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:
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 Aug 12 18:29:06 2024
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