Fluorine in PDB 9gef: Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
All present enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex:
5.6.2.2;
Protein crystallography data
The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef
was solved by
B.Wang,
S.Najmudin,
X.-S.Pan,
V.Mykhaylyk,
C.Orr,
A.Wagner,
L.Govada,
N.E.Chayen,
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)
|
79.39 /
2.62
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
158.533,
158.533,
210.82,
90,
90,
120
|
R / Rfree (%)
|
18 /
20.9
|
Other elements in 9gef:
The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
(pdb code 9gef). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 1 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:40.1
occ:1.00
|
F1
|
F:TE9101
|
0.0
|
40.1
|
1.0
|
C9
|
F:TE9101
|
1.3
|
36.1
|
1.0
|
C10
|
F:TE9101
|
2.3
|
37.2
|
1.0
|
C8
|
F:TE9101
|
2.4
|
35.4
|
1.0
|
N4
|
F:TE9101
|
2.7
|
37.6
|
1.0
|
C11
|
F:TE9101
|
2.9
|
37.7
|
1.0
|
C2
|
F:DT4
|
2.9
|
61.2
|
1.0
|
N1
|
F:DT4
|
3.0
|
62.3
|
1.0
|
N3
|
F:DT4
|
3.0
|
59.9
|
1.0
|
C8
|
F:DA5
|
3.1
|
48.7
|
1.0
|
N7
|
F:DA5
|
3.1
|
47.7
|
1.0
|
C6
|
F:DT4
|
3.2
|
62.9
|
1.0
|
C4
|
F:DT4
|
3.3
|
60.4
|
1.0
|
C5
|
F:DT4
|
3.4
|
62.1
|
1.0
|
O2
|
F:DT4
|
3.5
|
61.2
|
1.0
|
C14
|
F:TE9101
|
3.6
|
43.5
|
1.0
|
C7
|
F:TE9101
|
3.6
|
36.5
|
1.0
|
C2'
|
F:DT4
|
3.7
|
62.3
|
1.0
|
N9
|
F:DA5
|
3.7
|
47.7
|
1.0
|
C5
|
F:DA5
|
3.7
|
45.7
|
1.0
|
C1'
|
F:DT4
|
3.8
|
63.1
|
1.0
|
O4
|
F:DT4
|
4.1
|
59.0
|
1.0
|
C15
|
F:TE9101
|
4.1
|
37.8
|
1.0
|
C4
|
F:DA5
|
4.1
|
45.7
|
1.0
|
C13
|
F:TE9101
|
4.2
|
38.9
|
1.0
|
N1
|
H:DA1
|
4.2
|
66.8
|
1.0
|
C12
|
F:TE9101
|
4.3
|
38.7
|
1.0
|
O4'
|
F:DA5
|
4.4
|
51.1
|
1.0
|
C7
|
F:DT4
|
4.4
|
63.1
|
1.0
|
C1'
|
F:DA5
|
4.6
|
48.6
|
1.0
|
C6
|
F:DA5
|
4.6
|
44.0
|
1.0
|
C2
|
H:DA1
|
4.7
|
67.2
|
1.0
|
C6
|
F:TE9101
|
4.8
|
38.4
|
1.0
|
CL1
|
F:TE9101
|
5.0
|
87.8
|
1.0
|
C6
|
H:DA1
|
5.0
|
64.9
|
1.0
|
N6
|
F:DA5
|
5.0
|
43.8
|
1.0
|
C3'
|
F:DT4
|
5.0
|
64.8
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 2 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:49.1
occ:1.00
|
F2
|
F:TE9101
|
0.0
|
49.1
|
1.0
|
C16
|
F:TE9101
|
1.3
|
38.9
|
1.0
|
C2
|
F:TE9101
|
2.4
|
37.9
|
1.0
|
C17
|
F:TE9101
|
2.4
|
37.0
|
1.0
|
N3
|
F:TE9101
|
2.8
|
36.9
|
1.0
|
C3
|
F:TE9101
|
3.0
|
38.6
|
1.0
|
C2
|
E:DT15
|
3.0
|
42.3
|
1.0
|
N3
|
E:DT15
|
3.2
|
43.0
|
1.0
|
N1
|
E:DT15
|
3.2
|
42.1
|
1.0
|
O2
|
E:DT15
|
3.4
|
42.2
|
1.0
|
C2'
|
E:DT15
|
3.5
|
46.5
|
1.0
|
N2
|
F:TE9101
|
3.6
|
37.6
|
1.0
|
C18
|
F:TE9101
|
3.6
|
36.2
|
1.0
|
C6
|
E:DT15
|
3.6
|
43.1
|
1.0
|
C4
|
E:DT15
|
3.7
|
43.4
|
1.0
|
C1'
|
E:DT15
|
3.8
|
42.0
|
1.0
|
C5
|
E:DT15
|
3.9
|
43.5
|
1.0
|
C15
|
F:TE9101
|
4.0
|
37.8
|
1.0
|
C1
|
F:TE9101
|
4.1
|
34.8
|
1.0
|
CA
|
A:GLY457
|
4.1
|
48.5
|
1.0
|
C4
|
F:TE9101
|
4.2
|
40.0
|
1.0
|
N1
|
F:DA5
|
4.3
|
42.5
|
1.0
|
CL1
|
F:TE9101
|
4.3
|
87.8
|
1.0
|
O4
|
E:DT15
|
4.4
|
44.1
|
1.0
|
N
|
A:GLY457
|
4.5
|
49.5
|
1.0
|
C14
|
F:TE9101
|
4.6
|
43.5
|
1.0
|
C2
|
F:DA5
|
4.6
|
42.8
|
1.0
|
O1
|
F:TE9101
|
4.6
|
44.4
|
1.0
|
F3
|
F:TE9101
|
4.7
|
38.7
|
1.0
|
C5
|
F:TE9101
|
4.9
|
44.3
|
1.0
|
C7
|
F:TE9101
|
4.9
|
36.5
|
1.0
|
C7
|
E:DT15
|
5.0
|
44.7
|
1.0
|
C
|
A:ARG456
|
5.0
|
50.1
|
1.0
|
OP1
|
H:DA1
|
5.0
|
72.8
|
1.0
|
C3'
|
E:DT15
|
5.0
|
45.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 3 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F101
b:38.7
occ:1.00
|
F3
|
F:TE9101
|
0.0
|
38.7
|
1.0
|
C18
|
F:TE9101
|
1.3
|
36.2
|
1.0
|
C1
|
F:TE9101
|
2.4
|
34.8
|
1.0
|
C17
|
F:TE9101
|
2.4
|
37.0
|
1.0
|
N1
|
F:TE9101
|
2.7
|
32.1
|
1.0
|
OD1
|
A:ASP435
|
3.0
|
40.2
|
1.0
|
O5'
|
H:DA1
|
3.2
|
68.6
|
1.0
|
CA
|
A:ARG456
|
3.3
|
50.2
|
1.0
|
CA
|
A:GLY434
|
3.5
|
41.1
|
1.0
|
N2
|
F:TE9101
|
3.6
|
37.6
|
1.0
|
C16
|
F:TE9101
|
3.6
|
38.9
|
1.0
|
CG
|
A:ARG456
|
3.6
|
53.1
|
1.0
|
N
|
A:ASP435
|
3.6
|
40.6
|
1.0
|
CB
|
A:ARG456
|
3.7
|
51.2
|
1.0
|
O
|
A:LEU455
|
3.8
|
49.2
|
1.0
|
OP1
|
H:DA1
|
3.9
|
72.8
|
1.0
|
N
|
A:GLY457
|
3.9
|
49.5
|
1.0
|
P
|
H:DA1
|
3.9
|
70.1
|
1.0
|
C
|
A:ARG456
|
4.0
|
50.1
|
1.0
|
C4'
|
H:DA1
|
4.1
|
66.0
|
1.0
|
C2
|
F:TE9101
|
4.1
|
37.9
|
1.0
|
C
|
A:GLY434
|
4.1
|
41.6
|
1.0
|
CG
|
A:ASP435
|
4.2
|
40.8
|
1.0
|
C5'
|
H:DA1
|
4.2
|
66.0
|
1.0
|
N
|
A:ARG456
|
4.3
|
50.4
|
1.0
|
O4'
|
H:DA1
|
4.3
|
65.6
|
1.0
|
C
|
A:LEU455
|
4.4
|
49.9
|
1.0
|
OP2
|
H:DA1
|
4.5
|
71.0
|
1.0
|
N
|
A:GLY434
|
4.5
|
42.0
|
1.0
|
CD
|
A:ARG456
|
4.7
|
54.4
|
1.0
|
CB
|
A:ASP435
|
4.7
|
40.7
|
1.0
|
F2
|
F:TE9101
|
4.7
|
49.1
|
1.0
|
CA
|
A:ASP435
|
4.8
|
40.9
|
1.0
|
CL1
|
F:TE9101
|
4.8
|
87.8
|
1.0
|
CA
|
A:GLY457
|
5.0
|
48.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 4 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:37.9
occ:1.00
|
F1
|
H:TE9101
|
0.0
|
37.9
|
1.0
|
C9
|
H:TE9101
|
1.4
|
36.1
|
1.0
|
C10
|
H:TE9101
|
2.3
|
36.0
|
1.0
|
C8
|
H:TE9101
|
2.4
|
35.5
|
1.0
|
N4
|
H:TE9101
|
2.7
|
35.1
|
1.0
|
C2
|
H:DC4
|
2.7
|
59.0
|
1.0
|
C11
|
H:TE9101
|
2.8
|
37.5
|
1.0
|
N3
|
H:DC4
|
2.9
|
57.5
|
1.0
|
N1
|
H:DC4
|
3.0
|
60.0
|
1.0
|
N7
|
H:DG5
|
3.1
|
46.1
|
1.0
|
C8
|
H:DG5
|
3.2
|
47.6
|
1.0
|
O2
|
H:DC4
|
3.2
|
59.7
|
1.0
|
C4
|
H:DC4
|
3.3
|
57.0
|
1.0
|
C6
|
H:DC4
|
3.3
|
59.8
|
1.0
|
C2'
|
H:DC4
|
3.5
|
60.3
|
1.0
|
C5
|
H:DC4
|
3.5
|
58.3
|
1.0
|
C14
|
H:TE9101
|
3.6
|
42.0
|
1.0
|
C1'
|
H:DC4
|
3.6
|
61.3
|
1.0
|
C7
|
H:TE9101
|
3.6
|
36.0
|
1.0
|
C5
|
H:DG5
|
3.7
|
44.5
|
1.0
|
N9
|
H:DG5
|
3.8
|
47.2
|
1.0
|
C4
|
H:DG5
|
4.1
|
45.1
|
1.0
|
C15
|
H:TE9101
|
4.1
|
37.6
|
1.0
|
N4
|
H:DC4
|
4.2
|
56.0
|
1.0
|
C12
|
H:TE9101
|
4.2
|
40.6
|
1.0
|
C13
|
H:TE9101
|
4.2
|
37.1
|
1.0
|
N1
|
F:DG1
|
4.3
|
68.0
|
1.0
|
O4'
|
H:DG5
|
4.4
|
51.2
|
1.0
|
C6
|
H:DG5
|
4.6
|
42.6
|
1.0
|
C1'
|
H:DG5
|
4.6
|
48.8
|
1.0
|
N2
|
F:DG1
|
4.6
|
72.1
|
1.0
|
C3'
|
H:DC4
|
4.7
|
61.9
|
1.0
|
C2
|
F:DG1
|
4.8
|
69.6
|
1.0
|
C6
|
H:TE9101
|
4.8
|
36.2
|
1.0
|
O6
|
H:DG5
|
4.9
|
41.9
|
1.0
|
O4'
|
H:DC4
|
5.0
|
63.6
|
1.0
|
CL1
|
H:TE9101
|
5.0
|
83.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 5 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:38.9
occ:1.00
|
F2
|
H:TE9101
|
0.0
|
38.9
|
1.0
|
C16
|
H:TE9101
|
1.3
|
35.4
|
1.0
|
C2
|
H:TE9101
|
2.4
|
34.6
|
1.0
|
C17
|
H:TE9101
|
2.4
|
35.4
|
1.0
|
N3
|
H:TE9101
|
2.9
|
35.3
|
1.0
|
C2
|
G:DC15
|
3.0
|
40.8
|
1.0
|
C3
|
H:TE9101
|
3.0
|
34.4
|
1.0
|
N3
|
G:DC15
|
3.2
|
41.5
|
1.0
|
N1
|
G:DC15
|
3.3
|
40.2
|
1.0
|
O2
|
G:DC15
|
3.3
|
41.0
|
1.0
|
C2'
|
G:DC15
|
3.4
|
43.5
|
1.0
|
N2
|
H:TE9101
|
3.6
|
34.1
|
1.0
|
C4
|
G:DC15
|
3.6
|
41.5
|
1.0
|
C18
|
H:TE9101
|
3.6
|
34.2
|
1.0
|
C6
|
G:DC15
|
3.7
|
40.5
|
1.0
|
C1'
|
G:DC15
|
3.8
|
40.0
|
1.0
|
C5
|
G:DC15
|
3.9
|
41.0
|
1.0
|
C15
|
H:TE9101
|
4.0
|
37.6
|
1.0
|
C1
|
H:TE9101
|
4.1
|
32.0
|
1.0
|
C4
|
H:TE9101
|
4.2
|
35.7
|
1.0
|
CA
|
B:GLY457
|
4.2
|
47.8
|
1.0
|
N2
|
H:DG5
|
4.3
|
41.9
|
1.0
|
CL1
|
H:TE9101
|
4.3
|
83.5
|
1.0
|
N1
|
H:DG5
|
4.4
|
41.7
|
1.0
|
N4
|
G:DC15
|
4.4
|
42.3
|
1.0
|
N
|
B:GLY457
|
4.6
|
49.4
|
1.0
|
C14
|
H:TE9101
|
4.7
|
42.0
|
1.0
|
O
|
F:HOH205
|
4.7
|
21.0
|
1.0
|
C2
|
H:DG5
|
4.7
|
42.6
|
1.0
|
F3
|
H:TE9101
|
4.8
|
35.6
|
1.0
|
OP1
|
F:DG1
|
4.8
|
70.0
|
1.0
|
C3'
|
G:DC15
|
4.8
|
43.4
|
1.0
|
O2
|
H:TE9101
|
4.9
|
41.3
|
1.0
|
C5
|
H:TE9101
|
5.0
|
38.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 9gef
Go back to
Fluorine Binding Sites List in 9gef
Fluorine binding site 6 out
of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F101
b:35.6
occ:1.00
|
F3
|
H:TE9101
|
0.0
|
35.6
|
1.0
|
C18
|
H:TE9101
|
1.4
|
34.2
|
1.0
|
C1
|
H:TE9101
|
2.4
|
32.0
|
1.0
|
C17
|
H:TE9101
|
2.4
|
35.4
|
1.0
|
N1
|
H:TE9101
|
2.7
|
31.4
|
1.0
|
O5'
|
F:DG1
|
3.1
|
67.9
|
1.0
|
OD2
|
B:ASP435
|
3.1
|
38.9
|
1.0
|
CA
|
B:ARG456
|
3.4
|
52.6
|
1.0
|
CA
|
B:GLY434
|
3.5
|
39.5
|
1.0
|
N2
|
H:TE9101
|
3.6
|
34.1
|
1.0
|
N
|
B:ASP435
|
3.6
|
39.3
|
1.0
|
C16
|
H:TE9101
|
3.6
|
35.4
|
1.0
|
O
|
F:HOH205
|
3.8
|
21.0
|
1.0
|
OP1
|
F:DG1
|
3.8
|
70.0
|
1.0
|
P
|
F:DG1
|
3.8
|
68.3
|
1.0
|
CG
|
B:ARG456
|
3.8
|
57.6
|
1.0
|
CB
|
B:ARG456
|
3.9
|
54.2
|
1.0
|
N
|
B:GLY457
|
3.9
|
49.4
|
1.0
|
O
|
B:LEU455
|
3.9
|
53.0
|
1.0
|
C4'
|
F:DG1
|
4.1
|
66.6
|
1.0
|
C
|
B:ARG456
|
4.1
|
50.9
|
1.0
|
C2
|
H:TE9101
|
4.1
|
34.6
|
1.0
|
C
|
B:GLY434
|
4.1
|
40.0
|
1.0
|
O4'
|
F:DG1
|
4.1
|
66.3
|
1.0
|
C5'
|
F:DG1
|
4.1
|
65.9
|
1.0
|
CG
|
B:ASP435
|
4.2
|
39.9
|
1.0
|
OP2
|
F:DG1
|
4.3
|
69.7
|
1.0
|
N
|
B:ARG456
|
4.4
|
52.9
|
1.0
|
C
|
B:LEU455
|
4.5
|
52.4
|
1.0
|
N
|
B:GLY434
|
4.5
|
40.3
|
1.0
|
CB
|
B:ASP435
|
4.7
|
39.7
|
1.0
|
CD
|
B:ARG456
|
4.8
|
59.9
|
1.0
|
CL1
|
H:TE9101
|
4.8
|
83.5
|
1.0
|
F2
|
H:TE9101
|
4.8
|
38.9
|
1.0
|
CA
|
B:ASP435
|
4.8
|
39.9
|
1.0
|
CA
|
B:GLY457
|
4.9
|
47.8
|
1.0
|
|
Reference:
B.Wang,
S.Najmudin,
X.S.Pan,
V.Mykhaylyk,
C.Orr,
A.Wagner,
L.Govada,
N.E.Chayen,
L.M.Fisher,
M.R.Sanderson.
Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in Type II Dna Topoisomerases. Proc.Natl.Acad.Sci.Usa V. 121 57121 2024.
ISSN: ESSN 1091-6490
PubMed: 39361644
DOI: 10.1073/PNAS.2413357121
Page generated: Thu Oct 31 20:07:50 2024
|