 1.0 CB E:HIS178 3.8 80.2 1.0 N E:GLY301 3.9 80.9 1.0 HA2 E:GLY301 3.9 80.9 1.0 NE2 E:HIS178 3.9 80.2 1.0 HB3 E:ASP176 3.9 75.7 1.0 HB2 E:ASP176 4.0 75.7 1.0 HB3 E:ASP264 4.1 83.5 1.0 CD2 E:HIS178 4.2 80.2 1.0 HE2 E:HIS140 4.2 70.4 1.0 N E:HIS178 4.2 80.2 1.0 CB E:ASP264 4.3 83.5 1.0 HE1 E:HIS140 4.3 70.4 1.0 C E:GLY301 4.4 80.9 1.0 H E:ILE177 4.5 82.3 1.0 HE22 E:GLN260 4.6 62.8 1.0 OH E:TYR303 4.6 85.3 1.0 HB3 E:HIS178 4.6 80.2 1.0 H E:GLY302 4.6 84.4 1.0 HE2 E:HIS178 4.6 80.2 1.0 HB2 E:ASP264 4.6 83.5 1.0 HA E:ASP176 4.6 75.7 1.0 CA E:HIS178 4.7 80.2 1.0 CA E:ASP176 4.7 75.7 1.0 CG2 E:ILE177 4.7 82.3 1.0 HA3 E:GLY262 4.7 73.2 1.0 NE2 E:HIS140 4.8 70.4 1.0 N E:ILE177 4.8 82.3 1.0 H E:ASP264 4.8 83.5 1.0 CE1 E:HIS140 4.8 70.4 1.0 N E:GLY302 4.8 84.4 1.0 HH E:TYR303 4.9 85.3 1.0 C E:ASP176 5.0 75.7 1.0 HE2 E:TYR303 5.0 85.3 1.0 HG21 E:ILE177 5.0 82.3 1.0

R.E.Turnbull, L.Fairall, A.Saleh, E.Kelsall, K.L.Morris, T.J.Ragan, C.G.Savva, A.Chandru, C.J.Millard, O.V.Makarova, C.J.Smith, A.M.Roseman, A.M.Fry, S.M.Cowley, J.W.R.Schwabe. The Midac Histone Deacetylase Complex Is Essential For Embryonic Development and Has A Unique Multivalent Structure. Nat Commun V. 11 3252 2020.
ISSN: ESSN 2041-1723
PubMed: 32591534
DOI: 10.1038/S41467-020-17078-8