Fluorine in PDB 2v7v: X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
Enzymatic activity of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
All present enzymatic activity of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine:
2.5.1.63;
Protein crystallography data
The structure of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine, PDB code: 2v7v
was solved by
X.Zhu,
D.O'hagan,
J.H.Naismith,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.16 /
1.94
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.892,
129.946,
184.491,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
22.1
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
(pdb code 2v7v). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine, PDB code: 2v7v:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 2v7v
Go back to
Fluorine Binding Sites List in 2v7v
Fluorine binding site 1 out
of 3 in the X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1299
b:26.8
occ:1.00
|
F19
|
A:5FD1299
|
0.0
|
26.8
|
1.0
|
C5'
|
A:5FD1299
|
1.3
|
22.0
|
1.0
|
C4'
|
A:5FD1299
|
2.2
|
20.0
|
1.0
|
N
|
A:SER158
|
2.9
|
19.0
|
1.0
|
CB
|
A:SER158
|
3.1
|
19.4
|
1.0
|
C3'
|
A:5FD1299
|
3.1
|
16.5
|
1.0
|
OG
|
A:SER158
|
3.2
|
18.6
|
1.0
|
O4'
|
A:5FD1299
|
3.3
|
17.4
|
1.0
|
CD1
|
A:PHE156
|
3.3
|
19.9
|
1.0
|
O3'
|
A:5FD1299
|
3.4
|
19.2
|
1.0
|
N
|
A:TYR157
|
3.4
|
19.6
|
1.0
|
C
|
A:PHE156
|
3.5
|
19.7
|
1.0
|
CA
|
A:PHE156
|
3.5
|
20.0
|
1.0
|
CA
|
A:SER158
|
3.6
|
19.0
|
1.0
|
O
|
A:THR155
|
3.8
|
20.8
|
1.0
|
C
|
A:TYR157
|
4.0
|
19.7
|
1.0
|
CE1
|
A:PHE156
|
4.0
|
18.7
|
1.0
|
O
|
A:PHE156
|
4.2
|
18.9
|
1.0
|
CA
|
A:TYR157
|
4.2
|
19.4
|
1.0
|
N
|
A:PHE156
|
4.3
|
20.3
|
1.0
|
CG
|
A:PHE156
|
4.3
|
20.4
|
1.0
|
OG1
|
A:THR80
|
4.3
|
18.1
|
1.0
|
CD2
|
A:LEU17
|
4.4
|
19.0
|
1.0
|
CB
|
A:TYR77
|
4.4
|
18.1
|
1.0
|
C
|
A:THR155
|
4.4
|
20.6
|
1.0
|
O
|
A:HOH2156
|
4.4
|
44.4
|
1.0
|
C1'
|
A:5FD1299
|
4.4
|
16.5
|
1.0
|
C2'
|
A:5FD1299
|
4.5
|
15.1
|
1.0
|
CB
|
A:PHE156
|
4.5
|
19.9
|
1.0
|
N
|
A:ARG159
|
4.5
|
18.8
|
1.0
|
C
|
A:SER158
|
4.6
|
19.2
|
1.0
|
CB
|
A:THR80
|
4.7
|
20.3
|
1.0
|
CB
|
A:TYR157
|
4.9
|
19.9
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 2v7v
Go back to
Fluorine Binding Sites List in 2v7v
Fluorine binding site 2 out
of 3 in the X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1299
b:26.2
occ:1.00
|
F19
|
C:5FD1299
|
0.0
|
26.2
|
1.0
|
C5'
|
C:5FD1299
|
1.4
|
21.6
|
1.0
|
C4'
|
C:5FD1299
|
2.3
|
19.3
|
1.0
|
N
|
B:SER158
|
2.9
|
18.6
|
1.0
|
CB
|
B:SER158
|
3.0
|
19.2
|
1.0
|
C3'
|
C:5FD1299
|
3.1
|
19.2
|
1.0
|
OG
|
B:SER158
|
3.1
|
19.6
|
1.0
|
O3'
|
C:5FD1299
|
3.3
|
18.5
|
1.0
|
CD1
|
B:PHE156
|
3.3
|
21.7
|
1.0
|
N
|
B:TYR157
|
3.4
|
19.9
|
1.0
|
C
|
B:PHE156
|
3.5
|
19.8
|
1.0
|
CA
|
B:PHE156
|
3.5
|
20.0
|
1.0
|
CA
|
B:SER158
|
3.5
|
19.0
|
1.0
|
O4'
|
C:5FD1299
|
3.5
|
21.0
|
1.0
|
CE1
|
B:PHE156
|
3.9
|
23.0
|
1.0
|
C
|
B:TYR157
|
4.0
|
19.5
|
1.0
|
O
|
B:THR155
|
4.0
|
20.7
|
1.0
|
O
|
B:PHE156
|
4.1
|
19.2
|
1.0
|
CD2
|
B:LEU17
|
4.2
|
17.6
|
1.0
|
CA
|
B:TYR157
|
4.2
|
19.1
|
1.0
|
CG
|
B:PHE156
|
4.3
|
21.8
|
1.0
|
N
|
B:PHE156
|
4.4
|
20.1
|
1.0
|
N
|
B:ARG159
|
4.4
|
18.8
|
1.0
|
C2'
|
C:5FD1299
|
4.5
|
16.9
|
1.0
|
CB
|
B:TYR77
|
4.5
|
18.2
|
1.0
|
CB
|
B:PHE156
|
4.5
|
20.5
|
1.0
|
O
|
B:HOH2139
|
4.5
|
36.4
|
1.0
|
C
|
B:SER158
|
4.5
|
19.1
|
1.0
|
C1'
|
C:5FD1299
|
4.6
|
18.6
|
1.0
|
C
|
B:THR155
|
4.6
|
20.7
|
1.0
|
OG1
|
B:THR80
|
4.6
|
21.5
|
1.0
|
CB
|
B:THR80
|
4.8
|
20.8
|
1.0
|
CB
|
B:TYR157
|
4.9
|
20.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 2v7v
Go back to
Fluorine Binding Sites List in 2v7v
Fluorine binding site 3 out
of 3 in the X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of X-Ray Crystal Structure of 5'-Fluorodeoxyadenosine Synthase From Streptomyces Cattleya Complexed with 5'-Fluorodeoxyadenosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1300
b:24.4
occ:1.00
|
F19
|
C:5FD1300
|
0.0
|
24.4
|
1.0
|
C5'
|
C:5FD1300
|
1.4
|
20.8
|
1.0
|
C4'
|
C:5FD1300
|
2.3
|
18.7
|
1.0
|
N
|
C:SER158
|
2.9
|
18.7
|
1.0
|
CB
|
C:SER158
|
3.1
|
18.3
|
1.0
|
C3'
|
C:5FD1300
|
3.1
|
18.1
|
1.0
|
OG
|
C:SER158
|
3.1
|
19.4
|
1.0
|
O3'
|
C:5FD1300
|
3.3
|
18.1
|
1.0
|
CD1
|
C:PHE156
|
3.3
|
19.7
|
1.0
|
O4'
|
C:5FD1300
|
3.4
|
20.2
|
1.0
|
N
|
C:TYR157
|
3.4
|
19.6
|
1.0
|
C
|
C:PHE156
|
3.5
|
19.6
|
1.0
|
CA
|
C:SER158
|
3.5
|
19.0
|
1.0
|
CA
|
C:PHE156
|
3.5
|
19.7
|
1.0
|
O
|
C:THR155
|
4.0
|
20.9
|
1.0
|
C
|
C:TYR157
|
4.0
|
19.5
|
1.0
|
CE1
|
C:PHE156
|
4.0
|
19.7
|
1.0
|
O
|
C:PHE156
|
4.2
|
18.9
|
1.0
|
CA
|
C:TYR157
|
4.2
|
19.0
|
1.0
|
CG
|
C:PHE156
|
4.4
|
20.1
|
1.0
|
CD2
|
C:LEU17
|
4.4
|
19.2
|
1.0
|
CB
|
C:TYR77
|
4.4
|
17.9
|
1.0
|
O
|
C:HOH2134
|
4.4
|
37.1
|
1.0
|
N
|
C:PHE156
|
4.4
|
20.0
|
1.0
|
C2'
|
C:5FD1300
|
4.5
|
15.8
|
1.0
|
C1'
|
C:5FD1300
|
4.5
|
17.4
|
1.0
|
OG1
|
C:THR80
|
4.5
|
17.9
|
1.0
|
N
|
C:ARG159
|
4.5
|
18.9
|
1.0
|
C
|
C:THR155
|
4.5
|
20.8
|
1.0
|
CB
|
C:PHE156
|
4.5
|
19.5
|
1.0
|
C
|
C:SER158
|
4.6
|
19.1
|
1.0
|
CB
|
C:THR80
|
4.7
|
19.7
|
1.0
|
CB
|
C:TYR157
|
4.9
|
19.9
|
1.0
|
|
Reference:
X.Zhu,
D.A.Robinson,
A.R.Mcewan,
D.O'hagan,
J.H.Naismith.
Mechanism of Enzymatic Fluorination in Streptomyces Cattleya. J. Am. Chem. Soc. V. 129 14597 2007.
ISSN: ESSN 1520-5126
PubMed: 17985882
DOI: 10.1021/JA0731569
Page generated: Wed Jul 31 16:03:20 2024
|