Zinc in PDB 3f0r: Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
Enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form:
3.5.1.98;
Protein crystallography data
The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r
was solved by
D.P.Dowling,
S.L.Gantt,
S.G.Gattis,
C.A.Fierke,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.97 /
2.54
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.895,
90.705,
92.141,
90.00,
94.63,
90.00
|
R / Rfree (%)
|
21 /
25.8
|
Other elements in 3f0r:
The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
(pdb code 3f0r). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 3f0r
Go back to
Zinc Binding Sites List in 3f0r
Zinc binding site 1 out
of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn400
b:42.4
occ:1.00
|
OD2
|
A:ASP178
|
1.8
|
34.5
|
1.0
|
OD2
|
A:ASP267
|
2.0
|
26.4
|
1.0
|
O2
|
A:TSN801
|
2.2
|
77.7
|
1.0
|
O1
|
A:TSN801
|
2.2
|
77.6
|
1.0
|
ND1
|
A:HIS180
|
2.3
|
42.6
|
1.0
|
N1
|
A:TSN801
|
2.6
|
77.8
|
1.0
|
C13
|
A:TSN801
|
2.6
|
77.9
|
1.0
|
CG
|
A:ASP178
|
2.8
|
35.1
|
1.0
|
CE1
|
A:HIS180
|
3.1
|
39.3
|
1.0
|
CG
|
A:HIS180
|
3.1
|
39.2
|
1.0
|
CG
|
A:ASP267
|
3.2
|
31.9
|
1.0
|
OD1
|
A:ASP178
|
3.2
|
35.6
|
1.0
|
CB
|
A:HIS180
|
3.5
|
37.4
|
1.0
|
OD1
|
A:ASP267
|
3.7
|
30.6
|
1.0
|
N
|
A:HIS180
|
3.8
|
33.6
|
1.0
|
C12
|
A:TSN801
|
3.9
|
78.0
|
1.0
|
NE2
|
A:HIS180
|
4.1
|
43.1
|
1.0
|
CD2
|
A:HIS180
|
4.1
|
40.0
|
1.0
|
CA
|
A:GLY304
|
4.1
|
36.0
|
1.0
|
CB
|
A:ASP178
|
4.2
|
31.6
|
1.0
|
CA
|
A:HIS180
|
4.3
|
35.3
|
1.0
|
N
|
A:LEU179
|
4.3
|
37.4
|
1.0
|
NE2
|
A:HIS142
|
4.4
|
44.1
|
1.0
|
CB
|
A:ASP267
|
4.4
|
30.9
|
1.0
|
N
|
A:GLY304
|
4.5
|
39.0
|
1.0
|
NE2
|
A:HIS143
|
4.6
|
37.7
|
1.0
|
OH
|
A:TYR306
|
4.6
|
52.1
|
1.0
|
C11
|
A:TSN801
|
4.6
|
78.2
|
1.0
|
CB
|
A:LEU179
|
4.7
|
36.9
|
1.0
|
C
|
A:LEU179
|
4.8
|
36.3
|
1.0
|
CE1
|
A:HIS142
|
4.8
|
43.3
|
1.0
|
CE1
|
A:TYR306
|
4.9
|
47.6
|
1.0
|
CA
|
A:LEU179
|
4.9
|
36.4
|
1.0
|
C
|
A:ASP178
|
4.9
|
33.0
|
1.0
|
|
Zinc binding site 2 out
of 3 in 3f0r
Go back to
Zinc Binding Sites List in 3f0r
Zinc binding site 2 out
of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:35.4
occ:1.00
|
OD2
|
B:ASP267
|
1.9
|
27.8
|
1.0
|
OD2
|
B:ASP178
|
2.0
|
35.2
|
1.0
|
O2
|
B:TSN804
|
2.2
|
60.4
|
1.0
|
ND1
|
B:HIS180
|
2.3
|
34.4
|
1.0
|
O1
|
B:TSN804
|
2.4
|
55.0
|
1.0
|
CG
|
B:ASP178
|
2.9
|
36.3
|
1.0
|
C13
|
B:TSN804
|
2.9
|
59.5
|
1.0
|
N1
|
B:TSN804
|
3.0
|
59.6
|
1.0
|
CG
|
B:ASP267
|
3.0
|
35.5
|
1.0
|
OD1
|
B:ASP178
|
3.1
|
35.8
|
1.0
|
CE1
|
B:HIS180
|
3.2
|
34.6
|
1.0
|
CG
|
B:HIS180
|
3.3
|
33.1
|
1.0
|
OD1
|
B:ASP267
|
3.4
|
39.3
|
1.0
|
CB
|
B:HIS180
|
3.7
|
33.0
|
1.0
|
N
|
B:HIS180
|
3.8
|
32.0
|
1.0
|
CA
|
B:GLY304
|
4.1
|
39.4
|
1.0
|
N
|
B:LEU179
|
4.3
|
34.9
|
1.0
|
CB
|
B:ASP178
|
4.3
|
33.2
|
1.0
|
C12
|
B:TSN804
|
4.3
|
59.0
|
1.0
|
CB
|
B:ASP267
|
4.3
|
35.1
|
1.0
|
NE2
|
B:HIS180
|
4.3
|
36.7
|
1.0
|
CA
|
B:HIS180
|
4.4
|
31.7
|
1.0
|
CD2
|
B:HIS180
|
4.4
|
34.6
|
1.0
|
N
|
B:GLY304
|
4.4
|
39.8
|
1.0
|
NE2
|
B:HIS142
|
4.4
|
32.0
|
1.0
|
OH
|
B:TYR306
|
4.4
|
45.5
|
1.0
|
CB
|
B:LEU179
|
4.6
|
33.7
|
1.0
|
CE1
|
B:TYR306
|
4.7
|
42.6
|
1.0
|
C
|
B:LEU179
|
4.7
|
33.7
|
1.0
|
CE1
|
B:HIS142
|
4.8
|
32.4
|
1.0
|
CA
|
B:LEU179
|
4.8
|
32.1
|
1.0
|
C11
|
B:TSN804
|
4.9
|
59.4
|
1.0
|
NE2
|
B:HIS143
|
5.0
|
31.1
|
1.0
|
C
|
B:ASP178
|
5.0
|
34.5
|
1.0
|
|
Zinc binding site 3 out
of 3 in 3f0r
Go back to
Zinc Binding Sites List in 3f0r
Zinc binding site 3 out
of 3 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn406
b:48.0
occ:1.00
|
OD2
|
C:ASP267
|
2.1
|
58.6
|
1.0
|
OD1
|
C:ASP178
|
2.1
|
32.1
|
1.0
|
ND1
|
C:HIS180
|
2.2
|
55.3
|
1.0
|
O2
|
C:TSN802
|
2.3
|
88.1
|
1.0
|
O1
|
C:TSN802
|
2.5
|
86.8
|
1.0
|
OD2
|
C:ASP178
|
2.6
|
30.0
|
1.0
|
CG
|
C:ASP178
|
2.7
|
35.8
|
1.0
|
CE1
|
C:HIS180
|
2.8
|
57.4
|
1.0
|
C13
|
C:TSN802
|
3.0
|
89.7
|
1.0
|
CG
|
C:HIS180
|
3.0
|
55.8
|
1.0
|
N1
|
C:TSN802
|
3.1
|
88.5
|
1.0
|
CG
|
C:ASP267
|
3.1
|
58.0
|
1.0
|
OD1
|
C:ASP267
|
3.5
|
59.0
|
1.0
|
CB
|
C:HIS180
|
3.6
|
54.5
|
1.0
|
NE2
|
C:HIS180
|
3.8
|
57.6
|
1.0
|
N
|
C:HIS180
|
3.8
|
53.0
|
1.0
|
CD2
|
C:HIS180
|
3.9
|
55.9
|
1.0
|
CA
|
C:GLY304
|
3.9
|
53.2
|
1.0
|
CB
|
C:ASP178
|
4.2
|
37.5
|
1.0
|
N
|
C:LEU179
|
4.2
|
47.5
|
1.0
|
N
|
C:GLY304
|
4.3
|
52.6
|
1.0
|
C12
|
C:TSN802
|
4.3
|
90.5
|
1.0
|
CA
|
C:HIS180
|
4.3
|
53.5
|
1.0
|
CB
|
C:ASP267
|
4.4
|
56.0
|
1.0
|
OH
|
C:TYR306
|
4.4
|
59.0
|
1.0
|
NE2
|
C:HIS142
|
4.4
|
61.9
|
1.0
|
CB
|
C:LEU179
|
4.7
|
48.1
|
1.0
|
CE1
|
C:TYR306
|
4.7
|
58.2
|
1.0
|
C
|
C:LEU179
|
4.7
|
52.2
|
1.0
|
CA
|
C:LEU179
|
4.8
|
49.8
|
1.0
|
CE1
|
C:HIS142
|
4.9
|
62.6
|
1.0
|
C
|
C:ASP178
|
4.9
|
45.4
|
1.0
|
C
|
C:GLY304
|
4.9
|
54.3
|
1.0
|
C11
|
C:TSN802
|
5.0
|
92.3
|
1.0
|
CA
|
C:ASP178
|
5.0
|
43.6
|
1.0
|
CZ
|
C:TYR306
|
5.0
|
58.3
|
1.0
|
|
Reference:
D.P.Dowling,
S.L.Gantt,
S.G.Gattis,
C.A.Fierke,
D.W.Christianson.
Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors. Biochemistry V. 47 13554 2008.
ISSN: ISSN 0006-2960
PubMed: 19053282
DOI: 10.1021/BI801610C
Page generated: Thu Oct 24 13:00:57 2024
|