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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy