Calcium in PDB 5ix0: HDAC2 with Ligand BRD7232
Enzymatic activity of HDAC2 with Ligand BRD7232
All present enzymatic activity of HDAC2 with Ligand BRD7232:
3.5.1.98;
Protein crystallography data
The structure of HDAC2 with Ligand BRD7232, PDB code: 5ix0
was solved by
S.Steinbacher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.74 /
1.72
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.195,
97.473,
139.254,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18 /
20
|
Other elements in 5ix0:
The structure of HDAC2 with Ligand BRD7232 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the HDAC2 with Ligand BRD7232
(pdb code 5ix0). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
HDAC2 with Ligand BRD7232, PDB code: 5ix0:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 1 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:20.5
occ:1.00
|
O
|
A:PHE203
|
2.5
|
15.6
|
1.0
|
|
O
|
A:ASP181
|
2.5
|
14.4
|
1.0
|
|
OD1
|
A:ASP179
|
2.5
|
16.6
|
1.0
|
|
O
|
A:HIS183
|
2.6
|
15.7
|
1.0
|
|
O
|
A:ASP179
|
2.9
|
15.9
|
1.0
|
|
OG
|
A:SER202
|
3.0
|
17.3
|
1.0
|
|
CG
|
A:ASP179
|
3.3
|
16.1
|
1.0
|
|
C
|
A:PHE203
|
3.5
|
16.2
|
1.0
|
|
C
|
A:ASP181
|
3.5
|
14.7
|
1.0
|
|
C
|
A:ASP179
|
3.6
|
15.5
|
1.0
|
|
C
|
A:HIS183
|
3.7
|
16.5
|
1.0
|
|
N
|
A:ASP181
|
3.8
|
14.0
|
1.0
|
|
N
|
A:PHE203
|
3.8
|
16.5
|
1.0
|
|
CB
|
A:HIS204
|
3.9
|
16.5
|
1.0
|
|
CB
|
A:ASP179
|
3.9
|
15.7
|
1.0
|
|
CB
|
A:ASP181
|
4.0
|
14.3
|
1.0
|
|
CA
|
A:ASP181
|
4.0
|
14.2
|
1.0
|
|
C
|
A:ILE180
|
4.2
|
14.6
|
1.0
|
|
OD2
|
A:ASP179
|
4.2
|
16.9
|
1.0
|
|
N
|
A:ILE180
|
4.2
|
15.1
|
1.0
|
|
CB
|
A:SER202
|
4.2
|
17.2
|
1.0
|
|
N
|
A:HIS204
|
4.3
|
16.4
|
1.0
|
|
CA
|
A:HIS204
|
4.3
|
16.8
|
1.0
|
|
ND1
|
A:HIS204
|
4.3
|
16.7
|
1.0
|
|
CA
|
A:PHE203
|
4.3
|
16.3
|
1.0
|
|
CA
|
A:ILE180
|
4.3
|
14.8
|
1.0
|
|
CA
|
A:ASP179
|
4.3
|
15.2
|
1.0
|
|
N
|
A:HIS183
|
4.4
|
16.0
|
1.0
|
|
CA
|
A:SER202
|
4.4
|
16.6
|
1.0
|
|
CA
|
A:HIS184
|
4.4
|
17.3
|
1.0
|
|
N
|
A:HIS184
|
4.4
|
17.0
|
1.0
|
|
N
|
A:GLY185
|
4.5
|
17.3
|
1.0
|
|
C
|
A:SER202
|
4.5
|
16.8
|
1.0
|
|
C
|
A:ILE182
|
4.6
|
15.8
|
1.0
|
|
CG
|
A:HIS204
|
4.6
|
16.9
|
1.0
|
|
N
|
A:ILE182
|
4.6
|
15.1
|
1.0
|
|
CA
|
A:HIS183
|
4.7
|
16.7
|
1.0
|
|
C
|
A:HIS184
|
4.7
|
17.2
|
1.0
|
|
CE1
|
A:HIS145
|
4.8
|
16.8
|
1.0
|
|
O
|
A:ILE180
|
4.9
|
14.6
|
1.0
|
|
O
|
A:ILE182
|
4.9
|
15.9
|
1.0
|
|
CA
|
A:ILE182
|
5.0
|
15.9
|
1.0
|
|
Calcium binding site 2 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 2 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:28.4
occ:1.00
|
O
|
A:HOH575
|
2.4
|
21.8
|
1.0
|
|
O
|
A:PHE192
|
2.4
|
20.4
|
1.0
|
|
O
|
A:VAL198
|
2.5
|
22.1
|
1.0
|
|
O
|
A:THR195
|
2.7
|
22.5
|
1.0
|
|
O
|
A:HOH570
|
3.0
|
25.6
|
1.0
|
|
O
|
A:TYR227
|
3.2
|
19.9
|
1.0
|
|
C
|
A:PHE192
|
3.5
|
20.7
|
1.0
|
|
C
|
A:VAL198
|
3.7
|
21.1
|
1.0
|
|
CB
|
A:TYR227
|
3.7
|
22.3
|
1.0
|
|
C
|
A:TYR227
|
3.8
|
20.6
|
1.0
|
|
C
|
A:THR195
|
3.9
|
23.2
|
1.0
|
|
CB
|
A:PHE192
|
4.1
|
19.1
|
1.0
|
|
N
|
A:TYR193
|
4.4
|
20.9
|
1.0
|
|
CA
|
A:TYR193
|
4.4
|
21.4
|
1.0
|
|
N
|
A:THR195
|
4.4
|
23.1
|
1.0
|
|
CA
|
A:TYR227
|
4.4
|
21.8
|
1.0
|
|
CA
|
A:PHE192
|
4.4
|
19.9
|
1.0
|
|
C
|
A:TYR193
|
4.4
|
22.2
|
1.0
|
|
CG2
|
A:THR195
|
4.4
|
22.4
|
1.0
|
|
O
|
A:TYR193
|
4.5
|
22.8
|
1.0
|
|
CA
|
A:MET199
|
4.5
|
21.7
|
1.0
|
|
N
|
A:MET199
|
4.5
|
21.2
|
1.0
|
|
CA
|
A:VAL198
|
4.6
|
20.4
|
1.0
|
|
O
|
A:GLY224
|
4.6
|
23.5
|
1.0
|
|
CA
|
A:THR195
|
4.7
|
23.6
|
1.0
|
|
N
|
A:ALA228
|
4.7
|
20.3
|
1.0
|
|
CA
|
A:GLY224
|
4.7
|
25.3
|
1.0
|
|
N
|
A:THR200
|
4.7
|
18.8
|
1.0
|
|
CB
|
A:VAL198
|
4.7
|
19.7
|
1.0
|
|
N
|
A:VAL198
|
4.8
|
21.3
|
1.0
|
|
OG1
|
A:THR200
|
4.8
|
18.6
|
1.0
|
|
N
|
A:ASP196
|
4.9
|
24.3
|
1.0
|
|
CG
|
A:TYR227
|
5.0
|
23.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 3 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:18.6
occ:1.00
|
O
|
B:ASP181
|
2.5
|
11.4
|
1.0
|
|
O
|
B:PHE203
|
2.5
|
13.3
|
1.0
|
|
OD1
|
B:ASP179
|
2.5
|
12.6
|
1.0
|
|
O
|
B:HIS183
|
2.7
|
12.2
|
1.0
|
|
OG
|
B:SER202
|
2.9
|
13.7
|
1.0
|
|
O
|
B:ASP179
|
2.9
|
12.1
|
1.0
|
|
CG
|
B:ASP179
|
3.3
|
13.0
|
1.0
|
|
C
|
B:ASP181
|
3.5
|
11.7
|
1.0
|
|
C
|
B:ASP179
|
3.5
|
12.1
|
1.0
|
|
C
|
B:PHE203
|
3.5
|
13.3
|
1.0
|
|
N
|
B:ASP181
|
3.7
|
11.2
|
1.0
|
|
C
|
B:HIS183
|
3.7
|
13.0
|
1.0
|
|
CB
|
B:ASP179
|
3.8
|
12.6
|
1.0
|
|
N
|
B:PHE203
|
3.9
|
13.3
|
1.0
|
|
CB
|
B:HIS204
|
3.9
|
13.6
|
1.0
|
|
CA
|
B:ASP181
|
3.9
|
11.5
|
1.0
|
|
CB
|
B:ASP181
|
4.0
|
11.5
|
1.0
|
|
N
|
B:ILE180
|
4.1
|
11.9
|
1.0
|
|
C
|
B:ILE180
|
4.1
|
11.7
|
1.0
|
|
CB
|
B:SER202
|
4.2
|
13.5
|
1.0
|
|
OD2
|
B:ASP179
|
4.2
|
13.3
|
1.0
|
|
CA
|
B:ILE180
|
4.2
|
11.6
|
1.0
|
|
CA
|
B:ASP179
|
4.3
|
12.2
|
1.0
|
|
CA
|
B:HIS204
|
4.3
|
14.0
|
1.0
|
|
N
|
B:HIS204
|
4.3
|
13.7
|
1.0
|
|
CA
|
B:PHE203
|
4.4
|
13.8
|
1.0
|
|
ND1
|
B:HIS204
|
4.4
|
13.9
|
1.0
|
|
CA
|
B:SER202
|
4.4
|
13.3
|
1.0
|
|
N
|
B:HIS183
|
4.4
|
12.6
|
1.0
|
|
CA
|
B:HIS184
|
4.5
|
13.9
|
1.0
|
|
N
|
B:HIS184
|
4.5
|
13.8
|
1.0
|
|
C
|
B:SER202
|
4.5
|
13.8
|
1.0
|
|
N
|
B:GLY185
|
4.5
|
14.3
|
1.0
|
|
O
|
B:HOH554
|
4.5
|
13.4
|
1.0
|
|
C
|
B:ILE182
|
4.6
|
12.9
|
1.0
|
|
N
|
B:ILE182
|
4.6
|
11.9
|
1.0
|
|
CG
|
B:HIS204
|
4.6
|
14.0
|
1.0
|
|
CA
|
B:HIS183
|
4.7
|
13.3
|
1.0
|
|
CE1
|
B:HIS145
|
4.8
|
13.6
|
1.0
|
|
C
|
B:HIS184
|
4.8
|
14.1
|
1.0
|
|
O
|
B:ILE180
|
4.9
|
12.3
|
1.0
|
|
CA
|
B:ILE182
|
5.0
|
12.6
|
1.0
|
|
O
|
B:ILE182
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 4 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:26.1
occ:1.00
|
O
|
B:HOH590
|
2.3
|
18.8
|
1.0
|
|
O
|
B:VAL198
|
2.4
|
18.2
|
1.0
|
|
O
|
B:PHE192
|
2.4
|
19.1
|
1.0
|
|
O
|
B:THR195
|
2.6
|
21.1
|
1.0
|
|
O
|
B:HOH578
|
2.9
|
29.3
|
1.0
|
|
O
|
B:TYR227
|
3.1
|
19.5
|
1.0
|
|
C
|
B:PHE192
|
3.5
|
19.1
|
1.0
|
|
CB
|
B:TYR227
|
3.6
|
20.5
|
1.0
|
|
C
|
B:VAL198
|
3.6
|
18.3
|
1.0
|
|
C
|
B:TYR227
|
3.8
|
19.3
|
1.0
|
|
C
|
B:THR195
|
3.8
|
21.8
|
1.0
|
|
CB
|
B:PHE192
|
4.1
|
17.8
|
1.0
|
|
CA
|
B:TYR227
|
4.4
|
20.1
|
1.0
|
|
N
|
B:THR195
|
4.4
|
21.8
|
1.0
|
|
N
|
B:TYR193
|
4.4
|
19.8
|
1.0
|
|
CA
|
B:TYR193
|
4.4
|
20.1
|
1.0
|
|
CA
|
B:PHE192
|
4.4
|
18.4
|
1.0
|
|
C
|
B:TYR193
|
4.4
|
20.9
|
1.0
|
|
CG2
|
B:THR195
|
4.4
|
21.0
|
1.0
|
|
O
|
B:TYR193
|
4.4
|
20.5
|
1.0
|
|
CA
|
B:MET199
|
4.5
|
18.7
|
1.0
|
|
N
|
B:MET199
|
4.5
|
17.9
|
1.0
|
|
CA
|
B:VAL198
|
4.6
|
17.9
|
1.0
|
|
CA
|
B:THR195
|
4.6
|
22.3
|
1.0
|
|
O
|
B:GLY224
|
4.6
|
22.6
|
1.0
|
|
N
|
B:ALA228
|
4.7
|
18.8
|
1.0
|
|
N
|
B:VAL198
|
4.7
|
19.0
|
1.0
|
|
CB
|
B:VAL198
|
4.7
|
17.4
|
1.0
|
|
CA
|
B:GLY224
|
4.7
|
24.3
|
1.0
|
|
N
|
B:THR200
|
4.8
|
16.3
|
1.0
|
|
N
|
B:ASP196
|
4.8
|
22.8
|
1.0
|
|
OG1
|
B:THR200
|
4.9
|
16.1
|
1.0
|
|
CG
|
B:TYR227
|
4.9
|
21.5
|
1.0
|
|
Calcium binding site 5 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 5 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:25.0
occ:1.00
|
O
|
C:ASP181
|
2.4
|
19.3
|
1.0
|
|
OD1
|
C:ASP179
|
2.5
|
18.2
|
1.0
|
|
O
|
C:PHE203
|
2.5
|
20.0
|
1.0
|
|
O
|
C:HIS183
|
2.6
|
19.4
|
1.0
|
|
OG
|
C:SER202
|
3.0
|
18.7
|
1.0
|
|
O
|
C:ASP179
|
3.0
|
18.5
|
1.0
|
|
CG
|
C:ASP179
|
3.3
|
18.0
|
1.0
|
|
C
|
C:ASP181
|
3.4
|
19.5
|
1.0
|
|
C
|
C:PHE203
|
3.6
|
20.2
|
1.0
|
|
C
|
C:ASP179
|
3.6
|
18.6
|
1.0
|
|
C
|
C:HIS183
|
3.7
|
19.7
|
1.0
|
|
N
|
C:ASP181
|
3.7
|
19.2
|
1.0
|
|
CB
|
C:ASP179
|
3.9
|
18.2
|
1.0
|
|
N
|
C:PHE203
|
3.9
|
19.8
|
1.0
|
|
CB
|
C:HIS204
|
3.9
|
20.2
|
1.0
|
|
CA
|
C:ASP181
|
3.9
|
19.0
|
1.0
|
|
CB
|
C:ASP181
|
3.9
|
18.7
|
1.0
|
|
N
|
C:ILE180
|
4.2
|
18.8
|
1.0
|
|
C
|
C:ILE180
|
4.2
|
19.5
|
1.0
|
|
OD2
|
C:ASP179
|
4.2
|
17.6
|
1.0
|
|
CB
|
C:SER202
|
4.2
|
18.7
|
1.0
|
|
CA
|
C:ASP179
|
4.3
|
18.2
|
1.0
|
|
CA
|
C:ILE180
|
4.3
|
19.5
|
1.0
|
|
CA
|
C:HIS204
|
4.4
|
20.9
|
1.0
|
|
N
|
C:HIS204
|
4.4
|
20.4
|
1.0
|
|
N
|
C:HIS183
|
4.4
|
19.8
|
1.0
|
|
CA
|
C:PHE203
|
4.4
|
20.6
|
1.0
|
|
ND1
|
C:HIS204
|
4.4
|
19.8
|
1.0
|
|
CA
|
C:SER202
|
4.5
|
19.2
|
1.0
|
|
N
|
C:GLY185
|
4.5
|
19.5
|
1.0
|
|
CA
|
C:HIS184
|
4.5
|
19.9
|
1.0
|
|
N
|
C:HIS184
|
4.5
|
19.8
|
1.0
|
|
O
|
C:HOH509
|
4.5
|
21.7
|
1.0
|
|
C
|
C:SER202
|
4.5
|
19.7
|
1.0
|
|
N
|
C:ILE182
|
4.5
|
19.8
|
1.0
|
|
C
|
C:ILE182
|
4.5
|
19.9
|
1.0
|
|
CG
|
C:HIS204
|
4.7
|
20.1
|
1.0
|
|
CE1
|
C:HIS145
|
4.7
|
19.8
|
1.0
|
|
CA
|
C:HIS183
|
4.7
|
20.1
|
1.0
|
|
C
|
C:HIS184
|
4.8
|
19.5
|
1.0
|
|
CA
|
C:ILE182
|
4.9
|
20.2
|
1.0
|
|
O
|
C:ILE182
|
4.9
|
19.9
|
1.0
|
|
O
|
C:ILE180
|
4.9
|
20.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 5ix0
Go back to
Calcium Binding Sites List in 5ix0
Calcium binding site 6 out
of 6 in the HDAC2 with Ligand BRD7232
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of HDAC2 with Ligand BRD7232 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca403
b:28.7
occ:1.00
|
O
|
C:HOH591
|
2.3
|
18.6
|
1.0
|
|
O
|
C:PHE192
|
2.4
|
17.7
|
1.0
|
|
O
|
C:VAL198
|
2.4
|
20.1
|
1.0
|
|
O
|
C:THR195
|
2.6
|
20.4
|
1.0
|
|
O
|
C:HOH537
|
3.0
|
30.1
|
1.0
|
|
O
|
C:TYR227
|
3.3
|
20.3
|
1.0
|
|
C
|
C:PHE192
|
3.5
|
18.2
|
1.0
|
|
C
|
C:VAL198
|
3.6
|
20.2
|
1.0
|
|
CB
|
C:TYR227
|
3.7
|
22.5
|
1.0
|
|
C
|
C:THR195
|
3.8
|
20.9
|
1.0
|
|
C
|
C:TYR227
|
3.9
|
21.3
|
1.0
|
|
CB
|
C:PHE192
|
4.1
|
17.5
|
1.0
|
|
N
|
C:THR195
|
4.3
|
20.3
|
1.0
|
|
CG2
|
C:THR195
|
4.3
|
19.6
|
1.0
|
|
CA
|
C:TYR227
|
4.4
|
22.2
|
1.0
|
|
CA
|
C:PHE192
|
4.4
|
17.5
|
1.0
|
|
CA
|
C:MET199
|
4.4
|
21.6
|
1.0
|
|
N
|
C:TYR193
|
4.4
|
18.0
|
1.0
|
|
C
|
C:TYR193
|
4.4
|
19.6
|
1.0
|
|
CA
|
C:TYR193
|
4.4
|
19.0
|
1.0
|
|
O
|
C:TYR193
|
4.4
|
20.2
|
1.0
|
|
N
|
C:MET199
|
4.5
|
20.8
|
1.0
|
|
CA
|
C:THR195
|
4.6
|
20.8
|
1.0
|
|
O
|
C:GLY224
|
4.6
|
22.0
|
1.0
|
|
N
|
C:ALA228
|
4.6
|
21.1
|
1.0
|
|
CA
|
C:VAL198
|
4.6
|
19.7
|
1.0
|
|
CA
|
C:GLY224
|
4.7
|
22.6
|
1.0
|
|
N
|
C:THR200
|
4.7
|
20.1
|
1.0
|
|
N
|
C:VAL198
|
4.8
|
20.2
|
1.0
|
|
CB
|
C:VAL198
|
4.8
|
18.9
|
1.0
|
|
N
|
C:ASP196
|
4.9
|
22.2
|
1.0
|
|
OG1
|
C:THR200
|
4.9
|
18.8
|
1.0
|
|
CG
|
C:TYR227
|
4.9
|
23.5
|
1.0
|
|
N
|
C:THR194
|
5.0
|
19.9
|
1.0
|
|
C
|
C:MET199
|
5.0
|
20.8
|
1.0
|
|
Reference:
F.F.Wagner,
M.Weiwer,
S.Steinbacher,
A.Schomburg,
P.Reinemer,
J.P.Gale,
A.J.Campbell,
S.L.Fisher,
W.N.Zhao,
S.A.Reis,
K.M.Hennig,
M.Thomas,
P.Muller,
M.R.Jefson,
D.M.Fass,
S.J.Haggarty,
Y.L.Zhang,
E.B.Holson.
Kinetic and Structural Insights Into the Binding of Histone Deacetylase 1 and 2 (HDAC1, 2) Inhibitors. Bioorg.Med.Chem. V. 24 4008 2016.
ISSN: ESSN 1464-3391
PubMed: 27377864
DOI: 10.1016/J.BMC.2016.06.040
Page generated: Sun Jul 14 20:42:22 2024
|
