Fluorine in PDB 6hf0: M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Enzymatic activity of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
All present enzymatic activity of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.:
1.1.98.3;
Protein crystallography data
The structure of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone., PDB code: 6hf0
was solved by
K.Futterer,
S.M.Batt,
G.S.Besra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
78.29 /
2.38
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.640,
85.410,
80.410,
90.00,
103.20,
90.00
|
R / Rfree (%)
|
21.2 /
24.1
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
(pdb code 6hf0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone., PDB code: 6hf0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 1 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:68.0
occ:1.00
|
F28
|
A:G1H901
|
0.0
|
68.0
|
1.0
|
C7
|
A:G1H901
|
1.3
|
68.2
|
1.0
|
F29
|
A:G1H901
|
2.1
|
64.0
|
1.0
|
F27
|
A:G1H901
|
2.2
|
69.2
|
1.0
|
C6
|
A:G1H901
|
2.3
|
68.3
|
1.0
|
C5
|
A:G1H901
|
2.9
|
61.0
|
1.0
|
C
|
A:GLY133
|
3.2
|
50.3
|
1.0
|
CD2
|
A:HIS132
|
3.3
|
53.9
|
1.0
|
O
|
A:GLY133
|
3.3
|
46.3
|
1.0
|
C1
|
A:G1H901
|
3.5
|
62.8
|
1.0
|
CA
|
A:GLY133
|
3.5
|
49.3
|
1.0
|
N
|
A:LYS134
|
3.7
|
56.7
|
1.0
|
NE2
|
A:HIS132
|
4.0
|
51.0
|
1.0
|
CD
|
A:LYS367
|
4.0
|
54.5
|
1.0
|
N
|
A:GLY133
|
4.1
|
48.0
|
1.0
|
C4
|
A:G1H901
|
4.2
|
71.3
|
1.0
|
CA
|
A:LYS134
|
4.2
|
56.6
|
1.0
|
CG
|
A:HIS132
|
4.4
|
45.9
|
1.0
|
O4
|
A:FAD900
|
4.5
|
47.2
|
1.0
|
C
|
A:HIS132
|
4.5
|
41.0
|
1.0
|
O
|
A:HIS132
|
4.6
|
42.0
|
1.0
|
C2
|
A:G1H901
|
4.6
|
70.3
|
1.0
|
CE1
|
A:PHE369
|
4.7
|
45.2
|
1.0
|
C3
|
A:G1H901
|
4.9
|
65.8
|
1.0
|
CG
|
A:LYS134
|
4.9
|
66.8
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 2 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:69.2
occ:1.00
|
F27
|
A:G1H901
|
0.0
|
69.2
|
1.0
|
C7
|
A:G1H901
|
1.3
|
68.2
|
1.0
|
F29
|
A:G1H901
|
2.2
|
64.0
|
1.0
|
F28
|
A:G1H901
|
2.2
|
68.0
|
1.0
|
C6
|
A:G1H901
|
2.3
|
68.3
|
1.0
|
C1
|
A:G1H901
|
2.7
|
62.8
|
1.0
|
ND2
|
A:ASN385
|
3.1
|
55.0
|
1.0
|
C5
|
A:G1H901
|
3.6
|
61.0
|
1.0
|
CD2
|
A:HIS132
|
3.7
|
53.9
|
1.0
|
NE2
|
A:HIS132
|
3.8
|
51.0
|
1.0
|
CD
|
A:LYS367
|
3.8
|
54.5
|
1.0
|
CE1
|
A:PHE369
|
3.9
|
45.2
|
1.0
|
CB
|
A:LYS367
|
3.9
|
55.5
|
1.0
|
CG
|
A:ASN385
|
4.0
|
51.3
|
1.0
|
C2
|
A:G1H901
|
4.1
|
70.3
|
1.0
|
CG
|
A:LYS367
|
4.3
|
49.4
|
1.0
|
CZ
|
A:PHE369
|
4.3
|
43.0
|
1.0
|
NE2
|
A:GLN336
|
4.6
|
46.8
|
1.0
|
OD1
|
A:ASN385
|
4.7
|
50.6
|
1.0
|
C4
|
A:G1H901
|
4.7
|
71.3
|
1.0
|
CB
|
A:ASN385
|
4.8
|
45.0
|
1.0
|
SG
|
A:CYS387
|
4.9
|
70.4
|
1.0
|
CD1
|
A:PHE369
|
4.9
|
48.7
|
1.0
|
C3
|
A:G1H901
|
4.9
|
65.8
|
1.0
|
O
|
A:GLY133
|
4.9
|
46.3
|
1.0
|
CG
|
A:HIS132
|
4.9
|
45.9
|
1.0
|
N8
|
A:G1H901
|
5.0
|
79.8
|
1.0
|
CG1
|
A:VAL365
|
5.0
|
56.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 3 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F901
b:64.0
occ:1.00
|
F29
|
A:G1H901
|
0.0
|
64.0
|
1.0
|
C7
|
A:G1H901
|
1.3
|
68.2
|
1.0
|
F28
|
A:G1H901
|
2.1
|
68.0
|
1.0
|
F27
|
A:G1H901
|
2.2
|
69.2
|
1.0
|
C6
|
A:G1H901
|
2.3
|
68.3
|
1.0
|
C5
|
A:G1H901
|
2.9
|
61.0
|
1.0
|
C1
|
A:G1H901
|
3.3
|
62.8
|
1.0
|
CD
|
A:LYS367
|
3.4
|
54.5
|
1.0
|
CB
|
A:LYS367
|
3.6
|
55.5
|
1.0
|
CG
|
A:LYS367
|
4.0
|
49.4
|
1.0
|
CB
|
A:SER228
|
4.0
|
58.2
|
1.0
|
CG1
|
A:VAL365
|
4.1
|
56.0
|
1.0
|
C4
|
A:G1H901
|
4.2
|
71.3
|
1.0
|
CA
|
A:LYS134
|
4.3
|
56.6
|
1.0
|
CG
|
A:LYS134
|
4.4
|
66.8
|
1.0
|
O
|
A:GLY133
|
4.5
|
46.3
|
1.0
|
N
|
A:LYS134
|
4.5
|
56.7
|
1.0
|
C
|
A:GLY133
|
4.5
|
50.3
|
1.0
|
C2
|
A:G1H901
|
4.5
|
70.3
|
1.0
|
CE
|
A:LYS367
|
4.7
|
48.9
|
1.0
|
O
|
A:SER227
|
4.7
|
48.9
|
1.0
|
C3
|
A:G1H901
|
4.8
|
65.8
|
1.0
|
ND2
|
A:ASN385
|
4.9
|
55.0
|
1.0
|
CB
|
A:LYS134
|
4.9
|
57.1
|
1.0
|
CA
|
A:SER228
|
4.9
|
56.2
|
1.0
|
O
|
A:PHE366
|
4.9
|
56.8
|
1.0
|
CA
|
A:LYS367
|
5.0
|
52.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 4 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:65.3
occ:1.00
|
F28
|
B:G1H901
|
0.0
|
65.3
|
1.0
|
C7
|
B:G1H901
|
1.3
|
73.7
|
1.0
|
F29
|
B:G1H901
|
2.1
|
72.3
|
1.0
|
F27
|
B:G1H901
|
2.2
|
72.0
|
1.0
|
C6
|
B:G1H901
|
2.3
|
75.9
|
1.0
|
C5
|
B:G1H901
|
2.9
|
75.8
|
1.0
|
C
|
B:GLY133
|
3.3
|
51.5
|
1.0
|
O
|
B:GLY133
|
3.4
|
47.6
|
1.0
|
CD2
|
B:HIS132
|
3.4
|
56.5
|
1.0
|
C1
|
B:G1H901
|
3.4
|
61.0
|
1.0
|
CA
|
B:GLY133
|
3.7
|
49.2
|
1.0
|
N
|
B:LYS134
|
3.7
|
56.3
|
1.0
|
CD
|
B:LYS367
|
4.0
|
53.6
|
1.0
|
NE2
|
B:HIS132
|
4.0
|
54.1
|
1.0
|
N
|
B:GLY133
|
4.2
|
47.5
|
1.0
|
CA
|
B:LYS134
|
4.2
|
53.8
|
1.0
|
C4
|
B:G1H901
|
4.2
|
84.7
|
1.0
|
CG
|
B:HIS132
|
4.5
|
50.7
|
1.0
|
O4
|
B:FAD900
|
4.5
|
52.8
|
1.0
|
C2
|
B:G1H901
|
4.6
|
74.1
|
1.0
|
C
|
B:HIS132
|
4.6
|
46.3
|
1.0
|
O
|
B:HIS132
|
4.6
|
46.2
|
1.0
|
CE1
|
B:PHE369
|
4.7
|
48.8
|
1.0
|
CG
|
B:LYS134
|
4.9
|
67.9
|
1.0
|
C3
|
B:G1H901
|
4.9
|
80.3
|
1.0
|
CE
|
B:LYS367
|
5.0
|
46.2
|
1.0
|
CB
|
B:LYS367
|
5.0
|
55.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 5 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:72.0
occ:1.00
|
F27
|
B:G1H901
|
0.0
|
72.0
|
1.0
|
C7
|
B:G1H901
|
1.3
|
73.7
|
1.0
|
F29
|
B:G1H901
|
2.2
|
72.3
|
1.0
|
F28
|
B:G1H901
|
2.2
|
65.3
|
1.0
|
C6
|
B:G1H901
|
2.3
|
75.9
|
1.0
|
C1
|
B:G1H901
|
2.7
|
61.0
|
1.0
|
ND2
|
B:ASN385
|
3.1
|
58.2
|
1.0
|
C5
|
B:G1H901
|
3.6
|
75.8
|
1.0
|
CB
|
B:LYS367
|
3.8
|
55.8
|
1.0
|
CD
|
B:LYS367
|
3.8
|
53.6
|
1.0
|
CD2
|
B:HIS132
|
3.9
|
56.5
|
1.0
|
CE1
|
B:PHE369
|
4.0
|
48.8
|
1.0
|
NE2
|
B:HIS132
|
4.0
|
54.1
|
1.0
|
CG
|
B:ASN385
|
4.1
|
55.1
|
1.0
|
C2
|
B:G1H901
|
4.1
|
74.1
|
1.0
|
CG
|
B:LYS367
|
4.2
|
46.7
|
1.0
|
CZ
|
B:PHE369
|
4.5
|
42.9
|
1.0
|
C4
|
B:G1H901
|
4.7
|
84.7
|
1.0
|
NE2
|
B:GLN336
|
4.7
|
50.1
|
1.0
|
CB
|
B:ASN385
|
4.8
|
51.9
|
1.0
|
OD1
|
B:ASN385
|
4.8
|
57.6
|
1.0
|
SG
|
B:CYS387
|
4.8
|
78.1
|
1.0
|
CG1
|
B:VAL365
|
4.8
|
57.9
|
1.0
|
C3
|
B:G1H901
|
4.9
|
80.3
|
1.0
|
N8
|
B:G1H901
|
5.0
|
87.0
|
1.0
|
O
|
B:GLY133
|
5.0
|
47.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6hf0
Go back to
Fluorine Binding Sites List in 6hf0
Fluorine binding site 6 out
of 6 in the M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of M. Tuberculosis DPRE1 Covalently Bound to A Nitrobenzoxacinone. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F901
b:72.3
occ:1.00
|
F29
|
B:G1H901
|
0.0
|
72.3
|
1.0
|
C7
|
B:G1H901
|
1.3
|
73.7
|
1.0
|
F28
|
B:G1H901
|
2.1
|
65.3
|
1.0
|
F27
|
B:G1H901
|
2.2
|
72.0
|
1.0
|
C6
|
B:G1H901
|
2.3
|
75.9
|
1.0
|
C5
|
B:G1H901
|
2.9
|
75.8
|
1.0
|
CD
|
B:LYS367
|
3.4
|
53.6
|
1.0
|
C1
|
B:G1H901
|
3.4
|
61.0
|
1.0
|
CB
|
B:LYS367
|
3.6
|
55.8
|
1.0
|
CB
|
B:SER228
|
3.9
|
58.9
|
1.0
|
CG1
|
B:VAL365
|
4.1
|
57.9
|
1.0
|
CG
|
B:LYS367
|
4.1
|
46.7
|
1.0
|
CA
|
B:LYS134
|
4.2
|
53.8
|
1.0
|
CG
|
B:LYS134
|
4.2
|
67.9
|
1.0
|
C4
|
B:G1H901
|
4.2
|
84.7
|
1.0
|
N
|
B:LYS134
|
4.5
|
56.3
|
1.0
|
O
|
B:GLY133
|
4.5
|
47.6
|
1.0
|
C
|
B:GLY133
|
4.5
|
51.5
|
1.0
|
O
|
B:SER227
|
4.6
|
54.4
|
1.0
|
C2
|
B:G1H901
|
4.6
|
74.1
|
1.0
|
CE
|
B:LYS367
|
4.7
|
46.2
|
1.0
|
CA
|
B:SER228
|
4.8
|
57.5
|
1.0
|
CB
|
B:LYS134
|
4.8
|
57.9
|
1.0
|
OG
|
B:SER228
|
4.9
|
69.5
|
1.0
|
C3
|
B:G1H901
|
4.9
|
80.3
|
1.0
|
O
|
B:PHE366
|
5.0
|
58.5
|
1.0
|
ND2
|
B:ASN385
|
5.0
|
58.2
|
1.0
|
CA
|
B:LYS367
|
5.0
|
53.9
|
1.0
|
|
Reference:
A.Richter,
I.Rudolph,
U.Mollmann,
K.Voigt,
C.W.Chung,
O.M.P.Singh,
M.Rees,
A.Mendoza-Losana,
R.Bates,
L.Ballell,
S.Batt,
N.Veerapen,
K.Futterer,
G.Besra,
P.Imming,
A.Argyrou.
Novel Insight Into the Reaction of Nitro, Nitroso and Hydroxylamino Benzothiazinones and of Benzoxacinones with Mycobacterium Tuberculosis DPRE1. Sci Rep V. 8 13473 2018.
ISSN: ESSN 2045-2322
PubMed: 30194385
DOI: 10.1038/S41598-018-31316-6
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