Magnesium in PDB 6waa: K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
All present enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One):
5.6.2.2;
Protein crystallography data
The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa
was solved by
J.Noeske,
W.Shu,
C.Bellamacina,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.08 /
3.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.590,
157.481,
144.060,
90.00,
94.93,
90.00
|
R / Rfree (%)
|
27.4 /
30.1
|
Other elements in 6waa:
The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
(pdb code 6waa). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 1 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1503
b:35.1
occ:1.00
|
O
|
B:LYS1113
|
3.6
|
67.1
|
1.0
|
O
|
B:PHE1115
|
3.8
|
65.5
|
1.0
|
H
|
B:PHE1115
|
4.2
|
60.0
|
1.0
|
HA
|
B:SER1114
|
4.4
|
70.0
|
1.0
|
OP2
|
J:DA13
|
4.4
|
0.9
|
1.0
|
H3'
|
J:DA13
|
4.6
|
0.9
|
1.0
|
H2'
|
J:DA13
|
4.8
|
0.2
|
1.0
|
N
|
B:PHE1115
|
4.8
|
66.3
|
1.0
|
C
|
B:LYS1113
|
4.8
|
67.7
|
1.0
|
C
|
B:PHE1115
|
5.0
|
64.3
|
1.0
|
O5'
|
J:DA13
|
5.0
|
0.4
|
1.0
|
OP2
|
J:DT14
|
5.0
|
0.6
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 2 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1504
b:71.6
occ:1.00
|
OD2
|
B:ASP491
|
2.1
|
73.5
|
1.0
|
OD2
|
B:ASP493
|
2.1
|
74.8
|
1.0
|
CG
|
B:ASP491
|
2.7
|
74.7
|
1.0
|
OD1
|
B:ASP491
|
3.2
|
74.7
|
1.0
|
CG
|
B:ASP493
|
3.4
|
74.5
|
1.0
|
H5''
|
I:DT11
|
3.4
|
55.9
|
1.0
|
HO3'
|
I:DT11
|
3.7
|
59.6
|
1.0
|
CB
|
B:ASP491
|
3.8
|
76.1
|
1.0
|
HB3
|
B:ASP491
|
3.9
|
0.0
|
1.0
|
HB2
|
B:ASP491
|
3.9
|
0.0
|
1.0
|
OE2
|
B:GLU419
|
4.0
|
75.7
|
1.0
|
OD1
|
B:ASP493
|
4.1
|
73.9
|
1.0
|
OP1
|
I:DT11
|
4.1
|
49.9
|
1.0
|
HB3
|
B:ASP493
|
4.1
|
0.9
|
1.0
|
O3'
|
I:DT11
|
4.2
|
66.6
|
1.0
|
C5'
|
I:DT11
|
4.4
|
60.2
|
1.0
|
CB
|
B:ASP493
|
4.4
|
73.2
|
1.0
|
HA3
|
B:GLY566
|
4.5
|
0.5
|
1.0
|
HB2
|
B:ASP495
|
4.6
|
70.0
|
1.0
|
CD
|
B:GLU419
|
4.6
|
76.6
|
1.0
|
OE1
|
B:GLU419
|
4.7
|
77.6
|
1.0
|
O
|
B:LYS565
|
4.7
|
80.8
|
1.0
|
H
|
B:ASP493
|
4.8
|
80.5
|
1.0
|
H4'
|
I:DT11
|
4.8
|
51.4
|
1.0
|
H5'
|
I:DT11
|
4.9
|
55.9
|
1.0
|
C4'
|
I:DT11
|
4.9
|
65.4
|
1.0
|
HB2
|
B:ASP493
|
5.0
|
0.9
|
1.0
|
C3'
|
I:DT11
|
5.0
|
66.5
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 3 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1502
b:87.6
occ:1.00
|
OD2
|
D:ASP493
|
2.1
|
0.1
|
1.0
|
CG
|
D:ASP493
|
2.9
|
0.8
|
1.0
|
H5''
|
L:DT11
|
3.0
|
0.3
|
1.0
|
OD1
|
D:ASP493
|
3.2
|
0.2
|
1.0
|
HB3
|
D:ASP491
|
3.4
|
0.8
|
1.0
|
OD2
|
D:ASP491
|
3.5
|
0.2
|
1.0
|
OE2
|
D:GLU419
|
3.7
|
0.7
|
1.0
|
HB2
|
D:ASP495
|
3.8
|
0.9
|
1.0
|
C5'
|
L:DT11
|
3.9
|
0.5
|
1.0
|
HB2
|
D:ASP491
|
4.0
|
0.8
|
1.0
|
H5'
|
L:DT11
|
4.0
|
0.3
|
1.0
|
CB
|
D:ASP491
|
4.0
|
1.0
|
1.0
|
O3'
|
L:DT11
|
4.1
|
0.4
|
1.0
|
CB
|
D:ASP493
|
4.2
|
0.5
|
1.0
|
H4'
|
L:DT11
|
4.2
|
0.5
|
1.0
|
CG
|
D:ASP491
|
4.2
|
0.8
|
1.0
|
OP1
|
L:DT11
|
4.2
|
0.6
|
1.0
|
HB3
|
D:ASP493
|
4.2
|
0.1
|
1.0
|
CD
|
D:GLU419
|
4.3
|
0.3
|
1.0
|
C4'
|
L:DT11
|
4.5
|
0.9
|
1.0
|
OE1
|
D:GLU419
|
4.5
|
0.3
|
1.0
|
HB2
|
D:ASP493
|
4.6
|
0.1
|
1.0
|
H
|
D:GLY496
|
4.7
|
0.6
|
1.0
|
HO3'
|
L:DT11
|
4.7
|
0.5
|
1.0
|
CB
|
D:ASP495
|
4.8
|
0.4
|
1.0
|
C3'
|
L:DT11
|
4.8
|
0.9
|
1.0
|
O5'
|
L:DT11
|
5.0
|
0.6
|
1.0
|
H
|
D:ASP493
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 4 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1502
b:29.1
occ:1.00
|
O
|
F:PHE1115
|
3.7
|
62.8
|
1.0
|
O
|
F:LYS1113
|
3.8
|
60.8
|
1.0
|
OP2
|
N:DA13
|
3.8
|
0.3
|
1.0
|
H
|
F:PHE1115
|
4.2
|
49.9
|
1.0
|
HA
|
F:SER1114
|
4.5
|
49.9
|
1.0
|
H2'
|
N:DA13
|
4.7
|
0.3
|
1.0
|
N
|
F:PHE1115
|
4.8
|
58.0
|
1.0
|
O5'
|
N:DA13
|
4.8
|
0.3
|
1.0
|
C
|
F:PHE1115
|
4.9
|
63.4
|
1.0
|
CE1
|
F:PHE1115
|
4.9
|
55.0
|
1.0
|
CZ
|
F:PHE1115
|
4.9
|
51.9
|
1.0
|
P
|
N:DA13
|
5.0
|
0.8
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 5 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1503
b:64.2
occ:1.00
|
OD2
|
F:ASP493
|
2.1
|
70.5
|
1.0
|
OD2
|
F:ASP491
|
2.2
|
72.0
|
1.0
|
H5''
|
M:DT11
|
3.1
|
57.5
|
1.0
|
CG
|
F:ASP493
|
3.2
|
71.0
|
1.0
|
CG
|
F:ASP491
|
3.2
|
73.5
|
1.0
|
HB2
|
F:ASP491
|
3.5
|
0.4
|
1.0
|
OD1
|
F:ASP493
|
3.6
|
73.0
|
1.0
|
HB3
|
F:ASP491
|
3.6
|
0.4
|
1.0
|
CB
|
F:ASP491
|
3.7
|
73.8
|
1.0
|
OE2
|
F:GLU419
|
3.9
|
78.3
|
1.0
|
HB2
|
F:ASP495
|
4.0
|
76.8
|
1.0
|
OP1
|
M:DT11
|
4.0
|
52.3
|
1.0
|
C5'
|
M:DT11
|
4.0
|
53.8
|
1.0
|
H5'
|
M:DT11
|
4.1
|
57.5
|
1.0
|
OD1
|
F:ASP491
|
4.3
|
75.0
|
1.0
|
HB3
|
F:ASP493
|
4.4
|
0.6
|
1.0
|
CB
|
F:ASP493
|
4.4
|
69.5
|
1.0
|
O3'
|
M:DT11
|
4.4
|
61.3
|
1.0
|
HA3
|
F:GLY566
|
4.4
|
88.5
|
1.0
|
O
|
F:LYS565
|
4.5
|
75.1
|
1.0
|
H4'
|
M:DT11
|
4.6
|
54.1
|
1.0
|
CD
|
F:GLU419
|
4.7
|
80.0
|
1.0
|
OD2
|
F:ASP495
|
4.7
|
66.2
|
1.0
|
HB2
|
F:ASP493
|
4.8
|
0.6
|
1.0
|
C4'
|
M:DT11
|
4.8
|
55.7
|
1.0
|
CB
|
F:ASP495
|
4.9
|
69.8
|
1.0
|
HO3'
|
M:DT11
|
4.9
|
60.1
|
1.0
|
OE1
|
F:GLU419
|
5.0
|
80.2
|
1.0
|
O5'
|
M:DT11
|
5.0
|
53.7
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 6 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1504
b:30.7
occ:1.00
|
OP1
|
M:DA3
|
3.7
|
0.9
|
1.0
|
OP2
|
M:DA3
|
4.0
|
94.9
|
1.0
|
O
|
F:GLU450
|
4.1
|
99.2
|
1.0
|
P
|
M:DA3
|
4.4
|
98.8
|
1.0
|
OE2
|
F:GLU455
|
4.4
|
0.9
|
1.0
|
OE1
|
F:GLU455
|
4.4
|
0.1
|
1.0
|
HA
|
F:VAL451
|
4.7
|
0.2
|
1.0
|
HB3
|
F:GLU450
|
4.9
|
0.1
|
1.0
|
CD
|
F:GLU455
|
4.9
|
0.1
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 6waa
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Magnesium Binding Sites List in 6waa
Magnesium binding site 7 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg1503
b:85.0
occ:1.00
|
OD2
|
H:ASP493
|
2.0
|
97.3
|
1.0
|
OD2
|
H:ASP491
|
2.1
|
97.6
|
1.0
|
OD1
|
H:ASP493
|
2.2
|
0.7
|
1.0
|
CG
|
H:ASP493
|
2.4
|
99.8
|
1.0
|
HB3
|
H:ASP491
|
2.9
|
0.3
|
1.0
|
CG
|
H:ASP491
|
3.0
|
97.4
|
1.0
|
HB2
|
H:ASP491
|
3.1
|
0.3
|
1.0
|
CB
|
H:ASP491
|
3.2
|
98.2
|
1.0
|
CB
|
H:ASP493
|
3.8
|
0.1
|
1.0
|
HB2
|
H:ASP495
|
3.9
|
0.9
|
1.0
|
H5''
|
P:DT11
|
4.0
|
0.3
|
1.0
|
HB2
|
H:ASP493
|
4.1
|
0.2
|
1.0
|
HB3
|
H:ASP493
|
4.2
|
0.2
|
1.0
|
OD1
|
H:ASP491
|
4.2
|
96.8
|
1.0
|
H
|
H:ASP493
|
4.3
|
0.5
|
1.0
|
H
|
H:GLY496
|
4.4
|
93.8
|
1.0
|
OP1
|
P:DT11
|
4.5
|
88.5
|
1.0
|
CA
|
H:ASP491
|
4.7
|
97.6
|
1.0
|
OE2
|
H:GLU419
|
4.8
|
1.0
|
1.0
|
H
|
H:ASP495
|
4.8
|
0.0
|
1.0
|
HO3'
|
P:DT11
|
4.8
|
0.9
|
1.0
|
CA
|
H:ASP493
|
4.8
|
0.9
|
1.0
|
CB
|
H:ASP495
|
4.8
|
96.0
|
1.0
|
N
|
H:ASP493
|
4.9
|
99.8
|
1.0
|
C5'
|
P:DT11
|
4.9
|
95.3
|
1.0
|
OD2
|
H:ASP495
|
5.0
|
94.6
|
1.0
|
N
|
H:GLY496
|
5.0
|
99.9
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 6waa
Go back to
Magnesium Binding Sites List in 6waa
Magnesium binding site 8 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg101
b:39.9
occ:1.00
|
O6
|
I:DG8
|
3.3
|
78.7
|
1.0
|
H73
|
I:DT7
|
3.6
|
92.0
|
1.0
|
H71
|
I:DT7
|
3.8
|
92.0
|
1.0
|
O4
|
J:DT17
|
3.8
|
85.7
|
1.0
|
H61
|
J:DA18
|
3.8
|
65.7
|
1.0
|
N7
|
I:DG8
|
3.9
|
70.6
|
1.0
|
H62
|
J:DA18
|
3.9
|
65.7
|
1.0
|
C6
|
I:DG8
|
3.9
|
77.6
|
1.0
|
O4
|
I:DT9
|
3.9
|
79.3
|
1.0
|
C7
|
I:DT7
|
4.1
|
80.3
|
1.0
|
C5
|
I:DG8
|
4.2
|
74.2
|
1.0
|
H73
|
I:DT9
|
4.2
|
65.1
|
1.0
|
N6
|
J:DA18
|
4.2
|
86.1
|
1.0
|
H61
|
I:DA10
|
4.3
|
63.5
|
1.0
|
H73
|
J:DT17
|
4.6
|
67.9
|
1.0
|
N6
|
I:DA10
|
4.8
|
80.4
|
1.0
|
H72
|
I:DT7
|
4.8
|
92.0
|
1.0
|
H62
|
I:DA10
|
4.9
|
63.5
|
1.0
|
C4
|
J:DT17
|
4.9
|
81.4
|
1.0
|
C8
|
I:DG8
|
5.0
|
66.5
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 6waa
Go back to
Magnesium Binding Sites List in 6waa
Magnesium binding site 9 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg101
b:82.4
occ:1.00
|
H72
|
L:DT7
|
3.4
|
0.6
|
1.0
|
H73
|
L:DT9
|
4.0
|
0.2
|
1.0
|
O4
|
K:DT17
|
4.0
|
0.6
|
1.0
|
N7
|
L:DG8
|
4.1
|
1.0
|
1.0
|
C7
|
L:DT7
|
4.2
|
0.6
|
1.0
|
O4
|
L:DT9
|
4.2
|
0.4
|
1.0
|
O6
|
L:DG8
|
4.2
|
0.4
|
1.0
|
H71
|
L:DT7
|
4.3
|
0.6
|
1.0
|
H73
|
L:DT7
|
4.4
|
0.6
|
1.0
|
H61
|
K:DA18
|
4.4
|
0.5
|
1.0
|
H62
|
K:DA18
|
4.5
|
0.5
|
1.0
|
H73
|
K:DT17
|
4.6
|
0.8
|
1.0
|
H61
|
L:DA10
|
4.6
|
0.5
|
1.0
|
C5
|
L:DG8
|
4.7
|
0.1
|
1.0
|
C6
|
L:DG8
|
4.7
|
0.3
|
1.0
|
N6
|
K:DA18
|
4.8
|
0.4
|
1.0
|
C7
|
L:DT9
|
4.9
|
0.4
|
1.0
|
H72
|
L:DT9
|
4.9
|
0.2
|
1.0
|
C8
|
L:DG8
|
5.0
|
0.8
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 6waa
Go back to
Magnesium Binding Sites List in 6waa
Magnesium binding site 10 out
of 11 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg101
b:34.7
occ:1.00
|
H73
|
M:DT7
|
2.9
|
61.3
|
1.0
|
H71
|
M:DT7
|
3.1
|
61.3
|
1.0
|
C7
|
M:DT7
|
3.5
|
57.9
|
1.0
|
O6
|
M:DG8
|
3.5
|
61.0
|
1.0
|
N7
|
M:DG8
|
3.7
|
60.5
|
1.0
|
H72
|
M:DT7
|
4.0
|
61.3
|
1.0
|
O4
|
N:DT17
|
4.0
|
76.8
|
1.0
|
H73
|
M:DT9
|
4.1
|
58.5
|
1.0
|
O4
|
M:DT9
|
4.1
|
67.5
|
1.0
|
C6
|
M:DG8
|
4.2
|
60.5
|
1.0
|
C5
|
M:DG8
|
4.2
|
60.3
|
1.0
|
H61
|
N:DA18
|
4.3
|
63.7
|
1.0
|
H62
|
N:DA18
|
4.3
|
63.7
|
1.0
|
O
|
N:HOH201
|
4.5
|
56.1
|
1.0
|
C5
|
M:DT7
|
4.7
|
56.9
|
1.0
|
N6
|
N:DA18
|
4.7
|
72.1
|
1.0
|
H61
|
M:DA10
|
4.7
|
52.4
|
1.0
|
H73
|
N:DT17
|
4.8
|
82.8
|
1.0
|
C8
|
M:DG8
|
4.8
|
59.6
|
1.0
|
|
Reference:
C.K.Skepper,
D.Armstrong,
C.J.Balibar,
D.Bauer,
C.Bellamacina,
B.M.Benton,
D.Bussiere,
G.De Pascale,
J.De Vicente,
C.R.Dean,
B.Dhumale,
L.M.Fisher,
J.Fuller,
M.Fulsunder,
L.M.Holder,
C.Hu,
B.Kantariya,
G.Lapointe,
J.A.Leeds,
X.Li,
P.Lu,
A.Lvov,
S.Ma,
S.Madhavan,
S.Malekar,
D.Mckenney,
W.Mergo,
L.Metzger,
H.E.Moser,
D.Mutnick,
J.Noeske,
C.Osborne,
A.Patel,
D.Patel,
T.Patel,
K.Prajapati,
K.R.Prosen,
F.Reck,
D.L.Richie,
A.Rico,
M.R.Sanderson,
S.Satasia,
W.S.Sawyer,
J.Selvarajah,
N.Shah,
K.Shanghavi,
W.Shu,
K.V.Thompson,
M.Traebert,
A.Vala,
L.Vala,
D.A.Veselkov,
J.Vo,
M.Wang,
M.Widya,
S.L.Williams,
Y.Xu,
Q.Yue,
R.Zang,
B.Zhou,
A.Rivkin.
Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J.Med.Chem. V. 63 7773 2020.
ISSN: ISSN 0022-2623
PubMed: 32634310
DOI: 10.1021/ACS.JMEDCHEM.0C00347
Page generated: Tue Oct 1 22:56:26 2024
|