Sodium in PDB 6wi3: Histone Deacetylases Complex with Peptide Macrocycles
Enzymatic activity of Histone Deacetylases Complex with Peptide Macrocycles
All present enzymatic activity of Histone Deacetylases Complex with Peptide Macrocycles:
3.5.1.98;
Protein crystallography data
The structure of Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6wi3
was solved by
A.K.Bera,
P.Hosseinzadeh,
P.Watson,
D.Baker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.80 /
2.35
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.162,
97.593,
139.07,
90,
90,
90
|
|
R / Rfree (%)
|
19.7 /
25.4
|
Other elements in 6wi3:
The structure of Histone Deacetylases Complex with Peptide Macrocycles also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Histone Deacetylases Complex with Peptide Macrocycles
(pdb code 6wi3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6wi3:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 1 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:19.0
occ:1.00
|
O
|
A:ASP181
|
2.4
|
30.2
|
1.0
|
|
O
|
A:PHE203
|
2.5
|
31.4
|
1.0
|
|
O
|
A:ASP179
|
2.7
|
24.3
|
1.0
|
|
OD1
|
A:ASP179
|
2.7
|
28.0
|
1.0
|
|
O
|
A:HIS183
|
2.9
|
28.3
|
1.0
|
|
OG
|
A:SER202
|
3.0
|
28.9
|
1.0
|
|
CG
|
A:ASP179
|
3.3
|
26.4
|
1.0
|
|
C
|
A:ASP179
|
3.3
|
24.8
|
1.0
|
|
C
|
A:ASP181
|
3.4
|
30.2
|
1.0
|
|
C
|
A:PHE203
|
3.4
|
33.6
|
1.0
|
|
N
|
A:ASP181
|
3.5
|
27.0
|
1.0
|
|
N
|
A:PHE203
|
3.7
|
29.0
|
1.0
|
|
CB
|
A:ASP179
|
3.7
|
22.5
|
1.0
|
|
CA
|
A:ASP181
|
3.8
|
25.1
|
1.0
|
|
CB
|
A:HIS204
|
3.9
|
32.2
|
1.0
|
|
C
|
A:ILE180
|
3.9
|
20.7
|
1.0
|
|
C
|
A:HIS183
|
4.0
|
27.8
|
1.0
|
|
N
|
A:ILE180
|
4.0
|
18.3
|
1.0
|
|
CB
|
A:ASP181
|
4.0
|
24.2
|
1.0
|
|
OD2
|
A:ASP179
|
4.1
|
24.1
|
1.0
|
|
CB
|
A:SER202
|
4.1
|
27.2
|
1.0
|
|
CA
|
A:ASP179
|
4.1
|
22.9
|
1.0
|
|
CA
|
A:ILE180
|
4.1
|
22.3
|
1.0
|
|
CA
|
A:PHE203
|
4.2
|
27.5
|
1.0
|
|
N
|
A:HIS204
|
4.3
|
33.1
|
1.0
|
|
CA
|
A:SER202
|
4.3
|
30.2
|
1.0
|
|
C
|
A:SER202
|
4.3
|
29.4
|
1.0
|
|
CA
|
A:HIS204
|
4.3
|
30.8
|
1.0
|
|
N
|
A:GLY185
|
4.4
|
30.1
|
1.0
|
|
CA
|
A:HIS184
|
4.5
|
28.8
|
1.0
|
|
O
|
A:HOH549
|
4.5
|
25.0
|
1.0
|
|
ND1
|
A:HIS204
|
4.5
|
31.1
|
1.0
|
|
N
|
A:ILE182
|
4.6
|
27.0
|
1.0
|
|
N
|
A:HIS184
|
4.6
|
32.2
|
1.0
|
|
N
|
A:HIS183
|
4.6
|
24.3
|
1.0
|
|
CG
|
A:HIS204
|
4.7
|
30.7
|
1.0
|
|
O
|
A:ILE180
|
4.7
|
21.0
|
1.0
|
|
C
|
A:ILE182
|
4.8
|
28.2
|
1.0
|
|
C
|
A:HIS184
|
4.8
|
29.8
|
1.0
|
|
CA
|
A:HIS183
|
5.0
|
26.6
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 2 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:32.6
occ:1.00
|
O
|
A:PHE192
|
2.4
|
28.2
|
1.0
|
|
O
|
A:VAL198
|
2.4
|
23.4
|
1.0
|
|
O
|
A:HOH530
|
2.4
|
33.6
|
1.0
|
|
O
|
A:THR195
|
2.5
|
30.5
|
1.0
|
|
O
|
A:HOH572
|
2.8
|
32.4
|
1.0
|
|
O
|
A:TYR227
|
3.4
|
35.4
|
1.0
|
|
C
|
A:PHE192
|
3.6
|
34.8
|
1.0
|
|
C
|
A:VAL198
|
3.6
|
29.8
|
1.0
|
|
CB
|
A:TYR227
|
3.7
|
35.2
|
1.0
|
|
C
|
A:THR195
|
3.7
|
26.0
|
1.0
|
|
C
|
A:TYR227
|
4.1
|
34.4
|
1.0
|
|
CB
|
A:PHE192
|
4.1
|
29.2
|
1.0
|
|
N
|
A:THR195
|
4.3
|
31.6
|
1.0
|
|
CG2
|
A:THR195
|
4.3
|
37.3
|
1.0
|
|
CA
|
A:MET199
|
4.4
|
25.1
|
1.0
|
|
C
|
A:TYR193
|
4.4
|
38.2
|
1.0
|
|
N
|
A:MET199
|
4.4
|
27.5
|
1.0
|
|
O
|
A:TYR193
|
4.4
|
29.2
|
1.0
|
|
CA
|
A:TYR193
|
4.5
|
28.9
|
1.0
|
|
O
|
A:GLY224
|
4.5
|
31.5
|
1.0
|
|
N
|
A:TYR193
|
4.5
|
30.5
|
1.0
|
|
CA
|
A:PHE192
|
4.5
|
30.4
|
1.0
|
|
CA
|
A:TYR227
|
4.5
|
39.2
|
1.0
|
|
CA
|
A:THR195
|
4.6
|
30.4
|
1.0
|
|
CA
|
A:VAL198
|
4.6
|
26.8
|
1.0
|
|
CA
|
A:GLY224
|
4.6
|
36.7
|
1.0
|
|
N
|
A:VAL198
|
4.7
|
29.3
|
1.0
|
|
N
|
A:ASP196
|
4.7
|
30.5
|
1.0
|
|
CA
|
A:ASP196
|
4.8
|
34.8
|
1.0
|
|
CB
|
A:VAL198
|
4.8
|
29.3
|
1.0
|
|
CG
|
A:TYR227
|
4.9
|
35.5
|
1.0
|
|
N
|
A:THR200
|
4.9
|
30.9
|
1.0
|
|
N
|
A:ALA228
|
4.9
|
30.6
|
1.0
|
|
N
|
A:THR194
|
5.0
|
35.3
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 3 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na402
b:14.9
occ:1.00
|
O
|
B:ASP181
|
2.4
|
18.5
|
1.0
|
|
O
|
B:PHE203
|
2.5
|
27.7
|
1.0
|
|
OD1
|
B:ASP179
|
2.6
|
29.4
|
1.0
|
|
O
|
B:ASP179
|
2.9
|
26.7
|
1.0
|
|
O
|
B:HIS183
|
2.9
|
23.5
|
1.0
|
|
OG
|
B:SER202
|
3.0
|
28.0
|
1.0
|
|
CG
|
B:ASP179
|
3.2
|
25.4
|
1.0
|
|
C
|
B:ASP179
|
3.4
|
26.5
|
1.0
|
|
C
|
B:ASP181
|
3.4
|
26.0
|
1.0
|
|
N
|
B:ASP181
|
3.5
|
27.2
|
1.0
|
|
C
|
B:PHE203
|
3.5
|
22.8
|
1.0
|
|
CB
|
B:ASP179
|
3.6
|
18.4
|
1.0
|
|
N
|
B:PHE203
|
3.8
|
29.2
|
1.0
|
|
CA
|
B:ASP181
|
3.8
|
22.2
|
1.0
|
|
N
|
B:ILE180
|
3.9
|
20.1
|
1.0
|
|
C
|
B:ILE180
|
3.9
|
22.6
|
1.0
|
|
CB
|
B:HIS204
|
4.0
|
27.5
|
1.0
|
|
C
|
B:HIS183
|
4.0
|
25.6
|
1.0
|
|
OD2
|
B:ASP179
|
4.0
|
25.2
|
1.0
|
|
CB
|
B:ASP181
|
4.1
|
21.8
|
1.0
|
|
CA
|
B:ASP179
|
4.1
|
26.2
|
1.0
|
|
CA
|
B:ILE180
|
4.1
|
22.7
|
1.0
|
|
CB
|
B:SER202
|
4.2
|
26.6
|
1.0
|
|
CA
|
B:PHE203
|
4.3
|
22.8
|
1.0
|
|
CA
|
B:SER202
|
4.3
|
21.6
|
1.0
|
|
C
|
B:SER202
|
4.3
|
31.6
|
1.0
|
|
N
|
B:HIS204
|
4.4
|
26.1
|
1.0
|
|
CA
|
B:HIS204
|
4.4
|
29.4
|
1.0
|
|
O
|
B:HOH545
|
4.5
|
20.7
|
1.0
|
|
N
|
B:GLY185
|
4.5
|
24.4
|
1.0
|
|
CA
|
B:HIS184
|
4.5
|
28.8
|
1.0
|
|
ND1
|
B:HIS204
|
4.6
|
31.2
|
1.0
|
|
N
|
B:ILE182
|
4.6
|
23.6
|
1.0
|
|
N
|
B:HIS184
|
4.7
|
26.8
|
1.0
|
|
N
|
B:HIS183
|
4.7
|
21.2
|
1.0
|
|
O
|
B:ILE180
|
4.8
|
24.6
|
1.0
|
|
C
|
B:ILE182
|
4.8
|
26.0
|
1.0
|
|
CG
|
B:HIS204
|
4.8
|
30.3
|
1.0
|
|
C
|
B:HIS184
|
4.9
|
27.9
|
1.0
|
|
CE1
|
B:HIS145
|
5.0
|
24.2
|
1.0
|
|
CA
|
B:HIS183
|
5.0
|
24.0
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 4 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na403
b:40.7
occ:1.00
|
O
|
B:VAL198
|
2.4
|
33.8
|
1.0
|
|
O
|
B:PHE192
|
2.4
|
31.9
|
1.0
|
|
O
|
B:HOH549
|
2.5
|
30.4
|
1.0
|
|
O
|
B:HOH559
|
2.5
|
27.1
|
1.0
|
|
O
|
B:THR195
|
2.6
|
34.5
|
1.0
|
|
O
|
B:TYR227
|
3.1
|
36.0
|
1.0
|
|
CB
|
B:TYR227
|
3.6
|
37.4
|
1.0
|
|
C
|
B:PHE192
|
3.6
|
32.9
|
1.0
|
|
C
|
B:VAL198
|
3.6
|
36.1
|
1.0
|
|
C
|
B:TYR227
|
3.9
|
32.6
|
1.0
|
|
C
|
B:THR195
|
3.9
|
43.1
|
1.0
|
|
CB
|
B:PHE192
|
4.2
|
22.5
|
1.0
|
|
O
|
B:GLY224
|
4.3
|
40.6
|
1.0
|
|
CA
|
B:TYR227
|
4.4
|
40.3
|
1.0
|
|
CA
|
B:MET199
|
4.4
|
33.9
|
1.0
|
|
N
|
B:THR195
|
4.4
|
35.0
|
1.0
|
|
N
|
B:MET199
|
4.5
|
36.5
|
1.0
|
|
CG2
|
B:THR195
|
4.5
|
36.6
|
1.0
|
|
CA
|
B:TYR193
|
4.5
|
35.3
|
1.0
|
|
N
|
B:TYR193
|
4.5
|
29.2
|
1.0
|
|
CA
|
B:GLY224
|
4.5
|
42.4
|
1.0
|
|
C
|
B:TYR193
|
4.5
|
41.9
|
1.0
|
|
CA
|
B:PHE192
|
4.5
|
35.4
|
1.0
|
|
O
|
B:TYR193
|
4.6
|
41.4
|
1.0
|
|
CA
|
B:VAL198
|
4.7
|
38.0
|
1.0
|
|
CA
|
B:THR195
|
4.7
|
36.8
|
1.0
|
|
N
|
B:VAL198
|
4.7
|
33.7
|
1.0
|
|
N
|
B:ALA228
|
4.7
|
34.1
|
1.0
|
|
N
|
B:THR200
|
4.8
|
23.3
|
1.0
|
|
CG
|
B:TYR227
|
4.8
|
43.1
|
1.0
|
|
N
|
B:ASP196
|
4.8
|
38.4
|
1.0
|
|
CA
|
B:ASP196
|
4.9
|
43.1
|
1.0
|
|
CB
|
B:VAL198
|
4.9
|
38.3
|
1.0
|
|
C
|
B:GLY224
|
4.9
|
39.8
|
1.0
|
|
OG1
|
B:THR200
|
5.0
|
35.0
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 5 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na402
b:39.1
occ:1.00
|
O
|
C:ASP181
|
2.4
|
52.8
|
1.0
|
|
OD1
|
C:ASP179
|
2.6
|
44.5
|
1.0
|
|
O
|
C:PHE203
|
2.7
|
57.9
|
1.0
|
|
O
|
C:HIS183
|
2.8
|
48.6
|
1.0
|
|
OG
|
C:SER202
|
2.8
|
50.8
|
1.0
|
|
O
|
C:ASP179
|
3.0
|
50.8
|
1.0
|
|
C
|
C:PHE203
|
3.4
|
56.6
|
1.0
|
|
CG
|
C:ASP179
|
3.4
|
46.5
|
1.0
|
|
C
|
C:ASP181
|
3.5
|
54.6
|
1.0
|
|
CB
|
C:HIS204
|
3.5
|
50.5
|
1.0
|
|
C
|
C:ASP179
|
3.7
|
54.5
|
1.0
|
|
C
|
C:HIS183
|
3.7
|
54.5
|
1.0
|
|
N
|
C:PHE203
|
3.7
|
51.0
|
1.0
|
|
N
|
C:ASP181
|
3.8
|
49.4
|
1.0
|
|
CB
|
C:ASP179
|
3.8
|
48.3
|
1.0
|
|
CA
|
C:HIS204
|
4.0
|
54.1
|
1.0
|
|
CB
|
C:SER202
|
4.0
|
51.6
|
1.0
|
|
N
|
C:HIS204
|
4.0
|
48.7
|
1.0
|
|
CA
|
C:ASP181
|
4.0
|
47.6
|
1.0
|
|
CA
|
C:HIS184
|
4.1
|
54.2
|
1.0
|
|
C
|
C:SER202
|
4.1
|
54.9
|
1.0
|
|
CA
|
C:SER202
|
4.2
|
58.3
|
1.0
|
|
CA
|
C:PHE203
|
4.2
|
58.9
|
1.0
|
|
CB
|
C:ASP181
|
4.2
|
46.5
|
1.0
|
|
N
|
C:GLY185
|
4.2
|
51.3
|
1.0
|
|
N
|
C:HIS184
|
4.3
|
53.8
|
1.0
|
|
C
|
C:ILE180
|
4.3
|
48.7
|
1.0
|
|
ND1
|
C:HIS204
|
4.4
|
52.4
|
1.0
|
|
CA
|
C:ASP179
|
4.4
|
49.8
|
1.0
|
|
OD2
|
C:ASP179
|
4.4
|
50.7
|
1.0
|
|
CG
|
C:HIS204
|
4.4
|
57.0
|
1.0
|
|
N
|
C:ILE180
|
4.4
|
46.9
|
1.0
|
|
N
|
C:HIS183
|
4.5
|
48.9
|
1.0
|
|
C
|
C:HIS184
|
4.6
|
54.7
|
1.0
|
|
CA
|
C:ILE180
|
4.6
|
48.1
|
1.0
|
|
N
|
C:ILE182
|
4.6
|
51.5
|
1.0
|
|
C
|
C:ILE182
|
4.6
|
52.4
|
1.0
|
|
CA
|
C:HIS183
|
4.8
|
54.8
|
1.0
|
|
CE1
|
C:HIS145
|
4.9
|
50.7
|
1.0
|
|
CA
|
C:ILE182
|
5.0
|
57.0
|
1.0
|
|
O
|
C:SER202
|
5.0
|
54.5
|
1.0
|
|
O
|
C:ILE182
|
5.0
|
50.0
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6wi3
Go back to
Sodium Binding Sites List in 6wi3
Sodium binding site 6 out
of 6 in the Histone Deacetylases Complex with Peptide Macrocycles
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na403
b:58.8
occ:1.00
|
O
|
C:PHE192
|
2.4
|
52.1
|
1.0
|
|
O
|
C:VAL198
|
2.4
|
57.9
|
1.0
|
|
O
|
C:HOH509
|
2.5
|
44.6
|
1.0
|
|
O
|
C:THR195
|
2.7
|
51.2
|
1.0
|
|
O
|
C:HOH524
|
3.0
|
49.1
|
1.0
|
|
O
|
C:TYR227
|
3.2
|
52.6
|
1.0
|
|
C
|
C:VAL198
|
3.6
|
57.3
|
1.0
|
|
C
|
C:PHE192
|
3.6
|
48.3
|
1.0
|
|
CB
|
C:TYR227
|
3.7
|
53.6
|
1.0
|
|
C
|
C:TYR227
|
3.9
|
59.3
|
1.0
|
|
C
|
C:THR195
|
4.0
|
50.1
|
1.0
|
|
CA
|
C:MET199
|
4.1
|
56.8
|
1.0
|
|
CB
|
C:PHE192
|
4.3
|
48.0
|
1.0
|
|
N
|
C:MET199
|
4.3
|
56.8
|
1.0
|
|
O
|
C:GLY224
|
4.3
|
51.0
|
1.0
|
|
CA
|
C:TYR227
|
4.4
|
57.8
|
1.0
|
|
CA
|
C:TYR193
|
4.5
|
46.4
|
1.0
|
|
N
|
C:TYR193
|
4.5
|
42.5
|
1.0
|
|
N
|
C:THR195
|
4.5
|
47.7
|
1.0
|
|
C
|
C:TYR193
|
4.6
|
46.1
|
1.0
|
|
CA
|
C:PHE192
|
4.6
|
51.8
|
1.0
|
|
N
|
C:THR200
|
4.6
|
55.8
|
1.0
|
|
CG2
|
C:THR195
|
4.6
|
54.0
|
1.0
|
|
O
|
C:TYR193
|
4.7
|
45.8
|
1.0
|
|
CA
|
C:GLY224
|
4.7
|
48.0
|
1.0
|
|
N
|
C:ALA228
|
4.7
|
52.6
|
1.0
|
|
CA
|
C:VAL198
|
4.8
|
56.6
|
1.0
|
|
CA
|
C:THR195
|
4.8
|
50.5
|
1.0
|
|
C
|
C:MET199
|
4.9
|
59.0
|
1.0
|
|
N
|
C:ASP196
|
4.9
|
54.8
|
1.0
|
|
CG
|
C:TYR227
|
4.9
|
61.5
|
1.0
|
|
CA
|
C:ASP196
|
4.9
|
59.4
|
1.0
|
|
N
|
C:VAL198
|
5.0
|
51.0
|
1.0
|
|
CB
|
C:ALA228
|
5.0
|
50.0
|
1.0
|
|
Reference:
A.K.Bera,
P.Hosseinzadeh,
D.Baker.
Anchor Extension, A Structure-Guided Approach to Design Macrocycles Targeting Histone Deacetylases To Be Published.
Page generated: Tue Oct 8 14:35:44 2024
|
