Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 9gef
Go back to
Chlorine Binding Sites List in 9gef
Chlorine binding site 1 out
of 4 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 Chlorine with other atoms in the Cl 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
|
A:Cl1507
b:75.3
occ:1.00
|
N
|
A:GLU609
|
3.2
|
77.8
|
1.0
|
N
|
A:ASP610
|
3.5
|
79.1
|
1.0
|
CB
|
A:SER1008
|
3.6
|
70.0
|
1.0
|
O
|
A:ASP610
|
3.7
|
74.1
|
1.0
|
N
|
A:GLU1010
|
3.7
|
65.2
|
1.0
|
CB
|
A:ALA614
|
3.8
|
66.3
|
1.0
|
CB
|
A:GLU1010
|
3.8
|
67.5
|
1.0
|
CA
|
A:ILE608
|
3.9
|
72.8
|
1.0
|
C
|
A:ILE608
|
4.0
|
76.1
|
1.0
|
N
|
A:LEU1009
|
4.0
|
65.9
|
1.0
|
CA
|
A:GLU609
|
4.0
|
81.0
|
1.0
|
CB
|
A:GLU609
|
4.1
|
81.8
|
1.0
|
CG2
|
A:ILE608
|
4.2
|
72.3
|
1.0
|
C
|
A:GLU609
|
4.3
|
81.4
|
1.0
|
C
|
A:ASP610
|
4.3
|
75.6
|
1.0
|
O
|
A:THR607
|
4.3
|
67.4
|
1.0
|
CA
|
A:ASP610
|
4.3
|
78.6
|
1.0
|
CA
|
A:SER1008
|
4.3
|
69.3
|
1.0
|
OG
|
A:SER1008
|
4.4
|
68.5
|
1.0
|
CA
|
A:GLU1010
|
4.4
|
64.6
|
1.0
|
C
|
A:SER1008
|
4.4
|
66.6
|
1.0
|
CB
|
A:LEU1009
|
4.5
|
65.0
|
1.0
|
CA
|
A:ALA614
|
4.5
|
65.3
|
1.0
|
CA
|
A:LEU1009
|
4.6
|
64.3
|
1.0
|
N
|
A:ALA614
|
4.6
|
67.1
|
1.0
|
CB
|
A:ILE608
|
4.6
|
72.5
|
1.0
|
C
|
A:LEU1009
|
4.7
|
63.5
|
1.0
|
CB
|
A:ASP610
|
4.7
|
79.4
|
1.0
|
OE1
|
A:GLU1010
|
4.9
|
70.6
|
1.0
|
N
|
A:ILE608
|
4.9
|
71.9
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 9gef
Go back to
Chlorine Binding Sites List in 9gef
Chlorine binding site 2 out
of 4 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 Chlorine with other atoms in the Cl 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
|
B:Cl1509
b:76.8
occ:1.00
|
N
|
B:GLU609
|
3.3
|
82.4
|
1.0
|
CB
|
B:SER1008
|
3.5
|
70.4
|
1.0
|
N
|
B:GLU1010
|
3.6
|
66.6
|
1.0
|
CB
|
B:GLU1010
|
3.7
|
69.2
|
1.0
|
N
|
B:ASP610
|
3.7
|
81.8
|
1.0
|
CB
|
B:ALA614
|
3.8
|
70.6
|
1.0
|
O
|
B:ASP610
|
3.8
|
75.6
|
1.0
|
N
|
B:LEU1009
|
3.9
|
65.7
|
1.0
|
CA
|
B:ILE608
|
4.0
|
77.9
|
1.0
|
C
|
B:ILE608
|
4.1
|
80.9
|
1.0
|
CA
|
B:GLU609
|
4.2
|
84.5
|
1.0
|
CB
|
B:GLU609
|
4.2
|
84.2
|
1.0
|
CA
|
B:SER1008
|
4.3
|
69.1
|
1.0
|
CA
|
B:GLU1010
|
4.3
|
66.2
|
1.0
|
OE1
|
B:GLU1010
|
4.3
|
74.0
|
1.0
|
OG
|
B:SER1008
|
4.3
|
70.0
|
1.0
|
O
|
B:THR607
|
4.3
|
73.1
|
1.0
|
C
|
B:SER1008
|
4.3
|
66.3
|
1.0
|
CG2
|
B:ILE608
|
4.4
|
77.9
|
1.0
|
CB
|
B:LEU1009
|
4.4
|
64.8
|
1.0
|
C
|
B:GLU609
|
4.4
|
84.3
|
1.0
|
C
|
B:ASP610
|
4.4
|
77.8
|
1.0
|
CA
|
B:ALA614
|
4.5
|
69.4
|
1.0
|
CA
|
B:LEU1009
|
4.5
|
64.3
|
1.0
|
CA
|
B:ASP610
|
4.5
|
80.6
|
1.0
|
C
|
B:LEU1009
|
4.6
|
64.3
|
1.0
|
N
|
B:ALA614
|
4.6
|
71.0
|
1.0
|
CB
|
B:ILE608
|
4.7
|
78.0
|
1.0
|
CB
|
B:ASP610
|
4.8
|
80.1
|
1.0
|
CG
|
B:GLU609
|
4.9
|
85.4
|
1.0
|
CG
|
B:GLU1010
|
4.9
|
69.5
|
1.0
|
N
|
B:ILE608
|
5.0
|
77.1
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 9gef
Go back to
Chlorine Binding Sites List in 9gef
Chlorine binding site 3 out
of 4 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 Chlorine with other atoms in the Cl 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:Cl101
b:87.8
occ:1.00
|
CL1
|
F:TE9101
|
0.0
|
87.8
|
1.0
|
C14
|
F:TE9101
|
1.7
|
43.5
|
1.0
|
N2
|
F:TE9101
|
2.4
|
37.6
|
1.0
|
C2
|
F:TE9101
|
2.6
|
37.9
|
1.0
|
C10
|
F:TE9101
|
2.6
|
37.2
|
1.0
|
C13
|
F:TE9101
|
2.6
|
38.9
|
1.0
|
C15
|
F:TE9101
|
2.7
|
37.8
|
1.0
|
N4
|
F:TE9101
|
2.9
|
37.6
|
1.0
|
N3
|
F:TE9101
|
3.0
|
36.9
|
1.0
|
C1
|
F:TE9101
|
3.0
|
34.8
|
1.0
|
C16
|
F:TE9101
|
3.4
|
38.9
|
1.0
|
N1
|
F:TE9101
|
3.6
|
32.1
|
1.0
|
C18
|
F:TE9101
|
3.7
|
36.2
|
1.0
|
CB
|
A:ARG456
|
3.8
|
51.2
|
1.0
|
C12
|
F:TE9101
|
3.8
|
38.7
|
1.0
|
C17
|
F:TE9101
|
3.9
|
37.0
|
1.0
|
C9
|
F:TE9101
|
3.9
|
36.1
|
1.0
|
C2
|
F:DA5
|
4.0
|
42.8
|
1.0
|
C7
|
F:TE9101
|
4.0
|
36.5
|
1.0
|
N3
|
F:DA5
|
4.0
|
44.1
|
1.0
|
C11
|
F:TE9101
|
4.2
|
37.7
|
1.0
|
F2
|
F:TE9101
|
4.3
|
49.1
|
1.0
|
N1
|
F:DA5
|
4.3
|
42.5
|
1.0
|
C3
|
F:TE9101
|
4.4
|
38.6
|
1.0
|
C4
|
F:DA5
|
4.4
|
45.7
|
1.0
|
O
|
A:ARG456
|
4.4
|
50.2
|
1.0
|
C8
|
F:TE9101
|
4.5
|
35.4
|
1.0
|
N3
|
H:DA1
|
4.5
|
66.7
|
1.0
|
C
|
A:ARG456
|
4.5
|
50.1
|
1.0
|
CG
|
A:ARG456
|
4.6
|
53.1
|
1.0
|
CD
|
A:ARG456
|
4.6
|
54.4
|
1.0
|
CA
|
A:ARG456
|
4.6
|
50.2
|
1.0
|
C2
|
H:DA1
|
4.7
|
67.2
|
1.0
|
C6
|
F:DA5
|
4.8
|
44.0
|
1.0
|
F3
|
F:TE9101
|
4.8
|
38.7
|
1.0
|
O4
|
F:TE9101
|
4.8
|
41.5
|
1.0
|
C5
|
F:DA5
|
4.8
|
45.7
|
1.0
|
C4
|
H:DA1
|
4.9
|
65.0
|
1.0
|
F1
|
F:TE9101
|
5.0
|
40.1
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 9gef
Go back to
Chlorine Binding Sites List in 9gef
Chlorine binding site 4 out
of 4 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 Chlorine with other atoms in the Cl 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:Cl101
b:83.5
occ:1.00
|
CL1
|
H:TE9101
|
0.0
|
83.5
|
1.0
|
C14
|
H:TE9101
|
1.7
|
42.0
|
1.0
|
N2
|
H:TE9101
|
2.3
|
34.1
|
1.0
|
C2
|
H:TE9101
|
2.6
|
34.6
|
1.0
|
C10
|
H:TE9101
|
2.6
|
36.0
|
1.0
|
C13
|
H:TE9101
|
2.7
|
37.1
|
1.0
|
C15
|
H:TE9101
|
2.7
|
37.6
|
1.0
|
N4
|
H:TE9101
|
2.9
|
35.1
|
1.0
|
C1
|
H:TE9101
|
2.9
|
32.0
|
1.0
|
N3
|
H:TE9101
|
3.0
|
35.3
|
1.0
|
C16
|
H:TE9101
|
3.4
|
35.4
|
1.0
|
N1
|
H:TE9101
|
3.5
|
31.4
|
1.0
|
C18
|
H:TE9101
|
3.7
|
34.2
|
1.0
|
CB
|
B:ARG456
|
3.9
|
54.2
|
1.0
|
C17
|
H:TE9101
|
3.9
|
35.4
|
1.0
|
C2
|
H:DG5
|
3.9
|
42.6
|
1.0
|
C12
|
H:TE9101
|
3.9
|
40.6
|
1.0
|
C9
|
H:TE9101
|
3.9
|
36.1
|
1.0
|
C7
|
H:TE9101
|
4.0
|
36.0
|
1.0
|
N3
|
H:DG5
|
4.1
|
44.2
|
1.0
|
N2
|
H:DG5
|
4.1
|
41.9
|
1.0
|
C11
|
H:TE9101
|
4.2
|
37.5
|
1.0
|
N1
|
H:DG5
|
4.3
|
41.7
|
1.0
|
F2
|
H:TE9101
|
4.3
|
38.9
|
1.0
|
C3
|
H:TE9101
|
4.4
|
34.4
|
1.0
|
C8
|
H:TE9101
|
4.5
|
35.5
|
1.0
|
O
|
B:ARG456
|
4.5
|
51.4
|
1.0
|
C4
|
H:DG5
|
4.5
|
45.1
|
1.0
|
N3
|
F:DG1
|
4.5
|
68.9
|
1.0
|
CD
|
B:ARG456
|
4.6
|
59.9
|
1.0
|
C
|
B:ARG456
|
4.6
|
50.9
|
1.0
|
C2
|
F:DG1
|
4.6
|
69.6
|
1.0
|
CG
|
B:ARG456
|
4.6
|
57.6
|
1.0
|
CA
|
B:ARG456
|
4.6
|
52.6
|
1.0
|
F3
|
H:TE9101
|
4.8
|
35.6
|
1.0
|
N2
|
F:DG1
|
4.8
|
72.1
|
1.0
|
C6
|
H:DG5
|
4.8
|
42.6
|
1.0
|
C5
|
H:DG5
|
4.9
|
44.5
|
1.0
|
C4
|
F:DG1
|
4.9
|
66.3
|
1.0
|
F1
|
H:TE9101
|
5.0
|
37.9
|
1.0
|
O4
|
H:TE9101
|
5.0
|
49.0
|
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 18:12:31 2024
|