Fluorine in PDB 5xdt: Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Protein crystallography data
The structure of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707, PDB code: 5xdt
was solved by
J.Fujita,
Y.Maeda,
E.Mizohata,
T.Inoue,
M.Kaul,
A.K.Parhi,
E.J.Lavoie,
D.S.Pilch,
H.Matsumura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.95 /
1.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.553,
51.193,
86.449,
90.00,
108.68,
90.00
|
R / Rfree (%)
|
13.6 /
16.8
|
Other elements in 5xdt:
The structure of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
(pdb code 5xdt). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707, PDB code: 5xdt:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 5xdt
Go back to
Fluorine Binding Sites List in 5xdt
Fluorine binding site 1 out
of 5 in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:39.2
occ:0.80
|
F5
|
A:ZI7403
|
0.0
|
39.2
|
0.8
|
C15
|
A:ZI7403
|
1.3
|
36.2
|
0.8
|
CE
|
A:MET226
|
1.7
|
31.9
|
0.2
|
F4
|
A:ZI7403
|
2.1
|
41.8
|
0.8
|
F3
|
A:ZI7403
|
2.1
|
36.2
|
0.8
|
C12
|
A:ZI7403
|
2.4
|
35.6
|
0.8
|
C11
|
A:ZI7403
|
3.0
|
39.5
|
0.8
|
CE
|
A:MET218
|
3.2
|
17.4
|
0.7
|
SD
|
A:MET226
|
3.3
|
34.5
|
0.2
|
C13
|
A:ZI7403
|
3.5
|
32.5
|
0.8
|
SD
|
A:MET218
|
3.5
|
16.8
|
0.7
|
CE
|
A:MET218
|
3.5
|
21.7
|
0.3
|
CD1
|
A:ILE311
|
3.6
|
20.1
|
0.2
|
CG
|
A:MET226
|
3.7
|
32.7
|
0.2
|
CD1
|
A:ILE311
|
3.8
|
25.4
|
0.8
|
CG1
|
A:ILE311
|
3.8
|
19.7
|
0.2
|
CG2
|
A:ILE311
|
4.0
|
22.7
|
0.8
|
CG
|
A:MET226
|
4.0
|
39.0
|
0.8
|
CG2
|
A:ILE311
|
4.1
|
17.8
|
0.2
|
SD
|
A:MET218
|
4.2
|
23.1
|
0.3
|
N3
|
A:ZI7403
|
4.2
|
36.0
|
0.8
|
CG1
|
A:ILE311
|
4.3
|
26.0
|
0.8
|
CB
|
A:MET226
|
4.4
|
33.4
|
0.8
|
CB
|
A:MET226
|
4.4
|
31.4
|
0.2
|
CD1
|
A:ILE197
|
4.5
|
27.6
|
0.2
|
SD
|
A:MET226
|
4.5
|
49.0
|
0.8
|
CB
|
A:ILE311
|
4.6
|
19.0
|
0.2
|
C14
|
A:ZI7403
|
4.6
|
30.8
|
0.8
|
CB
|
A:ILE311
|
4.7
|
22.5
|
0.8
|
CD1
|
A:ILE162
|
4.9
|
27.2
|
1.0
|
C10
|
A:ZI7403
|
4.9
|
33.3
|
0.8
|
|
Fluorine binding site 2 out
of 5 in 5xdt
Go back to
Fluorine Binding Sites List in 5xdt
Fluorine binding site 2 out
of 5 in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:36.2
occ:0.80
|
F3
|
A:ZI7403
|
0.0
|
36.2
|
0.8
|
C15
|
A:ZI7403
|
1.3
|
36.2
|
0.8
|
F4
|
A:ZI7403
|
2.1
|
41.8
|
0.8
|
CE
|
A:MET226
|
2.1
|
31.9
|
0.2
|
F5
|
A:ZI7403
|
2.1
|
39.2
|
0.8
|
C12
|
A:ZI7403
|
2.4
|
35.6
|
0.8
|
C13
|
A:ZI7403
|
2.8
|
32.5
|
0.8
|
SD
|
A:MET226
|
3.0
|
34.5
|
0.2
|
CA
|
A:GLY193
|
3.2
|
21.4
|
1.0
|
O
|
A:GLY193
|
3.2
|
22.3
|
1.0
|
C
|
A:GLY193
|
3.4
|
20.1
|
1.0
|
C11
|
A:ZI7403
|
3.6
|
39.5
|
0.8
|
CD1
|
A:ILE197
|
3.7
|
27.6
|
0.2
|
CG
|
A:MET226
|
3.9
|
32.7
|
0.2
|
CE2
|
A:PHE100
|
3.9
|
21.5
|
1.0
|
SD
|
A:MET226
|
4.0
|
49.0
|
0.8
|
CZ
|
A:PHE100
|
4.2
|
24.6
|
1.0
|
C14
|
A:ZI7403
|
4.2
|
30.8
|
0.8
|
CG1
|
A:ILE197
|
4.2
|
24.8
|
0.8
|
CG
|
A:MET226
|
4.4
|
39.0
|
0.8
|
N
|
A:VAL194
|
4.4
|
20.1
|
1.0
|
N
|
A:GLY193
|
4.6
|
20.6
|
1.0
|
CD1
|
A:ILE197
|
4.7
|
27.5
|
0.8
|
CG1
|
A:ILE197
|
4.7
|
26.8
|
0.2
|
N3
|
A:ZI7403
|
4.7
|
36.0
|
0.8
|
CD1
|
A:ILE311
|
4.8
|
25.4
|
0.8
|
CD1
|
A:ILE311
|
4.8
|
20.1
|
0.2
|
CE
|
A:MET226
|
4.8
|
45.2
|
0.8
|
O
|
A:HOH665
|
4.9
|
22.1
|
0.2
|
C10
|
A:ZI7403
|
5.0
|
33.3
|
0.8
|
|
Fluorine binding site 3 out
of 5 in 5xdt
Go back to
Fluorine Binding Sites List in 5xdt
Fluorine binding site 3 out
of 5 in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:41.8
occ:0.80
|
F4
|
A:ZI7403
|
0.0
|
41.8
|
0.8
|
C15
|
A:ZI7403
|
1.3
|
36.2
|
0.8
|
F5
|
A:ZI7403
|
2.1
|
39.2
|
0.8
|
F3
|
A:ZI7403
|
2.1
|
36.2
|
0.8
|
C12
|
A:ZI7403
|
2.3
|
35.6
|
0.8
|
C11
|
A:ZI7403
|
2.9
|
39.5
|
0.8
|
CE
|
A:MET226
|
3.1
|
31.9
|
0.2
|
CD1
|
A:ILE197
|
3.2
|
27.6
|
0.2
|
CE
|
A:MET98
|
3.3
|
18.4
|
1.0
|
SD
|
A:MET218
|
3.4
|
16.8
|
0.7
|
C13
|
A:ZI7403
|
3.5
|
32.5
|
0.8
|
CG1
|
A:ILE197
|
3.7
|
24.8
|
0.8
|
CD1
|
A:ILE197
|
3.7
|
27.5
|
0.8
|
CE
|
A:MET218
|
3.7
|
17.4
|
0.7
|
CE
|
A:MET218
|
3.8
|
21.7
|
0.3
|
CZ
|
A:PHE100
|
3.9
|
24.6
|
1.0
|
CG1
|
A:ILE197
|
3.9
|
26.8
|
0.2
|
CE2
|
A:PHE100
|
3.9
|
21.5
|
1.0
|
N3
|
A:ZI7403
|
4.1
|
36.0
|
0.8
|
CD1
|
A:ILE311
|
4.4
|
20.1
|
0.2
|
O
|
A:GLY193
|
4.5
|
22.3
|
1.0
|
C14
|
A:ZI7403
|
4.6
|
30.8
|
0.8
|
SD
|
A:MET98
|
4.6
|
17.3
|
1.0
|
SD
|
A:MET226
|
4.6
|
34.5
|
0.2
|
CG1
|
A:VAL214
|
4.8
|
16.7
|
1.0
|
CG2
|
A:VAL129
|
4.8
|
16.9
|
1.0
|
SD
|
A:MET218
|
4.8
|
23.1
|
0.3
|
C10
|
A:ZI7403
|
4.9
|
33.3
|
0.8
|
CB
|
A:ILE197
|
4.9
|
23.8
|
0.2
|
C
|
A:GLY193
|
5.0
|
20.1
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 5xdt
Go back to
Fluorine Binding Sites List in 5xdt
Fluorine binding site 4 out
of 5 in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:22.4
occ:0.80
|
F2
|
A:ZI7403
|
0.0
|
22.4
|
0.8
|
C3
|
A:ZI7403
|
1.3
|
20.9
|
0.8
|
C4
|
A:ZI7403
|
2.3
|
24.2
|
0.8
|
C2
|
A:ZI7403
|
2.3
|
19.5
|
0.8
|
O2
|
A:ZI7403
|
2.6
|
31.5
|
0.8
|
C1
|
A:ZI7403
|
2.9
|
18.1
|
0.8
|
N1
|
A:ZI7403
|
3.0
|
17.2
|
0.8
|
OD1
|
A:ASN263
|
3.1
|
20.1
|
1.0
|
CG
|
A:ASN263
|
3.1
|
18.5
|
1.0
|
CB
|
A:ASN263
|
3.2
|
17.6
|
1.0
|
CD1
|
A:LEU209
|
3.4
|
23.5
|
1.0
|
C5
|
A:ZI7403
|
3.6
|
25.2
|
0.8
|
C7
|
A:ZI7403
|
3.6
|
20.2
|
0.8
|
CD1
|
A:LEU200
|
3.7
|
34.1
|
1.0
|
O1
|
A:ZI7403
|
3.8
|
19.0
|
0.8
|
CB
|
A:LEU209
|
3.8
|
19.3
|
1.0
|
CG
|
A:LEU209
|
3.9
|
20.2
|
1.0
|
ND2
|
A:ASN263
|
3.9
|
20.5
|
1.0
|
C8
|
A:ZI7403
|
3.9
|
37.3
|
0.8
|
C6
|
A:ZI7403
|
4.1
|
21.9
|
0.8
|
S1
|
A:ZI7403
|
4.4
|
33.1
|
0.8
|
CA
|
A:ASN263
|
4.4
|
16.9
|
1.0
|
CD2
|
A:LEU261
|
4.6
|
26.8
|
1.0
|
C9
|
A:ZI7403
|
4.6
|
32.7
|
0.8
|
CG
|
A:LEU200
|
4.6
|
28.7
|
1.0
|
F1
|
A:ZI7403
|
4.7
|
22.1
|
0.8
|
CB
|
A:LEU200
|
4.8
|
25.7
|
1.0
|
CA
|
A:LEU209
|
5.0
|
17.9
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 5xdt
Go back to
Fluorine Binding Sites List in 5xdt
Fluorine binding site 5 out
of 5 in the Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Staphylococcus Aureus Ftsz 12-316 Complexed with TXA707 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:22.1
occ:0.80
|
F1
|
A:ZI7403
|
0.0
|
22.1
|
0.8
|
C7
|
A:ZI7403
|
1.3
|
20.2
|
0.8
|
C2
|
A:ZI7403
|
2.3
|
19.5
|
0.8
|
C6
|
A:ZI7403
|
2.3
|
21.9
|
0.8
|
C1
|
A:ZI7403
|
2.8
|
18.1
|
0.8
|
O1
|
A:ZI7403
|
2.8
|
19.0
|
0.8
|
O
|
A:VAL203
|
3.1
|
24.7
|
1.0
|
CG2
|
A:VAL297
|
3.1
|
22.3
|
1.0
|
CG1
|
A:VAL203
|
3.4
|
26.2
|
1.0
|
CB
|
A:VAL203
|
3.4
|
25.4
|
1.0
|
CA
|
A:CA402
|
3.5
|
21.1
|
1.0
|
C3
|
A:ZI7403
|
3.6
|
20.9
|
0.8
|
C5
|
A:ZI7403
|
3.6
|
25.2
|
0.8
|
C
|
A:VAL203
|
3.6
|
21.8
|
1.0
|
N1
|
A:ZI7403
|
3.8
|
17.2
|
0.8
|
N
|
A:GLY205
|
3.8
|
19.2
|
1.0
|
CA
|
A:VAL203
|
4.1
|
23.5
|
1.0
|
CA
|
A:GLY205
|
4.1
|
18.6
|
1.0
|
C4
|
A:ZI7403
|
4.1
|
24.2
|
0.8
|
C
|
A:SER204
|
4.2
|
23.6
|
1.0
|
O
|
A:ASP199
|
4.2
|
21.8
|
1.0
|
N
|
A:SER204
|
4.4
|
23.5
|
1.0
|
CB
|
A:VAL297
|
4.5
|
19.9
|
1.0
|
CA
|
A:LEU200
|
4.5
|
22.0
|
1.0
|
O
|
A:LEU200
|
4.5
|
23.9
|
1.0
|
O
|
A:SER204
|
4.6
|
27.5
|
1.0
|
OD1
|
A:ASN208
|
4.6
|
19.7
|
1.0
|
CG2
|
A:VAL203
|
4.7
|
25.7
|
1.0
|
O
|
A:HOH739
|
4.7
|
36.5
|
1.0
|
N
|
A:VAL203
|
4.7
|
23.7
|
1.0
|
CA
|
A:SER204
|
4.7
|
24.3
|
0.7
|
F2
|
A:ZI7403
|
4.7
|
22.4
|
0.8
|
CA
|
A:SER204
|
4.7
|
24.2
|
0.3
|
CG1
|
A:VAL297
|
4.7
|
21.3
|
1.0
|
C
|
A:ASP199
|
4.9
|
20.8
|
1.0
|
C
|
A:LEU200
|
4.9
|
23.2
|
1.0
|
|
Reference:
J.Fujita,
Y.Maeda,
E.Mizohata,
T.Inoue,
M.Kaul,
A.K.Parhi,
E.J.Lavoie,
D.S.Pilch,
H.Matsumura.
Structural Flexibility of An Inhibitor Overcomes Drug Resistance Mutations in Staphylococcus Aureus Ftsz Acs Chem. Biol. V. 12 1947 2017.
ISSN: ESSN 1554-8937
PubMed: 28621933
DOI: 10.1021/ACSCHEMBIO.7B00323
Page generated: Thu Aug 1 16:52:32 2024
|