Fluorine in PDB 7jom: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Protein crystallography data
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317, PDB code: 7jom
was solved by
P.R.Watson,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
59.43 /
1.84
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.46,
96.45,
96.45,
90,
90,
90
|
R / Rfree (%)
|
16.8 /
20.7
|
Other elements in 7jom:
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
(pdb code 7jom). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317, PDB code: 7jom:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 1 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:24.1
occ:1.00
|
F23
|
A:TO3901
|
0.0
|
24.1
|
1.0
|
C22
|
A:TO3901
|
1.3
|
22.7
|
1.0
|
C24
|
A:TO3901
|
2.3
|
26.6
|
1.0
|
C21
|
A:TO3901
|
2.4
|
25.0
|
1.0
|
F25
|
A:TO3901
|
2.6
|
34.9
|
1.0
|
C20
|
A:TO3901
|
3.6
|
21.6
|
1.0
|
C26
|
A:TO3901
|
3.6
|
26.8
|
1.0
|
C28
|
A:TO3901
|
4.1
|
23.2
|
1.0
|
F27
|
A:TO3901
|
4.7
|
25.0
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 2 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:34.9
occ:1.00
|
F25
|
A:TO3901
|
0.0
|
34.9
|
1.0
|
C24
|
A:TO3901
|
1.3
|
26.6
|
1.0
|
C22
|
A:TO3901
|
2.3
|
22.7
|
1.0
|
C26
|
A:TO3901
|
2.3
|
26.8
|
1.0
|
F23
|
A:TO3901
|
2.6
|
24.1
|
1.0
|
F27
|
A:TO3901
|
2.7
|
25.0
|
1.0
|
C21
|
A:TO3901
|
3.5
|
25.0
|
1.0
|
C28
|
A:TO3901
|
3.5
|
23.2
|
1.0
|
C20
|
A:TO3901
|
4.0
|
21.6
|
1.0
|
F29
|
A:TO3901
|
4.6
|
27.1
|
1.0
|
O
|
A:HOH1163
|
4.7
|
19.4
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 3 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:25.0
occ:1.00
|
F27
|
A:TO3901
|
0.0
|
25.0
|
1.0
|
C26
|
A:TO3901
|
1.3
|
26.8
|
1.0
|
C28
|
A:TO3901
|
2.3
|
23.2
|
1.0
|
C24
|
A:TO3901
|
2.4
|
26.6
|
1.0
|
F29
|
A:TO3901
|
2.7
|
27.1
|
1.0
|
F25
|
A:TO3901
|
2.7
|
34.9
|
1.0
|
C20
|
A:TO3901
|
3.6
|
21.6
|
1.0
|
C22
|
A:TO3901
|
3.6
|
22.7
|
1.0
|
O
|
A:HOH1163
|
3.6
|
19.4
|
1.0
|
OG
|
A:SER531
|
3.8
|
18.4
|
1.0
|
O1
|
A:FMT906
|
3.9
|
30.7
|
1.0
|
C21
|
A:TO3901
|
4.1
|
25.0
|
1.0
|
C
|
A:FMT906
|
4.2
|
28.0
|
1.0
|
CA
|
A:SER531
|
4.3
|
11.3
|
1.0
|
CB
|
A:SER531
|
4.4
|
13.5
|
1.0
|
O2
|
A:FMT906
|
4.4
|
35.3
|
1.0
|
O
|
A:HOH1169
|
4.5
|
28.9
|
1.0
|
F23
|
A:TO3901
|
4.7
|
24.1
|
1.0
|
N
|
A:SER531
|
4.8
|
11.6
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 4 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:27.1
occ:1.00
|
F29
|
A:TO3901
|
0.0
|
27.1
|
1.0
|
C28
|
A:TO3901
|
1.3
|
23.2
|
1.0
|
C20
|
A:TO3901
|
2.3
|
21.6
|
1.0
|
C26
|
A:TO3901
|
2.3
|
26.8
|
1.0
|
F27
|
A:TO3901
|
2.7
|
25.0
|
1.0
|
O19
|
A:TO3901
|
2.8
|
13.7
|
1.0
|
S18
|
A:TO3901
|
2.9
|
14.9
|
1.0
|
C09
|
A:TO3901
|
3.1
|
12.7
|
1.0
|
O1
|
A:FMT906
|
3.3
|
30.7
|
1.0
|
OG
|
A:SER531
|
3.3
|
18.4
|
1.0
|
N10
|
A:TO3901
|
3.4
|
13.1
|
1.0
|
C24
|
A:TO3901
|
3.6
|
26.6
|
1.0
|
C21
|
A:TO3901
|
3.6
|
25.0
|
1.0
|
CB
|
A:SER531
|
3.7
|
13.5
|
1.0
|
C22
|
A:TO3901
|
4.1
|
22.7
|
1.0
|
O30
|
A:TO3901
|
4.1
|
14.8
|
1.0
|
C
|
A:FMT906
|
4.1
|
28.0
|
1.0
|
O
|
A:HOH1169
|
4.1
|
28.9
|
1.0
|
CE1
|
A:PHE583
|
4.2
|
12.2
|
1.0
|
CZ
|
A:PHE583
|
4.3
|
11.0
|
1.0
|
CA
|
A:SER531
|
4.3
|
11.3
|
1.0
|
C08
|
A:TO3901
|
4.3
|
10.5
|
1.0
|
C11
|
A:TO3901
|
4.4
|
13.3
|
1.0
|
F25
|
A:TO3901
|
4.6
|
34.9
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 5 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:28.2
occ:1.00
|
F23
|
B:TO3801
|
0.0
|
28.2
|
1.0
|
C22
|
B:TO3801
|
1.4
|
33.3
|
1.0
|
C24
|
B:TO3801
|
2.4
|
33.2
|
1.0
|
C21
|
B:TO3801
|
2.4
|
28.2
|
1.0
|
F25
|
B:TO3801
|
2.7
|
35.9
|
1.0
|
C20
|
B:TO3801
|
3.6
|
23.5
|
1.0
|
C26
|
B:TO3801
|
3.6
|
26.4
|
1.0
|
C28
|
B:TO3801
|
4.2
|
21.7
|
1.0
|
F27
|
B:TO3801
|
4.7
|
30.0
|
1.0
|
O19
|
B:TO3801
|
5.0
|
16.7
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 6 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:35.9
occ:1.00
|
F25
|
B:TO3801
|
0.0
|
35.9
|
1.0
|
C24
|
B:TO3801
|
1.3
|
33.2
|
1.0
|
C26
|
B:TO3801
|
2.3
|
26.4
|
1.0
|
C22
|
B:TO3801
|
2.3
|
33.3
|
1.0
|
F27
|
B:TO3801
|
2.6
|
30.0
|
1.0
|
F23
|
B:TO3801
|
2.7
|
28.2
|
1.0
|
C21
|
B:TO3801
|
3.5
|
28.2
|
1.0
|
C28
|
B:TO3801
|
3.5
|
21.7
|
1.0
|
C20
|
B:TO3801
|
3.9
|
23.5
|
1.0
|
F29
|
B:TO3801
|
4.6
|
19.3
|
1.0
|
O
|
B:HOH1059
|
4.8
|
17.1
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 7 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:30.0
occ:1.00
|
F27
|
B:TO3801
|
0.0
|
30.0
|
1.0
|
C26
|
B:TO3801
|
1.3
|
26.4
|
1.0
|
C28
|
B:TO3801
|
2.3
|
21.7
|
1.0
|
C24
|
B:TO3801
|
2.3
|
33.2
|
1.0
|
F25
|
B:TO3801
|
2.6
|
35.9
|
1.0
|
F29
|
B:TO3801
|
2.6
|
19.3
|
1.0
|
C20
|
B:TO3801
|
3.5
|
23.5
|
1.0
|
C22
|
B:TO3801
|
3.5
|
33.3
|
1.0
|
O
|
B:HOH1059
|
3.8
|
17.1
|
1.0
|
OG
|
B:SER531
|
3.9
|
13.8
|
1.0
|
C21
|
B:TO3801
|
4.0
|
28.2
|
1.0
|
O
|
B:HOH1068
|
4.4
|
23.8
|
1.0
|
CA
|
B:SER531
|
4.5
|
11.5
|
1.0
|
CB
|
B:SER531
|
4.5
|
11.4
|
1.0
|
F23
|
B:TO3801
|
4.7
|
28.2
|
1.0
|
S18
|
B:TO3801
|
4.9
|
16.5
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 7jom
Go back to
Fluorine Binding Sites List in 7jom
Fluorine binding site 8 out
of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:19.3
occ:1.00
|
F29
|
B:TO3801
|
0.0
|
19.3
|
1.0
|
C28
|
B:TO3801
|
1.3
|
21.7
|
1.0
|
C26
|
B:TO3801
|
2.3
|
26.4
|
1.0
|
C20
|
B:TO3801
|
2.3
|
23.5
|
1.0
|
F27
|
B:TO3801
|
2.6
|
30.0
|
1.0
|
O30
|
B:TO3801
|
2.9
|
14.2
|
1.0
|
S18
|
B:TO3801
|
2.9
|
16.5
|
1.0
|
C09
|
B:TO3801
|
3.2
|
12.4
|
1.0
|
OG
|
B:SER531
|
3.4
|
13.8
|
1.0
|
N10
|
B:TO3801
|
3.4
|
11.5
|
1.0
|
C24
|
B:TO3801
|
3.6
|
33.2
|
1.0
|
C21
|
B:TO3801
|
3.6
|
28.2
|
1.0
|
CB
|
B:SER531
|
3.7
|
11.4
|
1.0
|
O
|
B:HOH1068
|
4.0
|
23.8
|
1.0
|
C22
|
B:TO3801
|
4.1
|
33.3
|
1.0
|
O19
|
B:TO3801
|
4.1
|
16.7
|
1.0
|
CE1
|
B:PHE583
|
4.2
|
13.1
|
1.0
|
CA
|
B:SER531
|
4.3
|
11.5
|
1.0
|
CZ
|
B:PHE583
|
4.4
|
8.8
|
1.0
|
C08
|
B:TO3801
|
4.4
|
10.3
|
1.0
|
C11
|
B:TO3801
|
4.5
|
15.4
|
1.0
|
F25
|
B:TO3801
|
4.6
|
35.9
|
1.0
|
|
Reference:
P.R.Watson,
D.W.Christianson.
Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 To Be Published.
Page generated: Fri Aug 2 07:53:15 2024
|