Fluorine in PDB 2xct: The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
Enzymatic activity of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
All present enzymatic activity of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna:
5.99.1.3;
Protein crystallography data
The structure of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna, PDB code: 2xct
was solved by
B.D.Bax,
P.Chan,
D.S.Eggleston,
A.Fosberry,
D.R.Gentry,
F.Gorrec,
I.Giordano,
M.M.Hann,
A.Hennessy,
M.Hibbs,
J.Huang,
E.Jones,
J.Jones,
K.K.Brown,
C.J.Lewis,
E.May,
O.Singh,
C.Spitzfaden,
C.Shen,
A.Shillings,
A.Theobald,
A.Wohlkonig,
N.D.Pearson,
M.N.Gwynn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.956 /
3.35
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.984,
123.166,
170.418,
90.00,
90.25,
90.00
|
R / Rfree (%)
|
16.64 /
23.63
|
Other elements in 2xct:
The structure of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
(pdb code 2xct). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna, PDB code: 2xct:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 2xct
Go back to
Fluorine Binding Sites List in 2xct
Fluorine binding site 1 out
of 4 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F1020
b:70.5
occ:1.00
|
F1
|
G:CPF1020
|
0.0
|
70.5
|
1.0
|
C7
|
G:CPF1020
|
1.3
|
70.5
|
1.0
|
C6
|
G:CPF1020
|
2.4
|
70.5
|
1.0
|
C8
|
G:CPF1020
|
2.4
|
70.5
|
1.0
|
C14
|
G:CPF1020
|
2.6
|
70.5
|
1.0
|
N2
|
G:CPF1020
|
2.8
|
70.5
|
1.0
|
N7
|
H:DA13
|
3.0
|
75.3
|
1.0
|
C5
|
H:DA13
|
3.1
|
75.3
|
1.0
|
C2
|
H:DC12
|
3.5
|
0.7
|
1.0
|
N3
|
H:DC12
|
3.5
|
0.1
|
1.0
|
C6
|
H:DA13
|
3.5
|
74.5
|
1.0
|
N1
|
H:DC12
|
3.5
|
0.1
|
1.0
|
C8
|
H:DA13
|
3.5
|
76.0
|
1.0
|
C9
|
G:CPF1020
|
3.6
|
70.5
|
1.0
|
C5
|
G:CPF1020
|
3.6
|
70.5
|
1.0
|
C4
|
H:DC12
|
3.6
|
0.9
|
1.0
|
C6
|
H:DC12
|
3.7
|
0.9
|
1.0
|
C5
|
H:DC12
|
3.7
|
0.3
|
1.0
|
N6
|
H:DA13
|
3.7
|
73.9
|
1.0
|
C4
|
H:DA13
|
3.8
|
76.0
|
1.0
|
N1
|
G:DG9
|
3.9
|
92.2
|
1.0
|
N9
|
H:DA13
|
4.0
|
76.4
|
1.0
|
O2
|
H:DC12
|
4.0
|
0.0
|
1.0
|
C15
|
G:CPF1020
|
4.1
|
70.5
|
1.0
|
C10
|
G:CPF1020
|
4.1
|
70.5
|
1.0
|
N2
|
G:DG9
|
4.2
|
93.2
|
1.0
|
C2
|
G:DG9
|
4.3
|
92.4
|
1.0
|
C1'
|
H:DC12
|
4.3
|
0.8
|
1.0
|
C17
|
G:CPF1020
|
4.3
|
70.5
|
1.0
|
N4
|
H:DC12
|
4.4
|
0.4
|
1.0
|
N1
|
H:DA13
|
4.4
|
74.0
|
1.0
|
C2'
|
H:DC12
|
4.5
|
0.0
|
1.0
|
C6
|
G:DG9
|
4.6
|
91.6
|
1.0
|
N3
|
H:DA13
|
4.6
|
75.8
|
1.0
|
O6
|
G:DG9
|
4.8
|
91.5
|
1.0
|
C4
|
G:CPF1020
|
4.8
|
70.5
|
1.0
|
C2
|
H:DA13
|
4.8
|
74.5
|
1.0
|
C16
|
G:CPF1020
|
4.9
|
70.5
|
1.0
|
N3
|
G:CPF1020
|
4.9
|
70.5
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 2xct
Go back to
Fluorine Binding Sites List in 2xct
Fluorine binding site 2 out
of 4 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F1020
b:86.0
occ:1.00
|
F1
|
H:CPF1020
|
0.0
|
86.0
|
1.0
|
C7
|
H:CPF1020
|
1.4
|
86.0
|
1.0
|
C6
|
H:CPF1020
|
2.3
|
86.0
|
1.0
|
C8
|
H:CPF1020
|
2.4
|
86.0
|
1.0
|
C14
|
H:CPF1020
|
2.7
|
86.0
|
1.0
|
N2
|
H:CPF1020
|
2.9
|
86.0
|
1.0
|
N3
|
G:DC13
|
3.0
|
84.0
|
1.0
|
C4
|
G:DC13
|
3.2
|
83.5
|
1.0
|
C2
|
G:DC13
|
3.2
|
84.7
|
1.0
|
N2
|
H:DG9
|
3.3
|
91.8
|
1.0
|
N3
|
G:DC12
|
3.5
|
0.9
|
1.0
|
N1
|
G:DC13
|
3.5
|
85.2
|
1.0
|
C5
|
G:DC13
|
3.5
|
84.2
|
1.0
|
C5
|
H:CPF1020
|
3.6
|
86.0
|
1.0
|
C2
|
G:DC12
|
3.6
|
0.7
|
1.0
|
C6
|
G:DC13
|
3.7
|
84.9
|
1.0
|
C9
|
H:CPF1020
|
3.7
|
86.0
|
1.0
|
O2
|
G:DC13
|
3.8
|
85.0
|
1.0
|
N4
|
G:DC13
|
3.8
|
82.1
|
1.0
|
O2
|
G:DC12
|
3.8
|
0.1
|
1.0
|
C2
|
H:DG9
|
3.9
|
91.3
|
1.0
|
C4
|
G:DC12
|
4.1
|
0.5
|
1.0
|
C15
|
H:CPF1020
|
4.1
|
86.0
|
1.0
|
C17
|
H:CPF1020
|
4.2
|
86.0
|
1.0
|
C10
|
H:CPF1020
|
4.2
|
86.0
|
1.0
|
N1
|
G:DC12
|
4.3
|
0.1
|
1.0
|
N1
|
H:DG9
|
4.3
|
90.8
|
1.0
|
C1'
|
G:DC13
|
4.5
|
86.0
|
1.0
|
N3
|
H:DG9
|
4.6
|
91.5
|
1.0
|
N3
|
H:CPF1020
|
4.6
|
86.0
|
1.0
|
N4
|
G:DC12
|
4.6
|
0.6
|
1.0
|
C16
|
H:CPF1020
|
4.6
|
86.0
|
1.0
|
N1
|
F:DG8
|
4.6
|
53.0
|
1.0
|
O3
|
H:CPF1020
|
4.7
|
86.0
|
1.0
|
C4
|
H:CPF1020
|
4.7
|
86.0
|
1.0
|
C5
|
G:DC12
|
4.7
|
0.9
|
1.0
|
C6
|
G:DC12
|
4.8
|
0.7
|
1.0
|
O4'
|
G:DC13
|
4.8
|
86.2
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 2xct
Go back to
Fluorine Binding Sites List in 2xct
Fluorine binding site 3 out
of 4 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:F1020
b:86.1
occ:1.00
|
F1
|
X:CPF1020
|
0.0
|
86.1
|
1.0
|
C7
|
X:CPF1020
|
1.4
|
86.1
|
1.0
|
C6
|
X:CPF1020
|
2.4
|
86.1
|
1.0
|
C8
|
X:CPF1020
|
2.4
|
86.1
|
1.0
|
C14
|
X:CPF1020
|
2.5
|
86.1
|
1.0
|
N2
|
X:CPF1020
|
2.8
|
86.1
|
1.0
|
C5
|
X:DC13
|
2.9
|
71.6
|
1.0
|
C2
|
X:DC12
|
2.9
|
0.8
|
1.0
|
N3
|
X:DC12
|
2.9
|
0.7
|
1.0
|
C6
|
X:DC13
|
3.0
|
72.8
|
1.0
|
N1
|
X:DC12
|
3.2
|
0.6
|
1.0
|
C4
|
X:DC12
|
3.2
|
0.7
|
1.0
|
O2
|
X:DC12
|
3.4
|
0.8
|
1.0
|
C6
|
X:DC12
|
3.4
|
0.5
|
1.0
|
C4
|
X:DC13
|
3.4
|
72.2
|
1.0
|
C5
|
X:DC12
|
3.5
|
0.5
|
1.0
|
N1
|
X:DC13
|
3.6
|
74.6
|
1.0
|
C5
|
X:CPF1020
|
3.6
|
86.1
|
1.0
|
C9
|
X:CPF1020
|
3.7
|
86.1
|
1.0
|
N4
|
X:DC12
|
3.9
|
0.7
|
1.0
|
C1'
|
X:DC12
|
4.0
|
0.8
|
1.0
|
C15
|
X:CPF1020
|
4.0
|
86.1
|
1.0
|
N3
|
X:DC13
|
4.0
|
73.9
|
1.0
|
N4
|
X:DC13
|
4.1
|
71.0
|
1.0
|
C2
|
X:DC13
|
4.1
|
75.2
|
1.0
|
C10
|
X:CPF1020
|
4.2
|
86.1
|
1.0
|
C2'
|
X:DC12
|
4.2
|
0.7
|
1.0
|
N2
|
Y:DG9
|
4.2
|
95.8
|
1.0
|
C17
|
X:CPF1020
|
4.2
|
86.1
|
1.0
|
C1'
|
X:DC13
|
4.4
|
94.2
|
1.0
|
O4'
|
X:DC13
|
4.6
|
96.0
|
1.0
|
C4
|
X:CPF1020
|
4.7
|
86.1
|
1.0
|
O3
|
X:CPF1020
|
4.9
|
86.1
|
1.0
|
N3
|
X:CPF1020
|
4.9
|
86.1
|
1.0
|
C16
|
X:CPF1020
|
4.9
|
86.1
|
1.0
|
C2
|
Y:DG9
|
5.0
|
95.2
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 2xct
Go back to
Fluorine Binding Sites List in 2xct
Fluorine binding site 4 out
of 4 in the The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of The Twinned 3.35A Structure of S. Aureus Gyrase Complex with Ciprofloxacin and Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:F1020
b:76.7
occ:1.00
|
F1
|
Y:CPF1020
|
0.0
|
76.7
|
1.0
|
C7
|
Y:CPF1020
|
1.3
|
76.7
|
1.0
|
C6
|
Y:CPF1020
|
2.4
|
76.7
|
1.0
|
C8
|
Y:CPF1020
|
2.4
|
76.7
|
1.0
|
C14
|
Y:CPF1020
|
2.7
|
76.7
|
1.0
|
N2
|
Y:CPF1020
|
2.9
|
76.7
|
1.0
|
N7
|
Y:DA13
|
3.0
|
80.1
|
1.0
|
C4
|
Y:DC12
|
3.2
|
96.4
|
1.0
|
N3
|
Y:DC12
|
3.2
|
95.8
|
1.0
|
C2
|
Y:DC12
|
3.3
|
96.0
|
1.0
|
C5
|
Y:DC12
|
3.3
|
97.3
|
1.0
|
C6
|
Y:DC12
|
3.4
|
97.5
|
1.0
|
N1
|
Y:DC12
|
3.4
|
96.8
|
1.0
|
C5
|
Y:DA13
|
3.4
|
79.2
|
1.0
|
N6
|
Y:DA13
|
3.6
|
78.8
|
1.0
|
C5
|
Y:CPF1020
|
3.6
|
76.7
|
1.0
|
C9
|
Y:CPF1020
|
3.7
|
76.7
|
1.0
|
C6
|
Y:DA13
|
3.7
|
78.6
|
1.0
|
C8
|
Y:DA13
|
3.8
|
80.2
|
1.0
|
N4
|
Y:DC12
|
3.8
|
96.3
|
1.0
|
O2
|
Y:DC12
|
4.0
|
95.5
|
1.0
|
OP2
|
Y:DA13
|
4.1
|
0.1
|
1.0
|
C10
|
Y:CPF1020
|
4.2
|
76.7
|
1.0
|
C2'
|
Y:DC12
|
4.2
|
96.5
|
1.0
|
C15
|
Y:CPF1020
|
4.2
|
76.7
|
1.0
|
C4
|
Y:DA13
|
4.3
|
78.9
|
1.0
|
C1'
|
Y:DC12
|
4.3
|
97.1
|
1.0
|
C17
|
Y:CPF1020
|
4.4
|
76.7
|
1.0
|
C3'
|
Y:DC12
|
4.4
|
97.2
|
1.0
|
N9
|
Y:DA13
|
4.5
|
79.6
|
1.0
|
N1
|
Y:DA13
|
4.7
|
77.9
|
1.0
|
C4
|
Y:CPF1020
|
4.7
|
76.7
|
1.0
|
O5'
|
Y:DA13
|
4.8
|
0.9
|
1.0
|
O3
|
Y:CPF1020
|
4.8
|
76.7
|
1.0
|
P
|
Y:DA13
|
5.0
|
0.6
|
1.0
|
|
Reference:
B.D.Bax,
P.F.Chan,
D.S.Eggleston,
A.Fosberry,
D.R.Gentry,
F.Gorrec,
I.Giordano,
M.M.Hann,
A.Hennessy,
M.Hibbs,
J.Huang,
E.Jones,
J.Jones,
K.K.Brown,
C.J.Lewis,
E.W.May,
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ISSN: ISSN 0028-0836
PubMed: 20686482
DOI: 10.1038/NATURE09197
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