Fluorine in PDB 8c41: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
Protein crystallography data
The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41
was solved by
S.Najmudin,
X.S.Pan,
B.Wang,
N.E.Cheyen,
L.M.Fisher,
M.R.Sanderson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
115.01 /
2.39
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.471,
157.471,
212.339,
90,
90,
120
|
|
R / Rfree (%)
|
19.2 /
24.3
|
Other elements in 8c41:
The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
(pdb code 8c41). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 1 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:63.4
occ:1.00
|
F1
|
F:TE9101
|
0.0
|
63.4
|
1.0
|
|
C9
|
F:TE9101
|
1.4
|
62.4
|
1.0
|
|
C8
|
F:TE9101
|
2.3
|
60.3
|
1.0
|
|
C10
|
F:TE9101
|
2.4
|
62.4
|
1.0
|
|
H4
|
F:TE9101
|
2.5
|
60.6
|
1.0
|
|
H5
|
F:TE9101
|
2.7
|
61.7
|
1.0
|
|
N7
|
F:DA5
|
2.8
|
59.3
|
1.0
|
|
C2
|
F:DC4
|
2.8
|
73.0
|
1.0
|
|
N4
|
F:TE9101
|
2.8
|
62.6
|
1.0
|
|
C11
|
F:TE9101
|
2.9
|
61.7
|
1.0
|
|
N3
|
F:DC4
|
3.0
|
71.3
|
1.0
|
|
H6
|
F:TE9101
|
3.0
|
62.6
|
1.0
|
|
N1
|
F:DC4
|
3.0
|
77.8
|
1.0
|
|
H2'
|
F:DC4
|
3.0
|
86.4
|
1.0
|
|
C8
|
F:DA5
|
3.1
|
61.8
|
1.0
|
|
H8
|
F:DA5
|
3.2
|
61.4
|
1.0
|
|
C4
|
F:DC4
|
3.3
|
69.5
|
1.0
|
|
C6
|
F:DC4
|
3.3
|
76.0
|
1.0
|
|
O2
|
F:DC4
|
3.3
|
69.4
|
1.0
|
|
C5
|
F:DA5
|
3.4
|
59.1
|
1.0
|
|
C5
|
F:DC4
|
3.5
|
71.5
|
1.0
|
|
C14
|
F:TE9101
|
3.6
|
61.9
|
1.0
|
|
C7
|
F:TE9101
|
3.6
|
59.0
|
1.0
|
|
C1'
|
F:DC4
|
3.7
|
84.7
|
1.0
|
|
C2'
|
F:DC4
|
3.7
|
87.5
|
1.0
|
|
H62
|
F:DA5
|
3.8
|
61.2
|
1.0
|
|
H22
|
H:DG1
|
3.8
|
80.5
|
1.0
|
|
H1'
|
F:DC4
|
3.8
|
84.4
|
1.0
|
|
H6
|
F:DC4
|
3.9
|
75.0
|
1.0
|
|
N9
|
F:DA5
|
3.9
|
62.1
|
1.0
|
|
H1
|
H:DG1
|
4.1
|
79.4
|
1.0
|
|
C4
|
F:DA5
|
4.1
|
60.3
|
1.0
|
|
H5
|
F:DC4
|
4.1
|
72.2
|
1.0
|
|
N4
|
F:DC4
|
4.1
|
68.1
|
1.0
|
|
H2''
|
F:DC4
|
4.1
|
86.5
|
1.0
|
|
C15
|
F:TE9101
|
4.1
|
60.2
|
1.0
|
|
C6
|
F:DA5
|
4.2
|
59.6
|
1.0
|
|
C13
|
F:TE9101
|
4.2
|
62.9
|
1.0
|
|
N6
|
F:DA5
|
4.3
|
61.5
|
1.0
|
|
C12
|
F:TE9101
|
4.4
|
61.7
|
1.0
|
|
H41
|
F:DC4
|
4.4
|
68.4
|
1.0
|
|
H9
|
F:TE9101
|
4.5
|
62.0
|
1.0
|
|
N2
|
H:DG1
|
4.6
|
80.6
|
1.0
|
|
N1
|
H:DG1
|
4.6
|
79.4
|
1.0
|
|
H42
|
F:DC4
|
4.6
|
69.2
|
1.0
|
|
C6
|
F:TE9101
|
4.8
|
59.0
|
1.0
|
|
H10
|
F:TE9101
|
4.9
|
62.8
|
1.0
|
|
C2
|
H:DG1
|
4.9
|
81.1
|
1.0
|
|
H3'
|
F:DC4
|
4.9
|
87.8
|
1.0
|
|
H7
|
F:TE9101
|
4.9
|
61.5
|
1.0
|
|
O4'
|
F:DA5
|
4.9
|
61.6
|
1.0
|
|
O3
|
F:TE9101
|
4.9
|
57.4
|
1.0
|
|
C1'
|
F:DA5
|
5.0
|
61.5
|
1.0
|
|
C3'
|
F:DC4
|
5.0
|
88.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 2 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:61.3
occ:1.00
|
F2
|
F:TE9101
|
0.0
|
61.3
|
1.0
|
|
C16
|
F:TE9101
|
1.3
|
56.9
|
1.0
|
|
C17
|
F:TE9101
|
2.4
|
55.6
|
1.0
|
|
C2
|
F:TE9101
|
2.4
|
56.7
|
1.0
|
|
H2'
|
E:DT7
|
2.4
|
50.5
|
1.0
|
|
H11
|
F:TE9101
|
2.5
|
55.6
|
1.0
|
|
C2
|
E:DT7
|
2.8
|
45.3
|
1.0
|
|
N1
|
E:DT7
|
2.8
|
45.2
|
1.0
|
|
H2''
|
E:DT7
|
2.9
|
50.9
|
1.0
|
|
H3
|
F:TE9101
|
2.9
|
60.0
|
1.0
|
|
N3
|
F:TE9101
|
2.9
|
58.8
|
1.0
|
|
C2'
|
E:DT7
|
2.9
|
50.1
|
1.0
|
|
N3
|
E:DT7
|
3.2
|
46.1
|
1.0
|
|
C3
|
F:TE9101
|
3.2
|
59.6
|
1.0
|
|
O2
|
E:DT7
|
3.2
|
45.4
|
1.0
|
|
C6
|
E:DT7
|
3.2
|
45.6
|
1.0
|
|
C1'
|
E:DT7
|
3.4
|
47.0
|
1.0
|
|
HA3
|
A:GLY457
|
3.4
|
55.8
|
1.0
|
|
N2
|
F:TE9101
|
3.6
|
53.6
|
1.0
|
|
C18
|
F:TE9101
|
3.6
|
53.8
|
1.0
|
|
H3
|
E:DT7
|
3.6
|
46.1
|
1.0
|
|
C4
|
E:DT7
|
3.6
|
45.9
|
1.0
|
|
C5
|
E:DT7
|
3.6
|
45.6
|
1.0
|
|
H6
|
E:DT7
|
3.7
|
45.7
|
1.0
|
|
H1'
|
E:DT7
|
3.8
|
46.9
|
1.0
|
|
C1
|
F:TE9101
|
4.1
|
53.5
|
1.0
|
|
C15
|
F:TE9101
|
4.1
|
60.2
|
1.0
|
|
O5'
|
H:DG1
|
4.2
|
97.3
|
1.0
|
|
CL1
|
F:TE9101
|
4.2
|
65.9
|
1.0
|
|
CA
|
A:GLY457
|
4.2
|
56.5
|
1.0
|
|
HA2
|
A:GLY457
|
4.3
|
55.9
|
1.0
|
|
OP1
|
H:DG1
|
4.3
|
99.6
|
1.0
|
|
C3'
|
E:DT7
|
4.4
|
50.9
|
1.0
|
|
C4
|
F:TE9101
|
4.4
|
60.0
|
1.0
|
|
O4
|
E:DT7
|
4.5
|
44.7
|
1.0
|
|
H3'
|
E:DT7
|
4.6
|
52.0
|
1.0
|
|
H73
|
E:DT7
|
4.6
|
46.7
|
1.0
|
|
O4'
|
E:DT7
|
4.6
|
46.5
|
1.0
|
|
C14
|
F:TE9101
|
4.6
|
61.9
|
1.0
|
|
N
|
A:GLY457
|
4.6
|
55.4
|
1.0
|
|
N1
|
F:DA5
|
4.7
|
59.9
|
1.0
|
|
F3
|
F:TE9101
|
4.7
|
54.4
|
1.0
|
|
H2
|
F:DA5
|
4.7
|
59.8
|
1.0
|
|
C7
|
E:DT7
|
4.7
|
45.7
|
1.0
|
|
HO3'
|
E:DT7
|
4.9
|
72.2
|
0.0
|
|
H
|
A:LYS458
|
4.9
|
53.6
|
1.0
|
|
O
|
A:ARG456
|
4.9
|
53.0
|
1.0
|
|
P
|
H:DG1
|
5.0
|
97.7
|
1.0
|
|
C
|
A:ARG456
|
5.0
|
56.5
|
1.0
|
|
O4'
|
H:DG1
|
5.0
|
95.3
|
1.0
|
|
O2
|
F:TE9101
|
5.0
|
59.1
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 3 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:54.4
occ:1.00
|
F3
|
F:TE9101
|
0.0
|
54.4
|
1.0
|
|
C18
|
F:TE9101
|
1.3
|
53.8
|
1.0
|
|
C17
|
F:TE9101
|
2.4
|
55.6
|
1.0
|
|
C1
|
F:TE9101
|
2.4
|
53.5
|
1.0
|
|
H11
|
F:TE9101
|
2.6
|
55.6
|
1.0
|
|
H1
|
F:TE9101
|
2.6
|
54.2
|
1.0
|
|
HA2
|
A:GLY434
|
2.6
|
57.0
|
1.0
|
|
H
|
A:ASP435
|
2.6
|
54.2
|
1.0
|
|
HA
|
A:ARG456
|
2.7
|
57.9
|
1.0
|
|
N1
|
F:TE9101
|
2.8
|
53.1
|
1.0
|
|
H4'
|
H:DG1
|
3.1
|
97.0
|
1.0
|
|
N
|
A:ASP435
|
3.5
|
54.2
|
1.0
|
|
HD2
|
A:ARG456
|
3.5
|
62.0
|
1.0
|
|
OD2
|
A:ASP435
|
3.5
|
57.5
|
1.0
|
|
H
|
A:GLY457
|
3.5
|
56.0
|
1.0
|
|
OP2
|
H:DG1
|
3.5
|
93.8
|
1.0
|
|
CA
|
A:GLY434
|
3.6
|
58.0
|
1.0
|
|
H2
|
F:TE9101
|
3.6
|
53.3
|
1.0
|
|
N2
|
F:TE9101
|
3.6
|
53.6
|
1.0
|
|
C16
|
F:TE9101
|
3.6
|
56.9
|
1.0
|
|
CA
|
A:ARG456
|
3.6
|
58.0
|
1.0
|
|
O
|
A:LEU455
|
3.8
|
55.8
|
1.0
|
|
HD3
|
A:ARG456
|
3.8
|
62.3
|
1.0
|
|
N
|
A:GLY457
|
3.9
|
55.4
|
1.0
|
|
OP1
|
H:DG1
|
4.0
|
99.6
|
1.0
|
|
HA3
|
A:GLY434
|
4.0
|
57.0
|
1.0
|
|
C
|
A:GLY434
|
4.0
|
55.4
|
1.0
|
|
C4'
|
H:DG1
|
4.0
|
95.4
|
1.0
|
|
P
|
H:DG1
|
4.0
|
97.7
|
1.0
|
|
C
|
A:ARG456
|
4.1
|
56.5
|
1.0
|
|
HB2
|
A:ASP435
|
4.1
|
54.2
|
1.0
|
|
O5'
|
H:DG1
|
4.1
|
97.3
|
1.0
|
|
C2
|
F:TE9101
|
4.1
|
56.7
|
1.0
|
|
CG
|
A:ASP435
|
4.1
|
55.6
|
1.0
|
|
CD
|
A:ARG456
|
4.1
|
62.5
|
1.0
|
|
O4'
|
H:DG1
|
4.2
|
95.3
|
1.0
|
|
N
|
A:ARG456
|
4.4
|
58.2
|
1.0
|
|
C
|
A:LEU455
|
4.4
|
58.2
|
1.0
|
|
CB
|
A:ASP435
|
4.4
|
54.2
|
1.0
|
|
N
|
A:GLY434
|
4.5
|
57.4
|
1.0
|
|
H
|
A:GLY434
|
4.5
|
58.1
|
1.0
|
|
CA
|
A:ASP435
|
4.5
|
53.9
|
1.0
|
|
HB3
|
A:ARG456
|
4.6
|
59.4
|
1.0
|
|
CB
|
A:ARG456
|
4.6
|
59.5
|
1.0
|
|
C5'
|
H:DG1
|
4.7
|
93.8
|
1.0
|
|
F2
|
F:TE9101
|
4.7
|
61.3
|
1.0
|
|
H
|
A:SER436
|
4.8
|
54.3
|
1.0
|
|
CL1
|
F:TE9101
|
4.8
|
65.9
|
1.0
|
|
O3'
|
H:DG1
|
4.8
|
104.5
|
1.0
|
|
HA2
|
A:GLY457
|
4.9
|
55.9
|
1.0
|
|
CA
|
A:GLY457
|
4.9
|
56.5
|
1.0
|
|
O
|
A:ARG456
|
4.9
|
53.0
|
1.0
|
|
HA3
|
A:GLY457
|
4.9
|
55.8
|
1.0
|
|
CG
|
A:ARG456
|
5.0
|
61.5
|
1.0
|
|
OD1
|
A:ASP435
|
5.0
|
56.2
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 4 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:52.6
occ:1.00
|
F1
|
H:TE9101
|
0.0
|
52.6
|
1.0
|
|
C9
|
H:TE9101
|
1.3
|
54.2
|
1.0
|
|
C8
|
H:TE9101
|
2.3
|
54.4
|
1.0
|
|
C10
|
H:TE9101
|
2.4
|
56.4
|
1.0
|
|
H4
|
H:TE9101
|
2.5
|
54.4
|
1.0
|
|
H5
|
H:TE9101
|
2.7
|
58.5
|
1.0
|
|
N4
|
H:TE9101
|
2.8
|
59.3
|
1.0
|
|
N7
|
H:DA5
|
2.9
|
55.1
|
1.0
|
|
C11
|
H:TE9101
|
2.9
|
58.2
|
1.0
|
|
C2
|
H:DT4
|
2.9
|
86.9
|
1.0
|
|
H2'
|
H:DT4
|
2.9
|
81.7
|
1.0
|
|
H6
|
H:TE9101
|
2.9
|
59.4
|
1.0
|
|
N1
|
H:DT4
|
3.0
|
86.1
|
1.0
|
|
N3
|
H:DT4
|
3.0
|
86.8
|
1.0
|
|
C8
|
H:DA5
|
3.2
|
56.9
|
1.0
|
|
C6
|
H:DT4
|
3.2
|
85.3
|
1.0
|
|
C4
|
H:DT4
|
3.3
|
85.3
|
1.0
|
|
H8
|
H:DA5
|
3.3
|
56.8
|
1.0
|
|
C5
|
H:DT4
|
3.4
|
85.3
|
1.0
|
|
C5
|
H:DA5
|
3.5
|
55.2
|
1.0
|
|
H3
|
H:DT4
|
3.5
|
87.1
|
1.0
|
|
O2
|
H:DT4
|
3.5
|
82.3
|
1.0
|
|
C7
|
H:TE9101
|
3.6
|
54.0
|
1.0
|
|
C14
|
H:TE9101
|
3.6
|
56.8
|
1.0
|
|
C2'
|
H:DT4
|
3.7
|
82.4
|
1.0
|
|
C1'
|
H:DT4
|
3.7
|
84.3
|
1.0
|
|
H6
|
H:DT4
|
3.7
|
85.1
|
1.0
|
|
N9
|
H:DA5
|
3.9
|
58.2
|
1.0
|
|
H1'
|
H:DT4
|
4.0
|
84.0
|
1.0
|
|
C4
|
H:DA5
|
4.1
|
56.3
|
1.0
|
|
H2''
|
H:DT4
|
4.1
|
81.5
|
1.0
|
|
O4
|
H:DT4
|
4.1
|
88.2
|
1.0
|
|
C15
|
H:TE9101
|
4.1
|
55.0
|
1.0
|
|
C6
|
H:DA5
|
4.2
|
55.1
|
1.0
|
|
C13
|
H:TE9101
|
4.2
|
61.2
|
1.0
|
|
C12
|
H:TE9101
|
4.4
|
59.7
|
1.0
|
|
N6
|
H:DA5
|
4.4
|
56.2
|
1.0
|
|
H73
|
H:DT4
|
4.4
|
83.9
|
1.0
|
|
C7
|
H:DT4
|
4.4
|
83.4
|
1.0
|
|
N1
|
F:DA1
|
4.4
|
78.1
|
1.0
|
|
H62
|
H:DA5
|
4.5
|
55.8
|
1.0
|
|
H9
|
H:TE9101
|
4.6
|
60.0
|
1.0
|
|
H71
|
H:DT4
|
4.6
|
83.7
|
1.0
|
|
H61
|
H:DA5
|
4.7
|
56.2
|
1.0
|
|
C6
|
H:TE9101
|
4.8
|
53.2
|
1.0
|
|
H2
|
F:DA1
|
4.8
|
78.0
|
1.0
|
|
H3'
|
H:DT4
|
4.8
|
80.2
|
1.0
|
|
O4'
|
H:DA5
|
4.8
|
59.3
|
1.0
|
|
H10
|
H:TE9101
|
4.9
|
61.0
|
1.0
|
|
C3'
|
H:DT4
|
4.9
|
79.9
|
1.0
|
|
H7
|
H:TE9101
|
4.9
|
59.0
|
1.0
|
|
O3
|
H:TE9101
|
4.9
|
50.2
|
1.0
|
|
C1'
|
H:DA5
|
4.9
|
58.6
|
1.0
|
|
C2
|
F:DA1
|
4.9
|
77.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 5 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:52.4
occ:1.00
|
F2
|
H:TE9101
|
0.0
|
52.4
|
1.0
|
|
C16
|
H:TE9101
|
1.4
|
51.7
|
1.0
|
|
C17
|
H:TE9101
|
2.4
|
52.4
|
1.0
|
|
C2
|
H:TE9101
|
2.4
|
52.0
|
1.0
|
|
H2'
|
G:DT7
|
2.5
|
44.6
|
1.0
|
|
H11
|
H:TE9101
|
2.5
|
52.8
|
1.0
|
|
H3
|
H:TE9101
|
2.8
|
55.3
|
1.0
|
|
N1
|
G:DT7
|
2.8
|
40.6
|
1.0
|
|
H2''
|
G:DT7
|
2.9
|
44.4
|
1.0
|
|
C2
|
G:DT7
|
2.9
|
40.2
|
1.0
|
|
N3
|
H:TE9101
|
2.9
|
53.5
|
1.0
|
|
C2'
|
G:DT7
|
3.0
|
43.6
|
1.0
|
|
C3
|
H:TE9101
|
3.1
|
54.6
|
1.0
|
|
C6
|
G:DT7
|
3.1
|
40.7
|
1.0
|
|
N3
|
G:DT7
|
3.2
|
40.0
|
1.0
|
|
C1'
|
G:DT7
|
3.4
|
41.0
|
1.0
|
|
O2
|
G:DT7
|
3.4
|
40.6
|
1.0
|
|
C5
|
G:DT7
|
3.5
|
40.5
|
1.0
|
|
C4
|
G:DT7
|
3.6
|
40.1
|
1.0
|
|
H6
|
G:DT7
|
3.6
|
41.1
|
1.0
|
|
N2
|
H:TE9101
|
3.6
|
50.7
|
1.0
|
|
C18
|
H:TE9101
|
3.6
|
52.7
|
1.0
|
|
HA3
|
B:GLY457
|
3.7
|
57.8
|
1.0
|
|
H3
|
G:DT7
|
3.7
|
40.2
|
1.0
|
|
H1'
|
G:DT7
|
3.8
|
40.6
|
1.0
|
|
O
|
A:HOH1702
|
3.8
|
37.0
|
1.0
|
|
HA2
|
B:GLY457
|
4.0
|
57.7
|
1.0
|
|
C1
|
H:TE9101
|
4.1
|
51.2
|
1.0
|
|
C15
|
H:TE9101
|
4.1
|
55.0
|
1.0
|
|
OP1
|
F:DA1
|
4.2
|
86.7
|
1.0
|
|
CA
|
B:GLY457
|
4.3
|
58.0
|
1.0
|
|
O5'
|
F:DA1
|
4.3
|
89.2
|
1.0
|
|
C4
|
H:TE9101
|
4.4
|
55.1
|
1.0
|
|
CL1
|
H:TE9101
|
4.4
|
62.0
|
1.0
|
|
H73
|
G:DT7
|
4.4
|
42.4
|
1.0
|
|
O4
|
G:DT7
|
4.4
|
40.2
|
1.0
|
|
C3'
|
G:DT7
|
4.5
|
43.7
|
1.0
|
|
O
|
F:HOH204
|
4.5
|
24.0
|
1.0
|
|
C7
|
G:DT7
|
4.6
|
41.0
|
1.0
|
|
O4'
|
G:DT7
|
4.7
|
40.3
|
1.0
|
|
H3'
|
G:DT7
|
4.7
|
45.1
|
1.0
|
|
H2
|
H:DA5
|
4.7
|
56.0
|
1.0
|
|
C14
|
H:TE9101
|
4.8
|
56.8
|
1.0
|
|
F3
|
H:TE9101
|
4.8
|
53.6
|
1.0
|
|
O1
|
H:TE9101
|
4.8
|
60.4
|
1.0
|
|
N
|
B:GLY457
|
4.8
|
60.6
|
1.0
|
|
N1
|
H:DA5
|
4.8
|
54.7
|
1.0
|
|
H71
|
G:DT7
|
5.0
|
41.0
|
1.0
|
|
HO3'
|
G:DT7
|
5.0
|
62.4
|
0.0
|
|
Fluorine binding site 6 out
of 6 in 8c41
Go back to
Fluorine Binding Sites List in 8c41
Fluorine binding site 6 out
of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:53.6
occ:1.00
|
F3
|
H:TE9101
|
0.0
|
53.6
|
1.0
|
|
C18
|
H:TE9101
|
1.4
|
52.7
|
1.0
|
|
C1
|
H:TE9101
|
2.4
|
51.2
|
1.0
|
|
C17
|
H:TE9101
|
2.4
|
52.4
|
1.0
|
|
HA2
|
B:GLY434
|
2.5
|
47.6
|
1.0
|
|
H
|
B:ASP435
|
2.5
|
48.3
|
1.0
|
|
H1
|
H:TE9101
|
2.5
|
51.5
|
1.0
|
|
H11
|
H:TE9101
|
2.6
|
52.8
|
1.0
|
|
N1
|
H:TE9101
|
2.8
|
50.6
|
1.0
|
|
HA
|
B:ARG456
|
2.9
|
66.2
|
1.0
|
|
H4'
|
F:DA1
|
3.2
|
90.3
|
1.0
|
|
N
|
B:ASP435
|
3.3
|
48.5
|
1.0
|
|
CA
|
B:GLY434
|
3.3
|
47.7
|
1.0
|
|
OP2
|
F:DA1
|
3.4
|
84.2
|
1.0
|
|
HA3
|
B:GLY434
|
3.5
|
47.6
|
1.0
|
|
O
|
B:LEU455
|
3.5
|
58.2
|
1.0
|
|
H2
|
H:TE9101
|
3.6
|
51.3
|
1.0
|
|
N2
|
H:TE9101
|
3.6
|
50.7
|
1.0
|
|
C16
|
H:TE9101
|
3.6
|
51.7
|
1.0
|
|
O
|
F:HOH204
|
3.7
|
24.0
|
1.0
|
|
H
|
B:GLY457
|
3.7
|
60.6
|
1.0
|
|
OD2
|
B:ASP435
|
3.7
|
55.2
|
1.0
|
|
OP1
|
F:DA1
|
3.8
|
86.7
|
1.0
|
|
HD3
|
B:ARG456
|
3.8
|
79.5
|
1.0
|
|
CA
|
B:ARG456
|
3.8
|
65.9
|
1.0
|
|
C
|
B:GLY434
|
3.8
|
47.8
|
1.0
|
|
HB2
|
B:ASP435
|
3.9
|
49.7
|
1.0
|
|
P
|
F:DA1
|
3.9
|
88.0
|
1.0
|
|
N
|
B:GLY457
|
4.0
|
60.6
|
1.0
|
|
O5'
|
F:DA1
|
4.0
|
89.2
|
1.0
|
|
C4'
|
F:DA1
|
4.1
|
88.9
|
1.0
|
|
O4'
|
F:DA1
|
4.1
|
89.7
|
1.0
|
|
C2
|
H:TE9101
|
4.1
|
52.0
|
1.0
|
|
C
|
B:ARG456
|
4.2
|
63.5
|
1.0
|
|
HD2
|
B:ARG456
|
4.3
|
79.4
|
1.0
|
|
CG
|
B:ASP435
|
4.3
|
52.0
|
1.0
|
|
C
|
B:LEU455
|
4.4
|
60.7
|
1.0
|
|
CB
|
B:ASP435
|
4.4
|
49.3
|
1.0
|
|
CA
|
B:ASP435
|
4.4
|
48.7
|
1.0
|
|
N
|
B:GLY434
|
4.5
|
47.3
|
1.0
|
|
CD
|
B:ARG456
|
4.5
|
79.8
|
1.0
|
|
N
|
B:ARG456
|
4.5
|
62.9
|
1.0
|
|
H
|
B:GLY434
|
4.6
|
48.1
|
1.0
|
|
HB3
|
B:ARG456
|
4.6
|
73.0
|
1.0
|
|
HA2
|
B:GLY457
|
4.7
|
57.7
|
1.0
|
|
C5'
|
F:DA1
|
4.7
|
87.4
|
1.0
|
|
H
|
B:SER436
|
4.7
|
46.9
|
1.0
|
|
F2
|
H:TE9101
|
4.8
|
52.4
|
1.0
|
|
CB
|
B:ARG456
|
4.8
|
74.4
|
1.0
|
|
CA
|
B:GLY457
|
4.9
|
58.0
|
1.0
|
|
O3'
|
F:DA1
|
4.9
|
97.2
|
1.0
|
|
CL1
|
H:TE9101
|
4.9
|
62.0
|
1.0
|
|
HA
|
B:ASP435
|
5.0
|
48.8
|
1.0
|
|
Reference:
S.Najmudin,
X.S.Pan,
B.Wang,
N.E.Cheyen,
L.M.Fisher,
M.R.Sanderson.
The Nature of the Molecular Interactions at High Resolution of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin. To Be Published.
Page generated: Fri Aug 2 17:04:23 2024
|
