Fluorine in PDB 6pk2: Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Enzymatic activity of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
All present enzymatic activity of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis:
6.4.1.3;
Protein crystallography data
The structure of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis, PDB code: 6pk2
was solved by
M.C.M.Reddy,
Z.Nian,
T.C.B.Michele,
J.C.Sacchettini,
Tb Structuralgenomics Consortium (Tbsgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.44 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.120,
149.797,
152.958,
90.00,
90.04,
90.00
|
R / Rfree (%)
|
17.3 /
22.2
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
(pdb code 6pk2). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis, PDB code: 6pk2:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 1 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:42.5
occ:1.00
|
F17
|
A:ORJ501
|
0.0
|
42.5
|
1.0
|
C16
|
A:ORJ501
|
1.4
|
40.1
|
1.0
|
C15
|
A:ORJ501
|
2.4
|
37.2
|
1.0
|
C18
|
A:ORJ501
|
2.4
|
36.7
|
1.0
|
CA
|
B:GLY341
|
3.3
|
35.7
|
1.0
|
C14
|
A:ORJ501
|
3.6
|
39.3
|
1.0
|
CB
|
B:ALA300
|
3.7
|
38.1
|
1.0
|
C19
|
A:ORJ501
|
3.7
|
32.6
|
1.0
|
CD1
|
B:LEU295
|
3.8
|
37.4
|
1.0
|
CD2
|
B:LEU344
|
3.8
|
32.3
|
1.0
|
C13
|
A:ORJ501
|
4.2
|
35.2
|
1.0
|
CB
|
B:ALA370
|
4.2
|
38.2
|
1.0
|
C
|
B:GLY341
|
4.3
|
34.5
|
1.0
|
CB
|
B:LEU295
|
4.3
|
42.7
|
1.0
|
N
|
B:GLY341
|
4.3
|
38.1
|
1.0
|
O
|
B:GLY341
|
4.3
|
38.0
|
1.0
|
CG
|
B:LEU295
|
4.4
|
43.4
|
1.0
|
CB
|
B:LEU344
|
4.6
|
31.8
|
1.0
|
CD2
|
B:LEU295
|
4.6
|
37.5
|
1.0
|
CA
|
B:ALA300
|
4.7
|
40.2
|
1.0
|
CG
|
B:LEU344
|
4.7
|
34.6
|
1.0
|
O
|
B:VAL337
|
4.9
|
41.7
|
1.0
|
CG2
|
B:VAL337
|
4.9
|
41.4
|
1.0
|
OH
|
A:TYR141
|
4.9
|
49.9
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 2 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:32.4
occ:1.00
|
F17
|
B:ORJ501
|
0.0
|
32.4
|
1.0
|
C16
|
B:ORJ501
|
1.4
|
30.6
|
1.0
|
C15
|
B:ORJ501
|
2.4
|
33.5
|
1.0
|
C18
|
B:ORJ501
|
2.4
|
31.1
|
1.0
|
CA
|
A:GLY341
|
3.3
|
27.9
|
1.0
|
CB
|
A:ALA300
|
3.5
|
27.1
|
1.0
|
C14
|
B:ORJ501
|
3.7
|
34.5
|
1.0
|
C19
|
B:ORJ501
|
3.7
|
33.5
|
1.0
|
CD1
|
A:LEU295
|
3.9
|
34.8
|
1.0
|
CD2
|
A:LEU344
|
3.9
|
20.7
|
1.0
|
C13
|
B:ORJ501
|
4.2
|
29.1
|
1.0
|
CB
|
A:LEU295
|
4.2
|
30.1
|
1.0
|
N
|
A:GLY341
|
4.3
|
29.4
|
1.0
|
CD2
|
A:LEU295
|
4.4
|
32.0
|
1.0
|
C
|
A:GLY341
|
4.4
|
32.2
|
1.0
|
CG
|
A:LEU295
|
4.4
|
35.4
|
1.0
|
CB
|
A:ALA370
|
4.4
|
29.9
|
1.0
|
O
|
A:GLY341
|
4.4
|
32.1
|
1.0
|
CA
|
A:ALA300
|
4.5
|
31.0
|
1.0
|
CB
|
A:LEU344
|
4.6
|
26.3
|
1.0
|
CG2
|
A:VAL337
|
4.7
|
28.4
|
1.0
|
O
|
A:VAL337
|
4.7
|
33.8
|
1.0
|
CG
|
A:LEU344
|
4.8
|
25.9
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 3 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:33.9
occ:1.00
|
F17
|
C:ORJ501
|
0.0
|
33.9
|
1.0
|
C16
|
C:ORJ501
|
1.4
|
34.7
|
1.0
|
C15
|
C:ORJ501
|
2.4
|
34.8
|
1.0
|
C18
|
C:ORJ501
|
2.4
|
31.1
|
1.0
|
CA
|
D:GLY341
|
3.3
|
30.9
|
1.0
|
CB
|
D:ALA300
|
3.6
|
38.3
|
1.0
|
C14
|
C:ORJ501
|
3.7
|
39.1
|
1.0
|
C19
|
C:ORJ501
|
3.7
|
35.3
|
1.0
|
CD2
|
D:LEU344
|
3.8
|
26.3
|
1.0
|
CD1
|
D:LEU295
|
4.0
|
38.8
|
1.0
|
O
|
D:GLY341
|
4.2
|
34.0
|
1.0
|
C13
|
C:ORJ501
|
4.2
|
35.1
|
1.0
|
C
|
D:GLY341
|
4.2
|
33.1
|
1.0
|
CB
|
D:ALA370
|
4.3
|
33.6
|
1.0
|
N
|
D:GLY341
|
4.3
|
37.5
|
1.0
|
CB
|
D:LEU344
|
4.4
|
33.4
|
1.0
|
CB
|
D:LEU295
|
4.4
|
34.0
|
1.0
|
CD2
|
D:LEU295
|
4.4
|
38.2
|
1.0
|
CG
|
D:LEU295
|
4.5
|
39.1
|
1.0
|
CA
|
D:ALA300
|
4.6
|
37.9
|
1.0
|
CG
|
D:LEU344
|
4.7
|
36.7
|
1.0
|
O
|
D:VAL337
|
4.7
|
40.6
|
1.0
|
CG2
|
D:VAL337
|
4.8
|
36.4
|
1.0
|
O
|
D:ARG340
|
4.9
|
36.9
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 4 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:33.8
occ:1.00
|
F17
|
D:ORJ501
|
0.0
|
33.8
|
1.0
|
C16
|
D:ORJ501
|
1.4
|
35.9
|
1.0
|
C15
|
D:ORJ501
|
2.4
|
36.0
|
1.0
|
C18
|
D:ORJ501
|
2.5
|
31.9
|
1.0
|
CA
|
C:GLY341
|
3.3
|
32.6
|
1.0
|
C14
|
D:ORJ501
|
3.6
|
37.7
|
1.0
|
CB
|
C:ALA300
|
3.7
|
35.1
|
1.0
|
C19
|
D:ORJ501
|
3.7
|
34.9
|
1.0
|
CD1
|
C:LEU295
|
3.9
|
34.4
|
1.0
|
CD2
|
C:LEU344
|
4.0
|
34.2
|
1.0
|
CB
|
C:ALA370
|
4.2
|
30.8
|
1.0
|
C13
|
D:ORJ501
|
4.2
|
35.9
|
1.0
|
CB
|
C:LEU295
|
4.2
|
37.1
|
1.0
|
N
|
C:GLY341
|
4.3
|
35.8
|
1.0
|
C
|
C:GLY341
|
4.3
|
34.0
|
1.0
|
O
|
C:GLY341
|
4.4
|
37.0
|
1.0
|
CG
|
C:LEU295
|
4.4
|
40.4
|
1.0
|
CD2
|
C:LEU295
|
4.4
|
40.0
|
1.0
|
CB
|
C:LEU344
|
4.6
|
29.9
|
1.0
|
CA
|
C:ALA300
|
4.7
|
37.4
|
1.0
|
O
|
C:VAL337
|
4.7
|
41.8
|
1.0
|
CG2
|
C:VAL337
|
4.7
|
36.9
|
1.0
|
CG
|
C:LEU344
|
4.8
|
34.1
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 5 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F501
b:39.2
occ:1.00
|
F17
|
E:ORJ501
|
0.0
|
39.2
|
1.0
|
C16
|
E:ORJ501
|
1.4
|
40.8
|
1.0
|
C15
|
E:ORJ501
|
2.4
|
38.7
|
1.0
|
C18
|
E:ORJ501
|
2.4
|
37.0
|
1.0
|
CA
|
F:GLY341
|
3.3
|
33.2
|
1.0
|
CB
|
F:ALA300
|
3.7
|
38.9
|
1.0
|
C14
|
E:ORJ501
|
3.7
|
37.0
|
1.0
|
C19
|
E:ORJ501
|
3.7
|
36.1
|
1.0
|
CD1
|
F:LEU295
|
3.7
|
41.1
|
1.0
|
CD2
|
F:LEU344
|
3.9
|
26.4
|
1.0
|
CB
|
F:ALA370
|
4.2
|
34.9
|
1.0
|
C13
|
E:ORJ501
|
4.2
|
35.8
|
1.0
|
O
|
F:GLY341
|
4.2
|
37.7
|
1.0
|
C
|
F:GLY341
|
4.2
|
37.1
|
1.0
|
N
|
F:GLY341
|
4.4
|
41.0
|
1.0
|
CB
|
F:LEU295
|
4.4
|
42.2
|
1.0
|
CB
|
F:LEU344
|
4.4
|
30.1
|
1.0
|
CG
|
F:LEU295
|
4.5
|
43.3
|
1.0
|
CG
|
F:LEU344
|
4.7
|
32.3
|
1.0
|
CA
|
F:ALA300
|
4.8
|
40.1
|
1.0
|
O
|
F:VAL337
|
4.8
|
44.8
|
1.0
|
OH
|
E:TYR141
|
4.8
|
45.0
|
1.0
|
CD2
|
F:LEU295
|
4.8
|
40.8
|
1.0
|
CG2
|
F:VAL337
|
4.9
|
41.9
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 6 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F501
b:31.5
occ:1.00
|
F17
|
F:ORJ501
|
0.0
|
31.5
|
1.0
|
C16
|
F:ORJ501
|
1.4
|
28.4
|
1.0
|
C15
|
F:ORJ501
|
2.4
|
33.1
|
1.0
|
C18
|
F:ORJ501
|
2.4
|
29.2
|
1.0
|
CA
|
E:GLY341
|
3.4
|
27.0
|
1.0
|
CB
|
E:ALA300
|
3.5
|
25.2
|
1.0
|
CD1
|
E:LEU295
|
3.5
|
31.0
|
1.0
|
C14
|
F:ORJ501
|
3.7
|
30.2
|
1.0
|
C19
|
F:ORJ501
|
3.7
|
31.9
|
1.0
|
CD2
|
E:LEU344
|
3.9
|
20.3
|
1.0
|
CB
|
E:LEU295
|
4.2
|
30.4
|
1.0
|
C13
|
F:ORJ501
|
4.2
|
30.1
|
1.0
|
CB
|
E:ALA370
|
4.3
|
28.0
|
1.0
|
CG
|
E:LEU295
|
4.3
|
33.3
|
1.0
|
N
|
E:GLY341
|
4.4
|
28.2
|
1.0
|
C
|
E:GLY341
|
4.4
|
30.9
|
1.0
|
O
|
E:GLY341
|
4.4
|
30.6
|
1.0
|
CD2
|
E:LEU295
|
4.5
|
33.8
|
1.0
|
CA
|
E:ALA300
|
4.5
|
30.6
|
1.0
|
CB
|
E:LEU344
|
4.6
|
27.5
|
1.0
|
CG2
|
E:VAL337
|
4.7
|
32.5
|
1.0
|
O
|
E:VAL337
|
4.8
|
36.5
|
1.0
|
CG
|
E:LEU344
|
4.8
|
25.5
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6pk2
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Fluorine Binding Sites List in 6pk2
Fluorine binding site 7 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F501
b:36.4
occ:1.00
|
F17
|
G:ORJ501
|
0.0
|
36.4
|
1.0
|
C16
|
G:ORJ501
|
1.4
|
33.2
|
1.0
|
C15
|
G:ORJ501
|
2.4
|
37.4
|
1.0
|
C18
|
G:ORJ501
|
2.4
|
31.2
|
1.0
|
CA
|
G:GLY341
|
3.3
|
31.1
|
1.0
|
C14
|
G:ORJ501
|
3.6
|
36.7
|
1.0
|
C19
|
G:ORJ501
|
3.7
|
36.1
|
1.0
|
CB
|
G:ALA300
|
3.7
|
35.4
|
1.0
|
CD1
|
G:LEU295
|
3.9
|
37.3
|
1.0
|
CD2
|
G:LEU344
|
3.9
|
32.6
|
1.0
|
C13
|
G:ORJ501
|
4.2
|
36.0
|
1.0
|
CB
|
G:ALA370
|
4.2
|
29.6
|
1.0
|
CB
|
G:LEU295
|
4.2
|
34.5
|
1.0
|
N
|
G:GLY341
|
4.3
|
35.3
|
1.0
|
C
|
G:GLY341
|
4.3
|
33.5
|
1.0
|
O
|
G:GLY341
|
4.3
|
36.1
|
1.0
|
CG
|
G:LEU295
|
4.3
|
39.5
|
1.0
|
CD2
|
G:LEU295
|
4.4
|
39.5
|
1.0
|
CB
|
G:LEU344
|
4.6
|
31.8
|
1.0
|
CG2
|
G:VAL337
|
4.7
|
37.7
|
1.0
|
CA
|
G:ALA300
|
4.7
|
35.9
|
1.0
|
O
|
G:VAL337
|
4.7
|
42.8
|
1.0
|
CG
|
G:LEU344
|
4.8
|
33.5
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6pk2
Go back to
Fluorine Binding Sites List in 6pk2
Fluorine binding site 8 out
of 8 in the Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of the Carboxyltransferase Subunit of Acc (ACCD6) in Complex with Inhibitor Quizalofop-P Derivative From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F502
b:36.1
occ:1.00
|
F17
|
G:ORJ502
|
0.0
|
36.1
|
1.0
|
C16
|
G:ORJ502
|
1.4
|
36.5
|
1.0
|
C15
|
G:ORJ502
|
2.4
|
33.8
|
1.0
|
C18
|
G:ORJ502
|
2.4
|
31.7
|
1.0
|
CA
|
H:GLY341
|
3.3
|
31.2
|
1.0
|
CB
|
H:ALA300
|
3.6
|
39.0
|
1.0
|
CD1
|
H:LEU295
|
3.7
|
36.2
|
1.0
|
C14
|
G:ORJ502
|
3.7
|
38.0
|
1.0
|
C19
|
G:ORJ502
|
3.7
|
36.0
|
1.0
|
CD2
|
H:LEU344
|
3.8
|
28.3
|
1.0
|
O
|
H:GLY341
|
4.1
|
34.8
|
1.0
|
C13
|
G:ORJ502
|
4.2
|
38.0
|
1.0
|
C
|
H:GLY341
|
4.2
|
33.7
|
1.0
|
CB
|
H:ALA370
|
4.2
|
34.2
|
1.0
|
CB
|
H:LEU295
|
4.3
|
35.8
|
1.0
|
N
|
H:GLY341
|
4.3
|
35.5
|
1.0
|
CG
|
H:LEU295
|
4.4
|
33.9
|
1.0
|
CB
|
H:LEU344
|
4.4
|
32.9
|
1.0
|
CD2
|
H:LEU295
|
4.5
|
35.0
|
1.0
|
CA
|
H:ALA300
|
4.5
|
36.8
|
1.0
|
CG
|
H:LEU344
|
4.7
|
36.1
|
1.0
|
O
|
H:VAL337
|
4.7
|
39.6
|
1.0
|
CG2
|
H:VAL337
|
4.9
|
35.0
|
1.0
|
|
Reference:
M.C.M.Reddy,
Z.Nian,
J.C.Sacchettini.
Elucidating the Inhibition and Specificity of Binding of Herbicidal Aryloxyphenoxypropionates Derivatives to Mycobacterium Tuberculosis Carboxyltransferase Domain of Acetyl-Coenzyme A(ACCD6). To Be Published.
Page generated: Fri Aug 2 00:26:18 2024
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