Zinc in PDB 6who: 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: 6who
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)
|
48.74 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.541,
97.482,
138.977,
90,
90,
90
|
R / Rfree (%)
|
18.4 /
22.1
|
Other elements in 6who:
The structure of Histone Deacetylases Complex with Peptide Macrocycles also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Histone Deacetylases Complex with Peptide Macrocycles
(pdb code 6who). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6who:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 6who
Go back to
Zinc Binding Sites List in 6who
Zinc binding site 1 out
of 3 in the Histone Deacetylases Complex with Peptide Macrocycles
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:22.5
occ:1.00
|
OD2
|
A:ASP269
|
2.0
|
19.3
|
1.0
|
OD1
|
A:ASP181
|
2.0
|
23.2
|
1.0
|
ND1
|
A:HIS183
|
2.2
|
24.7
|
1.0
|
SH
|
F:U2M500
|
2.3
|
25.9
|
1.0
|
CG
|
A:ASP181
|
2.8
|
24.7
|
1.0
|
OD2
|
A:ASP181
|
2.9
|
19.6
|
1.0
|
CG
|
A:ASP269
|
3.0
|
27.6
|
1.0
|
CE1
|
A:HIS183
|
3.1
|
24.0
|
1.0
|
CG
|
A:HIS183
|
3.2
|
25.6
|
1.0
|
OD1
|
A:ASP269
|
3.4
|
26.2
|
1.0
|
CZ
|
F:U2M500
|
3.6
|
33.8
|
1.0
|
CB
|
A:HIS183
|
3.6
|
20.1
|
1.0
|
CE
|
F:U2M500
|
3.9
|
28.6
|
1.0
|
N
|
A:HIS183
|
3.9
|
19.9
|
1.0
|
CA
|
A:GLY306
|
4.1
|
23.4
|
1.0
|
CG2
|
A:ILE182
|
4.1
|
23.1
|
1.0
|
NE2
|
A:HIS145
|
4.2
|
21.8
|
1.0
|
NE2
|
A:HIS183
|
4.2
|
25.2
|
1.0
|
CB
|
A:ASP181
|
4.2
|
17.6
|
1.0
|
CD2
|
A:HIS183
|
4.3
|
24.9
|
1.0
|
CB
|
A:ASP269
|
4.3
|
19.9
|
1.0
|
CA
|
A:HIS183
|
4.4
|
21.5
|
1.0
|
NE2
|
A:HIS146
|
4.4
|
27.9
|
1.0
|
N
|
A:ILE182
|
4.4
|
20.8
|
1.0
|
OH
|
A:TYR308
|
4.5
|
24.2
|
1.0
|
CE2
|
A:TYR308
|
4.5
|
21.0
|
1.0
|
N
|
A:GLY306
|
4.6
|
21.7
|
1.0
|
CE1
|
A:HIS145
|
4.6
|
20.4
|
1.0
|
C
|
A:ILE182
|
4.9
|
21.2
|
1.0
|
C
|
A:ASP181
|
5.0
|
23.5
|
1.0
|
|
Zinc binding site 2 out
of 3 in 6who
Go back to
Zinc Binding Sites List in 6who
Zinc binding site 2 out
of 3 in the Histone Deacetylases Complex with Peptide Macrocycles
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:22.6
occ:1.00
|
OD2
|
B:ASP269
|
2.0
|
22.4
|
1.0
|
OD1
|
B:ASP181
|
2.0
|
29.8
|
1.0
|
ND1
|
B:HIS183
|
2.0
|
25.8
|
1.0
|
SH
|
G:U2M500
|
2.3
|
20.0
|
1.0
|
CG
|
B:ASP181
|
2.7
|
23.3
|
1.0
|
OD2
|
B:ASP181
|
2.7
|
19.8
|
1.0
|
CE1
|
B:HIS183
|
3.0
|
25.8
|
1.0
|
CG
|
B:ASP269
|
3.0
|
22.5
|
1.0
|
CG
|
B:HIS183
|
3.1
|
21.4
|
1.0
|
OD1
|
B:ASP269
|
3.4
|
22.6
|
1.0
|
CB
|
B:HIS183
|
3.4
|
20.3
|
1.0
|
CZ
|
G:U2M500
|
3.5
|
33.9
|
1.0
|
CE
|
G:U2M500
|
3.7
|
26.4
|
1.0
|
N
|
B:HIS183
|
3.8
|
15.4
|
1.0
|
NE2
|
B:HIS183
|
4.1
|
25.8
|
1.0
|
CA
|
B:GLY306
|
4.1
|
25.9
|
1.0
|
CB
|
B:ASP181
|
4.2
|
20.4
|
1.0
|
NE2
|
B:HIS145
|
4.2
|
21.7
|
1.0
|
CD2
|
B:HIS183
|
4.2
|
26.5
|
1.0
|
CG2
|
B:ILE182
|
4.2
|
17.8
|
1.0
|
CA
|
B:HIS183
|
4.2
|
23.3
|
1.0
|
CB
|
B:ASP269
|
4.3
|
15.5
|
1.0
|
N
|
B:ILE182
|
4.4
|
17.0
|
1.0
|
CE1
|
B:HIS145
|
4.5
|
21.6
|
1.0
|
NE2
|
B:HIS146
|
4.5
|
22.0
|
1.0
|
CE2
|
B:TYR308
|
4.6
|
22.2
|
1.0
|
OH
|
B:TYR308
|
4.6
|
21.9
|
1.0
|
N
|
B:GLY306
|
4.6
|
29.9
|
1.0
|
C
|
B:ILE182
|
4.8
|
25.0
|
1.0
|
C
|
B:ASP181
|
4.9
|
22.6
|
1.0
|
CA
|
B:ASP181
|
4.9
|
18.9
|
1.0
|
CA
|
B:ILE182
|
5.0
|
23.3
|
1.0
|
|
Zinc binding site 3 out
of 3 in 6who
Go back to
Zinc Binding Sites List in 6who
Zinc binding site 3 out
of 3 in the Histone Deacetylases Complex with Peptide Macrocycles
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:41.4
occ:1.00
|
OD2
|
C:ASP269
|
2.0
|
49.7
|
1.0
|
OD1
|
C:ASP181
|
2.2
|
47.1
|
1.0
|
ND1
|
C:HIS183
|
2.2
|
43.9
|
1.0
|
SH
|
H:U2M500
|
2.5
|
43.5
|
1.0
|
OD2
|
C:ASP181
|
2.7
|
40.2
|
1.0
|
CG
|
C:ASP181
|
2.8
|
44.9
|
1.0
|
CG
|
C:ASP269
|
3.1
|
43.8
|
1.0
|
CE1
|
C:HIS183
|
3.1
|
41.2
|
1.0
|
CG
|
C:HIS183
|
3.2
|
51.4
|
1.0
|
CB
|
C:HIS183
|
3.5
|
40.1
|
1.0
|
OD1
|
C:ASP269
|
3.5
|
39.3
|
1.0
|
CZ
|
H:U2M500
|
3.6
|
43.5
|
1.0
|
CE
|
H:U2M500
|
3.6
|
43.8
|
1.0
|
N
|
C:HIS183
|
3.9
|
46.1
|
1.0
|
CA
|
C:GLY306
|
4.1
|
46.2
|
1.0
|
CG2
|
C:ILE182
|
4.1
|
42.0
|
1.0
|
NE2
|
C:HIS145
|
4.2
|
36.1
|
1.0
|
NE2
|
C:HIS183
|
4.2
|
42.1
|
1.0
|
CB
|
C:ASP181
|
4.3
|
45.3
|
1.0
|
CD2
|
C:HIS183
|
4.3
|
45.0
|
1.0
|
CA
|
C:HIS183
|
4.3
|
47.6
|
1.0
|
CB
|
C:ASP269
|
4.3
|
54.3
|
1.0
|
N
|
C:ILE182
|
4.5
|
43.8
|
1.0
|
CE2
|
C:TYR308
|
4.5
|
46.4
|
1.0
|
NE2
|
C:HIS146
|
4.5
|
39.5
|
1.0
|
OH
|
C:TYR308
|
4.5
|
45.2
|
1.0
|
CE1
|
C:HIS145
|
4.5
|
41.2
|
1.0
|
N
|
C:GLY306
|
4.6
|
51.6
|
1.0
|
C
|
C:ILE182
|
4.8
|
43.1
|
1.0
|
CZ
|
C:TYR308
|
5.0
|
56.4
|
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 29 10:07:12 2024
|