Chlorine in PDB 8qmc: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
Enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
All present enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin:
5.6.2.2;
Protein crystallography data
The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc
was solved by
S.Najmudin,
X.S.Pan,
B.Wang,
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)
|
64.86 /
2.40
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.14,
157.14,
211.636,
90,
90,
120
|
R / Rfree (%)
|
24.1 /
29.9
|
Other elements in 8qmc:
The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
(pdb code 8qmc). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 8qmc
Go back to
Chlorine Binding Sites List in 8qmc
Chlorine binding site 1 out
of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1508
b:17.6
occ:1.00
|
HH12
|
A:ARG1371
|
2.6
|
30.0
|
0.0
|
HH22
|
A:ARG1426
|
2.7
|
16.0
|
1.0
|
HH21
|
A:ARG1426
|
2.8
|
15.5
|
1.0
|
NH2
|
A:ARG1426
|
3.1
|
15.9
|
1.0
|
NH1
|
A:ARG1371
|
3.4
|
10.1
|
1.0
|
HH21
|
A:ARG1371
|
3.5
|
10.1
|
1.0
|
HD11
|
A:LEU1378
|
3.6
|
14.8
|
1.0
|
O
|
A:HOH1793
|
3.7
|
8.2
|
1.0
|
HD12
|
A:LEU1378
|
3.9
|
14.9
|
1.0
|
HH11
|
A:ARG1371
|
4.0
|
30.0
|
0.0
|
NH2
|
A:ARG1371
|
4.1
|
10.1
|
1.0
|
CD1
|
A:LEU1378
|
4.2
|
15.0
|
1.0
|
CZ
|
A:ARG1371
|
4.2
|
9.9
|
1.0
|
HD23
|
A:LEU1422
|
4.3
|
11.8
|
1.0
|
CZ
|
A:ARG1426
|
4.4
|
16.2
|
1.0
|
HD13
|
A:LEU1378
|
4.5
|
14.7
|
1.0
|
HD21
|
A:LEU1422
|
4.7
|
11.9
|
1.0
|
HD22
|
A:LEU1422
|
4.7
|
12.0
|
1.0
|
HH22
|
A:ARG1371
|
4.7
|
10.2
|
1.0
|
CD2
|
A:LEU1422
|
4.8
|
12.0
|
1.0
|
HH12
|
A:ARG1426
|
4.9
|
30.0
|
0.0
|
O
|
A:HOH1602
|
4.9
|
11.4
|
1.0
|
HG22
|
A:ILE1374
|
5.0
|
12.4
|
1.0
|
HD23
|
A:LEU1378
|
5.0
|
15.7
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 8qmc
Go back to
Chlorine Binding Sites List in 8qmc
Chlorine binding site 2 out
of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl1505
b:15.2
occ:1.00
|
HH12
|
B:ARG1426
|
2.6
|
30.0
|
0.0
|
HH12
|
B:ARG1371
|
2.6
|
30.0
|
0.0
|
O
|
B:HOH1785
|
3.1
|
12.6
|
1.0
|
H12
|
B:MPD1501
|
3.3
|
12.0
|
1.0
|
NH1
|
B:ARG1426
|
3.3
|
17.5
|
1.0
|
HH11
|
B:ARG1426
|
3.4
|
30.0
|
0.0
|
NH1
|
B:ARG1371
|
3.5
|
8.0
|
1.0
|
HD11
|
B:LEU1378
|
3.6
|
7.7
|
1.0
|
HH11
|
B:ARG1371
|
3.9
|
30.0
|
0.0
|
HD12
|
B:LEU1378
|
3.9
|
7.6
|
1.0
|
HH21
|
B:ARG1371
|
4.0
|
7.7
|
1.0
|
C1
|
B:MPD1501
|
4.1
|
12.1
|
1.0
|
HD23
|
B:LEU1422
|
4.2
|
9.1
|
1.0
|
CD1
|
B:LEU1378
|
4.2
|
7.6
|
1.0
|
H11
|
B:MPD1501
|
4.3
|
12.4
|
1.0
|
HD22
|
B:LEU1422
|
4.3
|
9.3
|
1.0
|
CZ
|
B:ARG1371
|
4.4
|
7.6
|
1.0
|
NH2
|
B:ARG1371
|
4.4
|
7.6
|
1.0
|
HM3
|
B:MPD1501
|
4.4
|
12.4
|
1.0
|
HH21
|
B:ARG1426
|
4.4
|
17.3
|
1.0
|
H13
|
B:MPD1501
|
4.5
|
12.0
|
1.0
|
CZ
|
B:ARG1426
|
4.5
|
17.3
|
1.0
|
CD2
|
B:LEU1422
|
4.6
|
9.4
|
1.0
|
HD13
|
B:LEU1378
|
4.6
|
7.3
|
1.0
|
HD21
|
B:LEU1422
|
4.6
|
9.5
|
1.0
|
NH2
|
B:ARG1426
|
4.8
|
17.5
|
1.0
|
HD23
|
B:LEU1378
|
4.9
|
8.4
|
1.0
|
HG23
|
B:ILE1374
|
4.9
|
8.0
|
1.0
|
HG22
|
B:ILE1374
|
5.0
|
7.7
|
1.0
|
HH22
|
B:ARG1371
|
5.0
|
7.4
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 8qmc
Go back to
Chlorine Binding Sites List in 8qmc
Chlorine binding site 3 out
of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl101
b:25.2
occ:1.00
|
CL1
|
F:TE9101
|
0.0
|
25.2
|
1.0
|
C14
|
F:TE9101
|
1.7
|
25.5
|
1.0
|
H10
|
F:TE9101
|
2.3
|
26.9
|
1.0
|
N2
|
F:TE9101
|
2.3
|
23.7
|
1.0
|
C2
|
F:TE9101
|
2.5
|
23.2
|
1.0
|
C10
|
F:TE9101
|
2.7
|
26.8
|
1.0
|
C15
|
F:TE9101
|
2.7
|
24.7
|
1.0
|
HB3
|
A:ARG456
|
2.8
|
28.8
|
1.0
|
C13
|
F:TE9101
|
2.9
|
27.5
|
1.0
|
C1
|
F:TE9101
|
2.9
|
23.6
|
1.0
|
N4
|
F:TE9101
|
3.0
|
27.5
|
1.0
|
N3
|
F:TE9101
|
3.0
|
23.7
|
1.0
|
H9
|
F:TE9101
|
3.2
|
27.2
|
1.0
|
C16
|
F:TE9101
|
3.4
|
22.9
|
1.0
|
O
|
A:ARG456
|
3.4
|
27.4
|
1.0
|
N1
|
F:TE9101
|
3.5
|
24.0
|
1.0
|
H2
|
F:TE9101
|
3.5
|
24.5
|
1.0
|
HD3
|
A:ARG456
|
3.6
|
30.4
|
1.0
|
C18
|
F:TE9101
|
3.6
|
23.2
|
1.0
|
CB
|
A:ARG456
|
3.8
|
29.4
|
1.0
|
C17
|
F:TE9101
|
3.8
|
22.8
|
1.0
|
C2
|
F:DA5
|
3.9
|
21.3
|
1.0
|
C9
|
F:TE9101
|
4.0
|
27.5
|
1.0
|
C7
|
F:TE9101
|
4.0
|
25.6
|
1.0
|
C
|
A:ARG456
|
4.0
|
28.1
|
1.0
|
H2
|
F:DA5
|
4.0
|
20.9
|
1.0
|
H8
|
F:TE9101
|
4.1
|
30.0
|
0.0
|
N3
|
F:DA5
|
4.1
|
22.6
|
1.0
|
HB2
|
A:ARG456
|
4.2
|
29.6
|
1.0
|
N1
|
F:DA5
|
4.2
|
21.2
|
1.0
|
H1
|
F:TE9101
|
4.2
|
24.1
|
1.0
|
C12
|
F:TE9101
|
4.2
|
29.0
|
1.0
|
F2
|
F:TE9101
|
4.3
|
23.2
|
1.0
|
CA
|
A:ARG456
|
4.3
|
29.2
|
1.0
|
HA
|
A:ARG456
|
4.3
|
29.2
|
1.0
|
C11
|
F:TE9101
|
4.4
|
29.2
|
1.0
|
CD
|
A:ARG456
|
4.4
|
31.2
|
1.0
|
C3
|
F:TE9101
|
4.4
|
24.0
|
1.0
|
C4
|
F:DA5
|
4.5
|
23.8
|
1.0
|
HD2
|
A:ARG456
|
4.5
|
31.1
|
1.0
|
C8
|
F:TE9101
|
4.5
|
27.0
|
1.0
|
C6
|
F:DA5
|
4.6
|
22.4
|
1.0
|
O4
|
F:TE9101
|
4.6
|
29.3
|
1.0
|
H11
|
F:TE9101
|
4.6
|
22.6
|
1.0
|
F3
|
F:TE9101
|
4.7
|
23.9
|
1.0
|
CG
|
A:ARG456
|
4.7
|
31.0
|
1.0
|
N3
|
H:DA1
|
4.7
|
56.1
|
1.0
|
C5
|
F:DA5
|
4.7
|
23.5
|
1.0
|
H3
|
E:DT15
|
4.8
|
22.7
|
1.0
|
H6
|
F:TE9101
|
4.8
|
29.8
|
1.0
|
HA3
|
A:GLY457
|
4.9
|
26.6
|
1.0
|
H3
|
F:TE9101
|
4.9
|
23.7
|
1.0
|
N
|
A:GLY457
|
5.0
|
28.0
|
1.0
|
C2
|
H:DA1
|
5.0
|
55.0
|
1.0
|
O
|
H:HOH207
|
5.0
|
11.1
|
1.0
|
H7
|
F:TE9101
|
5.0
|
29.5
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 8qmc
Go back to
Chlorine Binding Sites List in 8qmc
Chlorine binding site 4 out
of 4 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl101
b:41.8
occ:1.00
|
CL1
|
H:TE9101
|
0.0
|
41.8
|
1.0
|
C14
|
H:TE9101
|
1.7
|
42.7
|
1.0
|
N2
|
H:TE9101
|
2.2
|
40.7
|
1.0
|
H10
|
H:TE9101
|
2.3
|
42.9
|
1.0
|
C2
|
H:TE9101
|
2.6
|
40.5
|
1.0
|
C10
|
H:TE9101
|
2.7
|
43.8
|
1.0
|
C15
|
H:TE9101
|
2.7
|
42.4
|
1.0
|
C13
|
H:TE9101
|
2.8
|
43.5
|
1.0
|
C1
|
H:TE9101
|
2.9
|
40.1
|
1.0
|
N4
|
H:TE9101
|
3.0
|
44.2
|
1.0
|
N3
|
H:TE9101
|
3.0
|
41.3
|
1.0
|
HB3
|
B:ARG456
|
3.0
|
26.7
|
1.0
|
H9
|
H:TE9101
|
3.1
|
43.3
|
1.0
|
N1
|
H:TE9101
|
3.4
|
40.2
|
1.0
|
O
|
B:ARG456
|
3.4
|
23.1
|
1.0
|
C16
|
H:TE9101
|
3.5
|
39.8
|
1.0
|
H2
|
H:TE9101
|
3.6
|
40.8
|
1.0
|
C18
|
H:TE9101
|
3.7
|
39.3
|
1.0
|
C
|
B:ARG456
|
3.9
|
24.5
|
1.0
|
H1
|
H:TE9101
|
3.9
|
39.9
|
1.0
|
C17
|
H:TE9101
|
3.9
|
39.2
|
1.0
|
CB
|
B:ARG456
|
3.9
|
27.3
|
1.0
|
C2
|
H:DG5
|
4.0
|
42.9
|
1.0
|
C9
|
H:TE9101
|
4.0
|
44.5
|
1.0
|
C7
|
H:TE9101
|
4.0
|
43.3
|
1.0
|
H22
|
H:DG5
|
4.0
|
41.8
|
1.0
|
N2
|
H:DG5
|
4.1
|
42.4
|
1.0
|
H8
|
H:TE9101
|
4.1
|
30.0
|
0.0
|
N3
|
H:DG5
|
4.2
|
43.5
|
1.0
|
C12
|
H:TE9101
|
4.2
|
44.4
|
1.0
|
HD3
|
B:ARG456
|
4.3
|
28.6
|
1.0
|
CA
|
B:ARG456
|
4.3
|
26.4
|
1.0
|
HA
|
B:ARG456
|
4.3
|
26.4
|
1.0
|
N1
|
H:DG5
|
4.3
|
43.1
|
1.0
|
C11
|
H:TE9101
|
4.3
|
45.2
|
1.0
|
HB2
|
B:ARG456
|
4.4
|
27.3
|
1.0
|
HA3
|
B:GLY457
|
4.4
|
22.7
|
1.0
|
C3
|
H:TE9101
|
4.4
|
41.4
|
1.0
|
F2
|
H:TE9101
|
4.4
|
40.1
|
1.0
|
H21
|
F:DG1
|
4.5
|
48.6
|
1.0
|
C8
|
H:TE9101
|
4.5
|
44.4
|
1.0
|
H1
|
H:DG5
|
4.6
|
42.7
|
1.0
|
H21
|
H:DG5
|
4.6
|
42.1
|
1.0
|
N
|
B:GLY457
|
4.6
|
24.0
|
1.0
|
C4
|
H:DG5
|
4.6
|
44.6
|
1.0
|
O4
|
H:TE9101
|
4.7
|
44.1
|
1.0
|
F3
|
H:TE9101
|
4.7
|
38.9
|
1.0
|
H6
|
H:TE9101
|
4.7
|
45.6
|
1.0
|
N3
|
F:DG1
|
4.8
|
47.5
|
1.0
|
H11
|
H:TE9101
|
4.8
|
38.6
|
1.0
|
C6
|
H:DG5
|
4.9
|
44.2
|
1.0
|
H3
|
H:TE9101
|
4.9
|
40.8
|
1.0
|
O
|
F:HOH201
|
4.9
|
8.9
|
1.0
|
CG
|
B:ARG456
|
4.9
|
28.8
|
1.0
|
H7
|
H:TE9101
|
5.0
|
44.5
|
1.0
|
HG2
|
B:ARG456
|
5.0
|
28.7
|
1.0
|
C2
|
F:DG1
|
5.0
|
46.1
|
1.0
|
|
Reference:
S.Najmudin,
X.S.Pan,
B.Wang,
N.E.Chayen,
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: Thu Oct 31 17:57:31 2024
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