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

Enzymatic activity of 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;

Other elements in 6z2j:

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

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex, PDB code: 6z2j:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6z2j

Go back to Potassium Binding Sites List in 6z2j
Potassium binding site 1 out of 4 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K503

b:80.5
occ:1.00
HB3 C:HIS199 2.6 73.3 1.0
OD1 C:ASP174 2.7 68.4 1.0
HA C:HIS179 2.8 76.8 1.0
O C:HIS178 2.8 81.1 1.0
O C:ASP174 2.8 68.4 1.0
OG C:SER197 2.8 68.6 1.0
CG C:ASP174 2.8 68.4 1.0
O C:ASP176 2.8 77.0 1.0
O C:PHE198 3.0 73.1 1.0
HB3 C:ASP174 3.0 68.4 1.0
OD2 C:ASP174 3.2 68.4 1.0
H C:GLY180 3.3 75.1 1.0
HD1 C:HIS199 3.4 73.3 1.0
CB C:ASP174 3.4 68.4 1.0
CB C:HIS199 3.6 73.3 1.0
C C:ASP174 3.7 68.4 1.0
CA C:HIS179 3.7 76.8 1.0
C C:PHE198 3.7 73.1 1.0
H C:PHE198 3.8 73.1 1.0
C C:HIS178 3.8 81.1 1.0
N C:GLY180 3.9 75.1 1.0
H C:ASP176 3.9 77.0 1.0
HA C:SER197 3.9 68.6 1.0
C C:ASP176 3.9 77.0 1.0
HB3 C:ASP176 3.9 77.0 1.0
CB C:SER197 4.0 68.6 1.0
N C:PHE198 4.0 73.1 1.0
ND1 C:HIS199 4.0 73.3 1.0
N C:ASP176 4.0 77.0 1.0
HB2 C:HIS199 4.1 73.3 1.0
HD2 C:HIS179 4.1 76.8 1.0
HA C:HIS199 4.1 73.3 1.0
CG C:HIS199 4.2 73.3 1.0
HB2 C:SER197 4.2 68.6 1.0
CA C:ASP174 4.2 68.4 1.0
N C:HIS179 4.2 76.8 1.0
HB2 C:ASP174 4.2 68.4 1.0
CA C:SER197 4.3 68.6 1.0
C C:HIS179 4.3 76.8 1.0
CA C:HIS199 4.3 73.3 1.0
C C:SER197 4.3 68.6 1.0
N C:HIS199 4.4 73.3 1.0
CA C:ASP176 4.4 77.0 1.0
C C:ILE175 4.4 73.3 1.0
CA C:PHE198 4.5 73.1 1.0
N C:ILE175 4.6 73.3 1.0
CB C:ASP176 4.6 77.0 1.0
HB2 C:HIS179 4.7 76.8 1.0
HB3 C:SER197 4.7 68.6 1.0
CB C:HIS179 4.7 76.8 1.0
HA C:ASP174 4.8 68.4 1.0
CD2 C:HIS179 4.8 76.8 1.0
HA C:ILE175 4.8 73.3 1.0
HA3 C:GLY180 4.8 75.1 1.0
O C:ILE175 4.9 73.3 1.0
CA C:ILE175 4.9 73.3 1.0
CA C:GLY180 5.0 75.1 1.0

Potassium binding site 2 out of 4 in 6z2j

Go back to Potassium Binding Sites List in 6z2j
Potassium binding site 2 out of 4 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
C:K504

b:58.1
occ:1.00
O C:PHE187 2.6 66.6 1.0
O C:THR190 2.8 65.7 1.0
O C:TYR222 2.8 62.4 1.0
HB3 C:TYR222 2.8 62.4 1.0
O C:VAL193 2.9 59.2 1.0
HB2 C:ALA223 3.1 64.9 1.0
C C:TYR222 3.5 62.4 1.0
HB2 C:TYR222 3.5 62.4 1.0
H C:THR190 3.5 65.7 1.0
CB C:TYR222 3.5 62.4 1.0
C C:PHE187 3.8 66.6 1.0
HB3 C:PHE187 3.9 66.6 1.0
HG23 C:THR190 3.9 65.7 1.0
C C:THR190 4.0 65.7 1.0
HA C:TYR188 4.0 73.7 1.0
CB C:ALA223 4.1 64.9 1.0
HA C:MET194 4.1 58.8 1.0
HG22 C:THR190 4.1 65.7 1.0
C C:VAL193 4.1 59.2 1.0
CA C:TYR222 4.1 62.4 1.0
N C:ALA223 4.2 64.9 1.0
N C:THR190 4.3 65.7 1.0
HB C:VAL193 4.3 59.2 1.0
HA C:ALA223 4.3 64.9 1.0
CA C:ALA223 4.4 64.9 1.0
CG2 C:THR190 4.5 65.7 1.0
HB2 C:PHE187 4.5 66.6 1.0
HA C:ASP191 4.5 65.1 1.0
HB3 C:ALA223 4.5 64.9 1.0
CB C:PHE187 4.5 66.6 1.0
C C:TYR188 4.5 73.7 1.0
CA C:TYR188 4.5 73.7 1.0
N C:TYR188 4.6 73.7 1.0
H C:VAL193 4.6 59.2 1.0
HB1 C:ALA223 4.7 64.9 1.0
HA2 C:GLY219 4.7 63.9 1.0
CA C:THR190 4.7 65.7 1.0
HA C:TYR222 4.7 62.4 1.0
CA C:PHE187 4.7 66.6 1.0
CG C:TYR222 4.7 62.4 1.0
H C:ALA223 4.8 64.9 1.0
N C:THR189 4.8 74.4 1.0
O C:TYR188 4.8 73.7 1.0
H C:THR195 4.8 63.5 1.0
CA C:MET194 4.9 58.8 1.0
H C:THR189 4.9 74.4 1.0
HD2 C:TYR222 4.9 62.4 1.0
O C:GLY219 4.9 63.9 1.0
N C:MET194 4.9 58.8 1.0
N C:ASP191 5.0 65.1 1.0

Potassium binding site 3 out of 4 in 6z2j

Go back to Potassium Binding Sites List in 6z2j
Potassium binding site 3 out of 4 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K503

b:81.6
occ:1.00
HB3 E:HIS199 2.6 72.2 1.0
OD1 E:ASP174 2.7 67.0 1.0
HA E:HIS179 2.8 76.7 1.0
O E:HIS178 2.8 80.2 1.0
OG E:SER197 2.8 67.0 1.0
O E:ASP174 2.8 67.0 1.0
CG E:ASP174 2.8 67.0 1.0
O E:ASP176 2.8 75.7 1.0
O E:PHE198 3.0 71.9 1.0
HB3 E:ASP174 3.0 67.0 1.0
OD2 E:ASP174 3.2 67.0 1.0
H E:GLY180 3.3 75.5 1.0
HD1 E:HIS199 3.4 72.2 1.0
CB E:ASP174 3.4 67.0 1.0
CB E:HIS199 3.6 72.2 1.0
C E:ASP174 3.7 67.0 1.0
CA E:HIS179 3.7 76.7 1.0
C E:PHE198 3.7 71.9 1.0
H E:PHE198 3.8 71.9 1.0
C E:HIS178 3.8 80.2 1.0
N E:GLY180 3.9 75.5 1.0
H E:ASP176 3.9 75.7 1.0
HA E:SER197 3.9 67.0 1.0
C E:ASP176 3.9 75.7 1.0
HB3 E:ASP176 3.9 75.7 1.0
CB E:SER197 4.0 67.0 1.0
N E:PHE198 4.0 71.9 1.0
ND1 E:HIS199 4.0 72.2 1.0
N E:ASP176 4.0 75.7 1.0
HB2 E:HIS199 4.1 72.2 1.0
HD2 E:HIS179 4.1 76.7 1.0
HA E:HIS199 4.1 72.2 1.0
CG E:HIS199 4.2 72.2 1.0
HB2 E:SER197 4.2 67.0 1.0
CA E:ASP174 4.2 67.0 1.0
N E:HIS179 4.2 76.7 1.0
HB2 E:ASP174 4.2 67.0 1.0
CA E:SER197 4.3 67.0 1.0
C E:HIS179 4.3 76.7 1.0
CA E:HIS199 4.3 72.2 1.0
C E:SER197 4.3 67.0 1.0
N E:HIS199 4.4 72.2 1.0
CA E:ASP176 4.4 75.7 1.0
C E:ILE175 4.4 71.3 1.0
CA E:PHE198 4.5 71.9 1.0
N E:ILE175 4.6 71.3 1.0
CB E:ASP176 4.6 75.7 1.0
HB2 E:HIS179 4.7 76.7 1.0
HB3 E:SER197 4.7 67.0 1.0
CB E:HIS179 4.7 76.7 1.0
HA E:ASP174 4.8 67.0 1.0
CD2 E:HIS179 4.8 76.7 1.0
HA E:ILE175 4.8 71.3 1.0
HA3 E:GLY180 4.8 75.5 1.0
O E:ILE175 4.9 71.3 1.0
CA E:ILE175 4.9 71.3 1.0
CA E:GLY180 5.0 75.5 1.0

Potassium binding site 4 out of 4 in 6z2j

Go back to Potassium Binding Sites List in 6z2j
Potassium binding site 4 out of 4 in the The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Structure of the Dimeric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K504

b:54.8
occ:1.00
O E:PHE187 2.6 67.6 1.0
O E:THR190 2.8 67.1 1.0
O E:TYR222 2.8 62.9 1.0
HB3 E:TYR222 2.8 62.9 1.0
O E:VAL193 2.9 60.4 1.0
HB1 E:ALA223 3.1 64.5 1.0
C E:TYR222 3.5 62.9 1.0
HB2 E:TYR222 3.5 62.9 1.0
H E:THR190 3.5 67.1 1.0
CB E:TYR222 3.5 62.9 1.0
C E:PHE187 3.8 67.6 1.0
HB3 E:PHE187 3.9 67.6 1.0
HG23 E:THR190 3.9 67.1 1.0
C E:THR190 4.0 67.1 1.0
HA E:TYR188 4.0 74.7 1.0
CB E:ALA223 4.1 64.5 1.0
HA E:MET194 4.1 58.5 1.0
HG22 E:THR190 4.1 67.1 1.0
C E:VAL193 4.1 60.4 1.0
CA E:TYR222 4.1 62.9 1.0
N E:ALA223 4.2 64.5 1.0
N E:THR190 4.3 67.1 1.0
HB E:VAL193 4.3 60.4 1.0
HA E:ALA223 4.3 64.5 1.0
CA E:ALA223 4.4 64.5 1.0
CG2 E:THR190 4.5 67.1 1.0
HB2 E:PHE187 4.5 67.6 1.0
HA E:ASP191 4.5 66.1 1.0
HB2 E:ALA223 4.5 64.5 1.0
CB E:PHE187 4.5 67.6 1.0
C E:TYR188 4.5 74.7 1.0
CA E:TYR188 4.5 74.7 1.0
N E:TYR188 4.6 74.7 1.0
H E:VAL193 4.6 60.4 1.0
HB3 E:ALA223 4.7 64.5 1.0
HA2 E:GLY219 4.7 66.6 1.0
CA E:THR190 4.7 67.1 1.0
HA E:TYR222 4.7 62.9 1.0
CA E:PHE187 4.7 67.6 1.0
CG E:TYR222 4.7 62.9 1.0
H E:ALA223 4.8 64.5 1.0
N E:THR189 4.8 76.2 1.0
O E:TYR188 4.8 74.7 1.0
H E:THR195 4.8 63.0 1.0
CA E:MET194 4.9 58.5 1.0
H E:THR189 4.9 76.2 1.0
HD2 E:TYR222 4.9 62.9 1.0
O E:GLY219 4.9 66.6 1.0
N E:MET194 4.9 58.5 1.0
N E:ASP191 5.0 66.1 1.0

Reference:

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
Page generated: Mon Dec 14 02:31:15 2020

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