Calcium in PDB 9jv3: Structure of Human HDAC2
Enzymatic activity of Structure of Human HDAC2
All present enzymatic activity of Structure of Human HDAC2:
3.5.1.98;
Protein crystallography data
The structure of Structure of Human HDAC2, PDB code: 9jv3
was solved by
T.Tojo,
Y.Itoh,
T.Kurohara,
Y.Li,
R.Singh,
R.Narozny,
A.Wiel,
Y.Miyake,
Y.Yamashita,
K.Kusakabe,
S.Uchida,
T.Suzuki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.57
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.024,
97.584,
138.967,
90,
90,
90
|
|
R / Rfree (%)
|
18.2 /
25.6
|
Other elements in 9jv3:
The structure of Structure of Human HDAC2 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Human HDAC2
(pdb code 9jv3). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Structure of Human HDAC2, PDB code: 9jv3:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 1 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:54.4
occ:1.00
|
O
|
A:ASP181
|
2.5
|
48.8
|
1.0
|
|
O
|
A:ASP179
|
2.5
|
50.0
|
1.0
|
|
O
|
A:PHE203
|
2.6
|
51.9
|
1.0
|
|
OD1
|
A:ASP179
|
2.6
|
49.2
|
1.0
|
|
O
|
A:HIS183
|
2.6
|
56.0
|
1.0
|
|
OG
|
A:SER202
|
2.8
|
50.7
|
1.0
|
|
CG
|
A:ASP179
|
3.3
|
48.3
|
1.0
|
|
C
|
A:ASP179
|
3.4
|
49.4
|
1.0
|
|
C
|
A:ASP181
|
3.5
|
47.6
|
1.0
|
|
C
|
A:PHE203
|
3.6
|
51.4
|
1.0
|
|
N
|
A:ASP181
|
3.7
|
47.2
|
1.0
|
|
C
|
A:HIS183
|
3.7
|
52.6
|
1.0
|
|
CB
|
A:ASP179
|
3.8
|
45.6
|
1.0
|
|
N
|
A:PHE203
|
3.8
|
50.8
|
1.0
|
|
CB
|
A:HIS204
|
3.8
|
48.6
|
1.0
|
|
CA
|
A:ASP181
|
4.0
|
46.0
|
1.0
|
|
C
|
A:ILE180
|
4.0
|
49.0
|
1.0
|
|
CB
|
A:ASP181
|
4.1
|
48.4
|
1.0
|
|
N
|
A:ILE180
|
4.1
|
49.0
|
1.0
|
|
OD2
|
A:ASP179
|
4.1
|
49.6
|
1.0
|
|
CB
|
A:SER202
|
4.1
|
46.9
|
1.0
|
|
CA
|
A:ILE180
|
4.2
|
47.9
|
1.0
|
|
CA
|
A:ASP179
|
4.2
|
46.4
|
1.0
|
|
CA
|
A:HIS184
|
4.3
|
52.0
|
1.0
|
|
CA
|
A:SER202
|
4.3
|
46.0
|
1.0
|
|
N
|
A:HIS184
|
4.4
|
54.4
|
1.0
|
|
CA
|
A:PHE203
|
4.4
|
49.5
|
1.0
|
|
CA
|
A:HIS204
|
4.4
|
52.9
|
1.0
|
|
C
|
A:SER202
|
4.4
|
48.7
|
1.0
|
|
N
|
A:HIS183
|
4.4
|
49.4
|
1.0
|
|
N
|
A:HIS204
|
4.4
|
51.1
|
1.0
|
|
ND1
|
A:HIS204
|
4.5
|
46.9
|
1.0
|
|
N
|
A:GLY185
|
4.5
|
52.0
|
1.0
|
|
C
|
A:ILE182
|
4.5
|
50.8
|
1.0
|
|
N
|
A:ILE182
|
4.6
|
49.7
|
1.0
|
|
O
|
A:HOH602
|
4.7
|
45.2
|
1.0
|
|
CG
|
A:HIS204
|
4.7
|
47.1
|
1.0
|
|
CA
|
A:HIS183
|
4.7
|
49.6
|
1.0
|
|
C
|
A:HIS184
|
4.7
|
53.7
|
1.0
|
|
O
|
A:ILE180
|
4.8
|
53.9
|
1.0
|
|
O
|
A:ILE182
|
4.9
|
52.0
|
1.0
|
|
CE1
|
A:HIS145
|
4.9
|
45.3
|
1.0
|
|
CA
|
A:ILE182
|
4.9
|
50.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 2 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:56.1
occ:1.00
|
O
|
A:VAL198
|
2.3
|
55.8
|
1.0
|
|
O
|
A:TYR227
|
2.3
|
62.2
|
1.0
|
|
O
|
A:THR195
|
2.4
|
57.1
|
1.0
|
|
O
|
A:HOH635
|
2.6
|
55.2
|
1.0
|
|
O
|
A:HOH667
|
2.6
|
62.6
|
1.0
|
|
O
|
A:PHE192
|
2.6
|
56.0
|
1.0
|
|
C
|
A:TYR227
|
3.4
|
56.7
|
1.0
|
|
CB
|
A:TYR227
|
3.6
|
60.1
|
1.0
|
|
C
|
A:VAL198
|
3.6
|
54.0
|
1.0
|
|
C
|
A:THR195
|
3.7
|
53.9
|
1.0
|
|
C
|
A:PHE192
|
3.7
|
58.8
|
1.0
|
|
CA
|
A:TYR227
|
4.1
|
57.3
|
1.0
|
|
CB
|
A:PHE192
|
4.2
|
55.0
|
1.0
|
|
N
|
A:THR195
|
4.3
|
55.1
|
1.0
|
|
N
|
A:ALA228
|
4.4
|
55.5
|
1.0
|
|
N
|
A:MET199
|
4.5
|
54.9
|
1.0
|
|
O
|
A:TYR193
|
4.5
|
53.8
|
1.0
|
|
O
|
A:GLY224
|
4.5
|
57.0
|
1.0
|
|
CA
|
A:MET199
|
4.5
|
55.2
|
1.0
|
|
CA
|
A:THR195
|
4.5
|
53.6
|
1.0
|
|
C
|
A:TYR193
|
4.5
|
54.8
|
1.0
|
|
CA
|
A:VAL198
|
4.5
|
53.8
|
1.0
|
|
N
|
A:TYR193
|
4.6
|
58.0
|
1.0
|
|
CG2
|
A:THR195
|
4.6
|
58.5
|
1.0
|
|
CA
|
A:TYR193
|
4.6
|
54.6
|
1.0
|
|
CA
|
A:PHE192
|
4.6
|
56.6
|
1.0
|
|
N
|
A:ASP196
|
4.7
|
51.5
|
1.0
|
|
CB
|
A:VAL198
|
4.7
|
52.9
|
1.0
|
|
N
|
A:VAL198
|
4.8
|
56.1
|
1.0
|
|
CA
|
A:GLY224
|
4.8
|
60.3
|
1.0
|
|
N
|
A:THR200
|
4.9
|
52.3
|
1.0
|
|
OG1
|
A:THR200
|
4.9
|
50.4
|
1.0
|
|
CG
|
A:TYR227
|
4.9
|
61.6
|
1.0
|
|
CA
|
A:ASP196
|
4.9
|
53.5
|
1.0
|
|
CB
|
A:ALA228
|
4.9
|
51.8
|
1.0
|
|
CA
|
A:ALA228
|
5.0
|
55.4
|
1.0
|
|
Calcium binding site 3 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 3 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:55.8
occ:1.00
|
O
|
B:ASP181
|
2.5
|
53.5
|
1.0
|
|
O
|
B:ASP179
|
2.6
|
57.8
|
1.0
|
|
OD1
|
B:ASP179
|
2.6
|
54.7
|
1.0
|
|
O
|
B:PHE203
|
2.6
|
55.0
|
1.0
|
|
O
|
B:HIS183
|
2.7
|
47.0
|
1.0
|
|
OG
|
B:SER202
|
2.8
|
55.2
|
1.0
|
|
CG
|
B:ASP179
|
3.2
|
52.3
|
1.0
|
|
C
|
B:ASP179
|
3.4
|
51.0
|
1.0
|
|
C
|
B:ASP181
|
3.4
|
48.3
|
1.0
|
|
N
|
B:ASP181
|
3.4
|
45.5
|
1.0
|
|
C
|
B:PHE203
|
3.6
|
48.5
|
1.0
|
|
C
|
B:HIS183
|
3.7
|
44.2
|
1.0
|
|
N
|
B:PHE203
|
3.8
|
52.8
|
1.0
|
|
CB
|
B:ASP179
|
3.8
|
48.0
|
1.0
|
|
CA
|
B:ASP181
|
3.8
|
46.4
|
1.0
|
|
CB
|
B:HIS204
|
3.8
|
53.6
|
1.0
|
|
CB
|
B:ASP181
|
4.0
|
44.1
|
1.0
|
|
OD2
|
B:ASP179
|
4.0
|
57.1
|
1.0
|
|
CB
|
B:SER202
|
4.0
|
49.4
|
1.0
|
|
C
|
B:ILE180
|
4.1
|
49.1
|
1.0
|
|
N
|
B:ILE180
|
4.1
|
49.0
|
1.0
|
|
CA
|
B:ASP179
|
4.2
|
49.5
|
1.0
|
|
CA
|
B:ILE180
|
4.2
|
47.4
|
1.0
|
|
N
|
B:GLY185
|
4.3
|
50.4
|
1.0
|
|
CA
|
B:HIS204
|
4.4
|
54.7
|
1.0
|
|
CA
|
B:PHE203
|
4.4
|
47.2
|
1.0
|
|
N
|
B:HIS204
|
4.4
|
51.1
|
1.0
|
|
O
|
B:HOH617
|
4.4
|
41.1
|
1.0
|
|
CA
|
B:SER202
|
4.4
|
47.5
|
1.0
|
|
CA
|
B:HIS184
|
4.5
|
46.9
|
1.0
|
|
N
|
B:HIS183
|
4.5
|
41.8
|
1.0
|
|
ND1
|
B:HIS204
|
4.5
|
53.7
|
1.0
|
|
N
|
B:HIS184
|
4.5
|
46.8
|
1.0
|
|
C
|
B:SER202
|
4.5
|
50.2
|
1.0
|
|
N
|
B:ILE182
|
4.5
|
47.5
|
1.0
|
|
C
|
B:ILE182
|
4.5
|
40.6
|
1.0
|
|
CG
|
B:HIS204
|
4.6
|
56.2
|
1.0
|
|
C
|
B:HIS184
|
4.7
|
47.2
|
1.0
|
|
CA
|
B:HIS183
|
4.7
|
45.0
|
1.0
|
|
O
|
B:ILE182
|
4.8
|
40.2
|
1.0
|
|
CA
|
B:ILE182
|
4.9
|
43.1
|
1.0
|
|
O
|
B:ILE180
|
4.9
|
52.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 4 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:51.3
occ:1.00
|
O
|
B:VAL198
|
2.3
|
49.5
|
1.0
|
|
O
|
B:TYR227
|
2.4
|
58.5
|
1.0
|
|
O
|
B:THR195
|
2.4
|
61.6
|
1.0
|
|
O
|
B:HOH683
|
2.6
|
51.1
|
1.0
|
|
O
|
B:HOH625
|
2.6
|
45.5
|
1.0
|
|
O
|
B:PHE192
|
2.6
|
50.4
|
1.0
|
|
C
|
B:TYR227
|
3.4
|
56.7
|
1.0
|
|
CB
|
B:TYR227
|
3.4
|
56.2
|
1.0
|
|
C
|
B:VAL198
|
3.6
|
52.5
|
1.0
|
|
C
|
B:THR195
|
3.7
|
54.4
|
1.0
|
|
C
|
B:PHE192
|
3.7
|
51.6
|
1.0
|
|
CA
|
B:TYR227
|
4.0
|
60.5
|
1.0
|
|
CB
|
B:PHE192
|
4.1
|
49.7
|
1.0
|
|
CA
|
B:MET199
|
4.4
|
48.0
|
1.0
|
|
N
|
B:THR195
|
4.4
|
60.2
|
1.0
|
|
N
|
B:MET199
|
4.5
|
46.7
|
1.0
|
|
N
|
B:ALA228
|
4.5
|
55.7
|
1.0
|
|
O
|
B:GLY224
|
4.6
|
52.2
|
1.0
|
|
CA
|
B:THR195
|
4.6
|
54.0
|
1.0
|
|
CG2
|
B:THR195
|
4.6
|
48.1
|
1.0
|
|
CA
|
B:PHE192
|
4.6
|
51.3
|
1.0
|
|
CA
|
B:VAL198
|
4.6
|
50.4
|
1.0
|
|
N
|
B:TYR193
|
4.6
|
50.5
|
1.0
|
|
CA
|
B:TYR193
|
4.6
|
49.5
|
1.0
|
|
N
|
B:THR200
|
4.7
|
48.1
|
1.0
|
|
N
|
B:ASP196
|
4.7
|
53.5
|
1.0
|
|
C
|
B:TYR193
|
4.7
|
52.0
|
1.0
|
|
CB
|
B:VAL198
|
4.7
|
51.3
|
1.0
|
|
CG
|
B:TYR227
|
4.8
|
57.4
|
1.0
|
|
N
|
B:VAL198
|
4.8
|
51.4
|
1.0
|
|
O
|
B:TYR193
|
4.8
|
54.1
|
1.0
|
|
CA
|
B:ASP196
|
4.9
|
51.8
|
1.0
|
|
CA
|
B:GLY224
|
5.0
|
61.1
|
1.0
|
|
OG1
|
B:THR200
|
5.0
|
49.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 5 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca502
b:65.2
occ:1.00
|
O
|
C:ASP181
|
2.5
|
67.0
|
1.0
|
|
O
|
C:ASP179
|
2.5
|
60.2
|
1.0
|
|
OD1
|
C:ASP179
|
2.6
|
57.6
|
1.0
|
|
O
|
C:PHE203
|
2.6
|
56.1
|
1.0
|
|
O
|
C:HIS183
|
2.6
|
60.5
|
1.0
|
|
OG
|
C:SER202
|
2.8
|
56.2
|
1.0
|
|
CG
|
C:ASP179
|
3.2
|
60.2
|
1.0
|
|
C
|
C:ASP179
|
3.3
|
59.9
|
1.0
|
|
N
|
C:ASP181
|
3.4
|
63.8
|
1.0
|
|
C
|
C:ASP181
|
3.5
|
65.2
|
1.0
|
|
CB
|
C:ASP179
|
3.6
|
58.2
|
1.0
|
|
C
|
C:PHE203
|
3.6
|
57.0
|
1.0
|
|
C
|
C:HIS183
|
3.7
|
60.3
|
1.0
|
|
CA
|
C:ASP181
|
3.8
|
61.9
|
1.0
|
|
CB
|
C:ASP181
|
3.9
|
57.5
|
1.0
|
|
N
|
C:PHE203
|
3.9
|
57.9
|
1.0
|
|
CB
|
C:HIS204
|
3.9
|
51.0
|
1.0
|
|
C
|
C:ILE180
|
4.0
|
59.4
|
1.0
|
|
N
|
C:ILE180
|
4.0
|
56.6
|
1.0
|
|
CB
|
C:SER202
|
4.1
|
58.0
|
1.0
|
|
CA
|
C:ASP179
|
4.1
|
61.2
|
1.0
|
|
OD2
|
C:ASP179
|
4.1
|
59.9
|
1.0
|
|
CA
|
C:ILE180
|
4.2
|
56.1
|
1.0
|
|
CA
|
C:HIS184
|
4.4
|
62.5
|
1.0
|
|
N
|
C:HIS184
|
4.4
|
57.3
|
1.0
|
|
CA
|
C:SER202
|
4.4
|
59.8
|
1.0
|
|
N
|
C:GLY185
|
4.4
|
61.4
|
1.0
|
|
CA
|
C:PHE203
|
4.4
|
58.5
|
1.0
|
|
N
|
C:HIS183
|
4.4
|
60.8
|
1.0
|
|
C
|
C:SER202
|
4.5
|
60.3
|
1.0
|
|
N
|
C:HIS204
|
4.5
|
51.0
|
1.0
|
|
CA
|
C:HIS204
|
4.5
|
54.9
|
1.0
|
|
ND1
|
C:HIS204
|
4.6
|
58.4
|
1.0
|
|
N
|
C:ILE182
|
4.7
|
60.5
|
1.0
|
|
CA
|
C:HIS183
|
4.7
|
60.9
|
1.0
|
|
C
|
C:ILE182
|
4.7
|
58.7
|
1.0
|
|
C
|
C:HIS184
|
4.7
|
62.5
|
1.0
|
|
CG
|
C:HIS204
|
4.7
|
54.6
|
1.0
|
|
O
|
C:ILE180
|
4.7
|
62.0
|
1.0
|
|
O
|
C:HOH605
|
4.8
|
69.4
|
1.0
|
|
CE1
|
C:HIS145
|
5.0
|
56.7
|
1.0
|
|
Calcium binding site 6 out
of 6 in 9jv3
Go back to
Calcium Binding Sites List in 9jv3
Calcium binding site 6 out
of 6 in the Structure of Human HDAC2
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Human HDAC2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:54.9
occ:1.00
|
O
|
C:VAL198
|
2.3
|
60.7
|
1.0
|
|
O
|
C:TYR227
|
2.4
|
55.1
|
1.0
|
|
O
|
C:THR195
|
2.4
|
54.9
|
1.0
|
|
O
|
C:HOH628
|
2.6
|
50.9
|
1.0
|
|
O
|
C:HOH636
|
2.6
|
54.0
|
1.0
|
|
O
|
C:PHE192
|
2.6
|
51.9
|
1.0
|
|
C
|
C:TYR227
|
3.4
|
57.7
|
1.0
|
|
CB
|
C:TYR227
|
3.5
|
55.4
|
1.0
|
|
C
|
C:VAL198
|
3.6
|
59.0
|
1.0
|
|
C
|
C:PHE192
|
3.7
|
50.6
|
1.0
|
|
C
|
C:THR195
|
3.7
|
55.6
|
1.0
|
|
CA
|
C:TYR227
|
4.1
|
58.0
|
1.0
|
|
CB
|
C:PHE192
|
4.2
|
47.0
|
1.0
|
|
CA
|
C:MET199
|
4.3
|
59.4
|
1.0
|
|
N
|
C:ALA228
|
4.4
|
56.2
|
1.0
|
|
N
|
C:MET199
|
4.4
|
59.3
|
1.0
|
|
CG2
|
C:THR195
|
4.5
|
51.8
|
1.0
|
|
N
|
C:THR195
|
4.5
|
54.7
|
1.0
|
|
CA
|
C:PHE192
|
4.6
|
50.4
|
1.0
|
|
N
|
C:TYR193
|
4.6
|
47.2
|
1.0
|
|
N
|
C:THR200
|
4.6
|
60.9
|
1.0
|
|
CA
|
C:TYR193
|
4.6
|
52.1
|
1.0
|
|
CA
|
C:THR195
|
4.6
|
54.8
|
1.0
|
|
CA
|
C:VAL198
|
4.6
|
56.8
|
1.0
|
|
O
|
C:TYR193
|
4.6
|
55.3
|
1.0
|
|
C
|
C:TYR193
|
4.6
|
53.0
|
1.0
|
|
N
|
C:ASP196
|
4.7
|
54.5
|
1.0
|
|
O
|
C:GLY224
|
4.7
|
58.0
|
1.0
|
|
OG1
|
C:THR200
|
4.8
|
49.1
|
1.0
|
|
N
|
C:VAL198
|
4.8
|
57.4
|
1.0
|
|
CG
|
C:TYR227
|
4.8
|
55.6
|
1.0
|
|
CA
|
C:GLY224
|
4.8
|
59.6
|
1.0
|
|
CB
|
C:VAL198
|
4.8
|
54.6
|
1.0
|
|
CA
|
C:ALA228
|
4.9
|
61.0
|
1.0
|
|
CB
|
C:ALA228
|
4.9
|
52.8
|
1.0
|
|
CA
|
C:ASP196
|
4.9
|
57.6
|
1.0
|
|
C
|
C:MET199
|
4.9
|
62.1
|
1.0
|
|
Reference:
T.Tojo,
Y.Itoh,
T.Kurohara,
Y.Li,
R.Singh,
R.Narozny,
A.Wiel,
Y.Miyake,
Y.Yamashita,
K.Kusakabe,
S.Uchida,
T.Suzuki.
Discovery of An HDAC2-Selective Inhibitor Based on Enzyme-Inhibitor Binding Thermodynamics and Kinetics, and Its Potential As A Therapeutic Drug For Neurological Disorders To Be Published.
Page generated: Sat Dec 13 13:09:01 2025
|
