Fluorine in PDB 7t5z: P. Aeruginosa Lpxa in Complex with Ligand L8

Enzymatic activity of P. Aeruginosa Lpxa in Complex with Ligand L8

All present enzymatic activity of P. Aeruginosa Lpxa in Complex with Ligand L8:
2.3.1.129;

Protein crystallography data

The structure of P. Aeruginosa Lpxa in Complex with Ligand L8, PDB code: 7t5z was solved by M.Sacco, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.04 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.83, 82.85, 221.21, 90, 90, 90
R / Rfree (%) 19 / 22.7

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the P. Aeruginosa Lpxa in Complex with Ligand L8 (pdb code 7t5z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the P. Aeruginosa Lpxa in Complex with Ligand L8, PDB code: 7t5z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 7t5z

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Fluorine binding site 1 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:40.5
occ:1.00
 F01 B:F6I301 0.0 40.5 1.0
C02 B:F6I301 1.3 38.5 1.0
F03 B:F6I301 2.2 43.3 1.0
C05 B:F6I301 2.3 36.1 1.0
F04 B:F6I301 2.3 46.6 1.0
C10 B:F6I301 2.6 34.7 1.0
C06 B:F6I301 3.5 36.7 1.0
CB B:ALA136 3.5 17.4 1.0
CB A:ASN133 3.9 17.2 1.0
CA A:GLY151 3.9 19.8 1.0
CE1 A:TYR152 3.9 19.5 1.0
CD1 A:TYR152 3.9 19.6 1.0
C09 B:F6I301 4.0 35.8 1.0
CG1 A:VAL132 4.3 17.9 1.0
O A:ASN133 4.4 16.3 1.0
CG A:ASN133 4.5 18.8 1.0
C07 B:F6I301 4.6 39.0 1.0
C A:GLY151 4.7 19.6 1.0
CD2 B:LEU154 4.7 19.2 1.0
N A:GLY151 4.8 20.8 1.0
CA A:ASN133 4.8 16.6 1.0
C08 B:F6I301 4.8 37.0 1.0
CA B:ALA136 4.9 18.4 1.0
N A:ASN133 4.9 17.1 1.0
OD1 A:ASN133 4.9 19.7 1.0
ND2 A:ASN133 5.0 20.2 1.0

Fluorine binding site 2 out of 18 in 7t5z

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Fluorine binding site 2 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:43.3
occ:1.00
 F03 B:F6I301 0.0 43.3 1.0
C02 B:F6I301 1.4 38.5 1.0
F01 B:F6I301 2.2 40.5 1.0
F04 B:F6I301 2.2 46.6 1.0
C05 B:F6I301 2.3 36.1 1.0
C06 B:F6I301 3.1 36.7 1.0
C10 B:F6I301 3.2 34.7 1.0
CB B:ALA136 3.6 17.4 1.0
O B:ALA136 3.6 19.7 1.0
N B:ALA138 3.8 19.7 1.0
CA B:ALA138 3.8 20.7 1.0
CB B:ALA138 3.9 20.9 1.0
C B:ALA136 3.9 18.8 1.0
O B:VAL155 4.0 20.9 1.0
C07 B:F6I301 4.3 39.0 1.0
C B:LEU137 4.3 19.0 1.0
C09 B:F6I301 4.4 35.8 1.0
CA B:ALA136 4.4 18.4 1.0
N B:VAL155 4.6 21.0 1.0
N B:LEU137 4.6 19.4 1.0
CA B:LEU137 4.8 20.2 1.0
C B:VAL155 4.8 22.2 1.0
C08 B:F6I301 4.8 37.0 1.0
SD A:MET169 4.8 40.3 1.0
O B:LEU137 4.9 19.6 1.0
CD2 B:LEU154 5.0 19.2 1.0

Fluorine binding site 3 out of 18 in 7t5z

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Fluorine binding site 3 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:46.6
occ:1.00
 F04 B:F6I301 0.0 46.6 1.0
C02 B:F6I301 1.4 38.5 1.0
F03 B:F6I301 2.2 43.3 1.0
F01 B:F6I301 2.3 40.5 1.0
C05 B:F6I301 2.3 36.1 1.0
C06 B:F6I301 2.6 36.7 1.0
C10 B:F6I301 3.6 34.7 1.0
CA A:GLY151 3.6 19.8 1.0
N A:GLY151 3.8 20.8 1.0
SD A:MET169 3.9 40.3 1.0
C07 B:F6I301 4.0 39.0 1.0
CB A:MET169 4.0 31.9 1.0
CG1 A:VAL132 4.1 17.9 1.0
C A:GLY151 4.5 19.6 1.0
O A:GLY151 4.6 20.8 1.0
CG A:MET169 4.6 34.8 1.0
C09 B:F6I301 4.6 35.8 1.0
CB B:ALA138 4.8 20.9 1.0
C08 B:F6I301 4.8 37.0 1.0
O13 B:F6I301 4.9 53.3 1.0

Fluorine binding site 4 out of 18 in 7t5z

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Fluorine binding site 4 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:39.9
occ:1.00
 F01 B:F6I302 0.0 39.9 1.0
C02 B:F6I302 1.4 34.7 1.0
F04 B:F6I302 2.2 35.2 1.0
F03 B:F6I302 2.2 39.1 1.0
C05 B:F6I302 2.3 32.5 1.0
C10 B:F6I302 2.6 29.9 1.0
CB C:ALA136 3.3 21.9 1.0
C06 B:F6I302 3.6 32.1 1.0
CB B:ASN133 3.7 19.4 1.0
CE1 B:TYR152 3.8 19.1 1.0
CD1 B:TYR152 3.9 18.5 1.0
CA B:GLY151 3.9 18.5 1.0
C09 B:F6I302 4.0 31.0 1.0
CG B:ASN133 4.4 20.5 1.0
O B:ASN133 4.5 21.0 1.0
CG1 B:VAL132 4.6 18.8 1.0
C07 B:F6I302 4.7 33.8 1.0
CA C:ALA136 4.7 22.9 1.0
CD2 C:LEU154 4.7 24.9 1.0
C B:GLY151 4.7 18.5 1.0
CA B:ASN133 4.8 19.4 1.0
N B:GLY151 4.8 19.9 1.0
ND2 B:ASN133 4.9 20.5 1.0
C08 B:F6I302 4.9 31.4 1.0
N B:ASN133 4.9 18.9 1.0
OD1 B:ASN133 5.0 23.0 1.0
C B:ASN133 5.0 19.9 1.0

Fluorine binding site 5 out of 18 in 7t5z

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Fluorine binding site 5 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:39.1
occ:1.00
 F03 B:F6I302 0.0 39.1 1.0
C02 B:F6I302 1.4 34.7 1.0
F04 B:F6I302 2.2 35.2 1.0
F01 B:F6I302 2.2 39.9 1.0
C05 B:F6I302 2.4 32.5 1.0
C06 B:F6I302 3.1 32.1 1.0
CB C:ALA136 3.1 21.9 1.0
C10 B:F6I302 3.3 29.9 1.0
O C:ALA136 3.7 26.5 1.0
C C:ALA136 3.9 23.1 1.0
SD B:MET169 3.9 51.2 1.0
CA C:ALA138 4.0 26.4 1.0
N C:ALA138 4.0 25.6 1.0
CB C:ALA138 4.0 27.9 1.0
CA C:ALA136 4.1 22.9 1.0
O C:VAL155 4.1 23.1 1.0
C07 B:F6I302 4.4 33.8 1.0
C09 B:F6I302 4.5 31.0 1.0
C C:LEU137 4.6 24.8 1.0
N C:LEU137 4.6 24.7 1.0
N C:VAL155 4.6 23.8 1.0
CB C:LEU154 4.6 23.2 1.0
CG B:MET169 4.7 41.4 1.0
CD2 C:LEU154 4.7 24.9 1.0
CA C:LEU154 4.8 22.5 1.0
C08 B:F6I302 4.9 31.4 1.0
C C:VAL155 5.0 23.6 1.0

Fluorine binding site 6 out of 18 in 7t5z

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Fluorine binding site 6 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:35.2
occ:1.00
 F04 B:F6I302 0.0 35.2 1.0
C02 B:F6I302 1.4 34.7 1.0
F01 B:F6I302 2.2 39.9 1.0
F03 B:F6I302 2.2 39.1 1.0
C05 B:F6I302 2.4 32.5 1.0
C06 B:F6I302 2.8 32.1 1.0
SD B:MET169 3.1 51.2 1.0
CG B:MET169 3.1 41.4 1.0
CA B:GLY151 3.5 18.5 1.0
C10 B:F6I302 3.6 29.9 1.0
N B:GLY151 3.8 19.9 1.0
C07 B:F6I302 4.2 33.8 1.0
C B:GLY151 4.2 18.5 1.0
O B:GLY151 4.4 18.9 1.0
CG1 B:VAL132 4.4 18.8 1.0
CB B:MET169 4.6 34.7 1.0
CE B:MET169 4.6 47.2 1.0
C09 B:F6I302 4.7 31.0 1.0
CB C:ALA136 4.7 21.9 1.0
CD1 B:TYR152 4.7 18.5 1.0
CD2 C:LEU154 4.8 24.9 1.0
CB C:LEU154 4.8 23.2 1.0
C08 B:F6I302 4.9 31.4 1.0

Fluorine binding site 7 out of 18 in 7t5z

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Fluorine binding site 7 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:47.9
occ:1.00
 F01 C:F6I301 0.0 47.9 1.0
C02 C:F6I301 1.3 43.1 1.0
F04 C:F6I301 2.2 44.9 1.0
F03 C:F6I301 2.2 54.8 1.0
C05 C:F6I301 2.3 42.6 1.0
C10 C:F6I301 2.6 39.3 1.0
CB A:ALA136 3.4 17.3 1.0
C06 C:F6I301 3.5 37.6 1.0
CE1 C:TYR152 3.7 20.9 1.0
CB C:ASN133 3.8 21.0 1.0
CD1 C:TYR152 3.9 20.8 1.0
CA C:GLY151 3.9 19.6 1.0
C09 C:F6I301 4.0 41.1 1.0
CG C:ASN133 4.3 21.6 1.0
O C:ASN133 4.3 20.5 1.0
CG1 C:VAL132 4.5 25.8 1.0
CE C:MET169 4.5 45.6 1.0
C07 C:F6I301 4.6 40.5 1.0
ND2 C:ASN133 4.7 22.6 1.0
C C:GLY151 4.7 19.4 1.0
CA C:ASN133 4.7 20.9 1.0
CA A:ALA136 4.8 18.2 1.0
C08 C:F6I301 4.8 40.3 1.0
N C:GLY151 4.8 19.7 1.0
OD1 C:ASN133 4.8 19.8 1.0
N C:ASN133 4.8 21.2 1.0
C C:ASN133 4.9 22.8 1.0
CD2 A:LEU154 5.0 25.9 1.0
CZ C:TYR152 5.0 21.9 1.0

Fluorine binding site 8 out of 18 in 7t5z

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Fluorine binding site 8 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:54.8
occ:1.00
 F03 C:F6I301 0.0 54.8 1.0
C02 C:F6I301 1.4 43.1 1.0
F04 C:F6I301 2.2 44.9 1.0
F01 C:F6I301 2.2 47.9 1.0
C05 C:F6I301 2.4 42.6 1.0
C06 C:F6I301 3.1 37.6 1.0
CB A:ALA136 3.3 17.3 1.0
CE C:MET169 3.3 45.6 1.0
C10 C:F6I301 3.3 39.3 1.0
O A:ALA136 3.6 17.8 1.0
N A:ALA138 4.0 19.4 1.0
C A:ALA136 4.0 17.3 1.0
CA A:ALA138 4.1 21.5 1.0
CB A:ALA138 4.2 22.0 1.0
CA A:ALA136 4.2 18.2 1.0
O A:VAL155 4.3 21.0 1.0
C07 C:F6I301 4.4 40.5 1.0
C09 C:F6I301 4.5 41.1 1.0
C A:LEU137 4.6 18.8 1.0
CB A:LEU154 4.7 22.5 1.0
N A:LEU137 4.7 18.1 1.0
N A:VAL155 4.8 19.7 1.0
CA A:LEU154 4.8 20.8 1.0
CD2 A:LEU154 4.8 25.9 1.0
SD C:MET169 4.9 46.4 1.0
C08 C:F6I301 5.0 40.3 1.0

Fluorine binding site 9 out of 18 in 7t5z

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Fluorine binding site 9 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:44.9
occ:1.00
 F04 C:F6I301 0.0 44.9 1.0
C02 C:F6I301 1.3 43.1 1.0
F03 C:F6I301 2.2 54.8 1.0
F01 C:F6I301 2.2 47.9 1.0
C05 C:F6I301 2.3 42.6 1.0
CE C:MET169 2.6 45.6 1.0
C06 C:F6I301 2.8 37.6 1.0
CA C:GLY151 3.4 19.6 1.0
C10 C:F6I301 3.5 39.3 1.0
N C:GLY151 3.7 19.7 1.0
C07 C:F6I301 4.1 40.5 1.0
C C:GLY151 4.2 19.4 1.0
CB C:MET169 4.2 35.5 1.0
CG1 C:VAL132 4.3 25.8 1.0
O C:GLY151 4.3 17.7 1.0
SD C:MET169 4.4 46.4 1.0
C09 C:F6I301 4.7 41.1 1.0
CD1 C:TYR152 4.7 20.8 1.0
CB A:ALA136 4.8 17.3 1.0
C08 C:F6I301 4.9 40.3 1.0
CG C:MET169 4.9 37.6 1.0
C C:SER150 5.0 21.6 1.0

Fluorine binding site 10 out of 18 in 7t5z

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Fluorine binding site 10 out of 18 in the P. Aeruginosa Lpxa in Complex with Ligand L8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of P. Aeruginosa Lpxa in Complex with Ligand L8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:54.0
occ:1.00
 F01 E:F6I301 0.0 54.0 1.0
C02 E:F6I301 1.4 53.8 1.0
F03 E:F6I301 2.2 58.7 1.0
F04 E:F6I301 2.3 50.1 1.0
C05 E:F6I301 2.4 53.1 1.0
C10 E:F6I301 2.7 48.7 1.0
CB D:ALA136 3.6 18.9 1.0
C06 E:F6I301 3.6 51.6 1.0
CE1 E:TYR152 3.6 24.4 1.0
CD1 E:TYR152 3.7 22.3 1.0
CA E:GLY151 3.8 20.3 1.0
CB E:ASN133 3.9 20.9 1.0
C09 E:F6I301 4.1 50.7 1.0
O E:ASN133 4.3 18.4 1.0
CG E:ASN133 4.5 20.9 1.0
CG1 E:VAL132 4.5 24.5 1.0
C E:GLY151 4.5 19.9 1.0
N E:GLY151 4.7 21.2 1.0
C07 E:F6I301 4.7 55.5 1.0
CA E:ASN133 4.8 20.9 1.0
ND2 E:ASN133 4.9 20.3 1.0
CA D:ALA136 4.9 19.2 1.0
CZ E:TYR152 4.9 27.0 1.0
C E:ASN133 4.9 20.5 1.0
C08 E:F6I301 4.9 51.7 1.0
N E:TYR152 4.9 19.8 1.0
N E:ASN133 5.0 21.3 1.0

Reference:

M.D.Sacco, K.Defrees, X.Zhang, W.Lawless, E.Nwanochie, A.Balsizer, S.E.Darch, A.R.Renslo, Y.Chen. Structure-Based Ligand Design Targeting Pseudomonas Aeruginosa Lpxa in Lipid A Biosynthesis. Acs Infect Dis. V. 8 1231 2022.
ISSN: ESSN 2373-8227
PubMed: 35653508
DOI: 10.1021/ACSINFECDIS.1C00650
Page generated: Wed Apr 5 01:09:09 2023

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