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Magnesium in PDB 7lhz: K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)

Enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)

All present enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25):
5.6.2.2;

Protein crystallography data

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25), PDB code: 7lhz 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) 46.92 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.185, 159.818, 144.059, 90, 94.94, 90
R / Rfree (%) 28.3 / 30.8

Other elements in 7lhz:

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) (pdb code 7lhz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25), PDB code: 7lhz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7lhz

Go back to Magnesium Binding Sites List in 7lhz
Magnesium binding site 1 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


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 (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1502

b:85.7
occ:1.00
 OD2 C:ASP493 2.0 90.1 1.0
OD2 C:ASP491 2.0 85.7 1.0
OD1 C:ASP491 2.1 83.1 1.0
HB2 C:ASP493 2.3 62.5 1.0
CG C:ASP491 2.4 85.6 1.0
CG C:ASP493 2.8 86.5 1.0
CB C:ASP493 2.9 82.9 1.0
OE2 C:GLU419 3.3 76.8 1.0
HB3 C:ASP493 3.3 62.5 1.0
OE1 C:GLU419 3.4 79.7 1.0
CD C:GLU419 3.7 79.4 1.0
HB2 C:ASP495 3.7 59.9 1.0
H C:ASP493 3.8 62.5 1.0
CB C:ASP491 3.9 87.7 1.0
H C:GLY496 3.9 60.8 1.0
OD1 C:ASP493 4.0 84.5 1.0
HO3' P:DT411 4.2 57.1 1.0
H C:ASP491 4.2 70.2 1.0
H5'' P:DT411 4.2 50.7 1.0
HB2 C:ASP491 4.3 69.5 1.0
CA C:ASP493 4.3 79.2 1.0
N C:GLY496 4.3 76.5 1.0
HB3 C:ASP491 4.3 69.5 1.0
HA2 C:GLY566 4.4 80.1 1.0
H3' P:DT411 4.4 54.3 1.0
N C:ASP493 4.4 82.8 1.0
HA3 C:GLY496 4.4 61.7 1.0
CB C:ASP495 4.5 80.0 1.0
HA2 C:GLY496 4.6 61.7 1.0
HB3 C:ASP495 4.6 59.9 1.0
CA C:GLY496 4.7 79.3 1.0
CA C:ASP491 4.7 86.3 1.0
O3' P:DT411 4.8 79.2 1.0
N C:ASP491 4.8 87.2 1.0
HA C:ASP493 4.9 61.6 1.0
C C:ASP491 4.9 80.8 1.0
O C:ASP491 4.9 77.2 1.0
H4' P:DT411 4.9 53.9 1.0
C C:ASP495 4.9 79.3 1.0
C3' P:DT411 4.9 77.6 1.0

Magnesium binding site 2 out of 4 in 7lhz

Go back to Magnesium Binding Sites List in 7lhz
Magnesium binding site 2 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


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 (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1501

b:91.9
occ:1.00
 OD2 D:ASP493 2.0 88.8 1.0
OD2 D:ASP491 2.1 95.1 1.0
CG D:ASP491 3.2 96.9 1.0
CG D:ASP493 3.2 90.5 1.0
HB2 D:ASP491 3.6 81.6 1.0
HB3 D:ASP491 3.7 81.6 1.0
CB D:ASP491 3.7 96.2 1.0
H5'' J:DT611 3.8 75.4 1.0
OD1 D:ASP493 3.9 91.8 1.0
HB2 D:ASP493 4.1 78.9 1.0
OD1 D:ASP491 4.2 98.5 1.0
OE1 D:GLU419 4.2 90.8 1.0
CB D:ASP493 4.3 91.1 1.0
HA3 D:GLY566 4.4 85.1 1.0
HA2 D:GLY566 4.6 85.1 1.0
OP1 J:DT611 4.6 84.7 1.0
HB3 D:ASP493 4.7 78.9 1.0
O3' J:DT611 4.7 97.7 1.0
OE2 D:GLU419 4.7 86.6 1.0
HE1 C:TYR1120 4.7 73.3 1.0
CD D:GLU419 4.7 89.2 1.0
C5' J:DT611 4.8 92.5 1.0
H D:LEU567 4.8 80.2 1.0
H D:ASP493 4.9 79.4 1.0
CA D:GLY566 5.0 106.4 1.0

Magnesium binding site 3 out of 4 in 7lhz

Go back to Magnesium Binding Sites List in 7lhz
Magnesium binding site 3 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


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 (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:82.9
occ:1.00
 OD2 A:ASP493 1.8 79.4 1.0
OD2 A:ASP491 1.9 81.8 1.0
CG A:ASP491 2.1 80.3 1.0
CG A:ASP493 2.1 77.9 1.0
OD1 A:ASP493 2.1 79.0 1.0
OD1 A:ASP491 2.2 78.1 1.0
HB2 A:ASP491 3.2 62.6 1.0
CB A:ASP491 3.2 81.7 1.0
H A:ASP493 3.4 55.6 1.0
CB A:ASP493 3.5 74.4 1.0
HB2 A:ASP493 3.6 56.7 1.0
HA2 A:GLY566 3.6 78.0 1.0
HA3 A:GLY566 3.8 78.0 1.0
HB3 A:ASP491 3.8 62.6 1.0
O A:LYS565 3.8 85.2 1.0
N A:ASP493 4.0 75.2 1.0
HB3 A:ASP493 4.1 56.7 1.0
CA A:GLY566 4.2 88.5 1.0
CA A:ASP493 4.3 73.2 1.0
C A:ASP491 4.3 76.9 1.0
CA A:ASP491 4.3 80.6 1.0
OE1 A:GLU419 4.4 77.0 1.0
O A:ASP491 4.5 74.8 1.0
HA A:ASP493 4.5 55.3 1.0
H A:ASP491 4.6 63.3 1.0
N A:ALA492 4.6 78.3 1.0
HB2 A:ASP495 4.7 57.0 1.0
H A:GLY496 4.7 55.8 1.0
H A:ALA492 4.7 59.5 1.0
OE2 A:GLU419 4.7 75.3 1.0
H A:LEU567 4.8 74.6 1.0
C A:LYS565 4.8 85.3 1.0
CD A:GLU419 4.9 76.8 1.0
N A:ASP491 4.9 81.2 1.0
N A:GLY566 5.0 88.0 1.0

Magnesium binding site 4 out of 4 in 7lhz

Go back to Magnesium Binding Sites List in 7lhz
Magnesium binding site 4 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


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 (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:108.1
occ:1.00
 OD2 B:ASP493 2.0 101.4 1.0
OD2 B:ASP491 2.1 104.8 1.0
OD1 B:ASP493 2.1 101.8 1.0
CG B:ASP493 2.3 102.2 1.0
CG B:ASP491 3.0 105.3 1.0
OD1 B:ASP491 3.7 105.1 1.0
HB3 B:ASP491 3.7 90.0 1.0
CB B:ASP493 3.8 102.8 1.0
H B:ASP493 3.9 88.6 1.0
CB B:ASP491 4.0 105.8 1.0
HB2 B:ASP493 4.1 85.7 1.0
HB2 B:ASP491 4.3 90.0 1.0
HB3 B:ASP493 4.3 85.7 1.0
HA3 B:GLY566 4.4 89.8 1.0
N B:ASP493 4.5 105.3 1.0
HA B:ASP493 4.6 87.1 1.0
CA B:ASP493 4.6 104.3 1.0
HA2 B:GLY566 4.8 89.8 1.0
H5'' H:DT211 4.8 82.7 1.0
H B:LEU567 4.8 87.7 1.0

Reference:

G.Lapointe, C.K.Skepper, L.M.Holder, D.Armstrong, C.Bellamacina, J.Blais, D.Bussiere, J.Bian, C.Cepura, H.Chan, C.R.Dean, G.De Pascale, B.Dhumale, L.M.Fisher, M.Fulsunder, B.Kantariya, J.Kim, S.King, L.Kossy, U.Kulkarni, J.Lakshman, J.A.Leeds, X.Ling, A.Lvov, S.Ma, S.Malekar, D.Mckenney, W.Mergo, L.Metzger, K.Mhaske, H.E.Moser, M.Mostafavi, S.Namballa, J.Noeske, C.Osborne, A.Patel, D.Patel, T.Patel, P.Piechon, V.Polyakov, K.Prajapati, K.R.Prosen, F.Reck, D.L.Richie, M.R.Sanderson, S.Satasia, B.Savani, J.Selvarajah, V.Sethuraman, W.Shu, K.Tashiro, K.V.Thompson, K.Vaarla, L.Vala, D.A.Veselkov, J.Vo, B.Vora, T.Wagner, L.Wedel, S.L.Williams, S.Yendluri, Q.Yue, A.Yifru, Y.Zhang, A.Rivkin. Discovery and Optimization of Dna Gyrase and Topoisomerase IV Inhibitors with Potent Activity Against Fluoroquinolone-Resistant Gram-Positive Bacteria. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33929852
DOI: 10.1021/ACS.JMEDCHEM.1C00375
Page generated: Wed Oct 2 23:22:17 2024

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