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Fluorine in PDB 5zni: Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine

Enzymatic activity of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine

All present enzymatic activity of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine:
2.4.2.1;

Protein crystallography data

The structure of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine, PDB code: 5zni was solved by D.Chen, P.Nordlund, J.M.Dziekan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.94 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 95.591, 95.591, 136.571, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine (pdb code 5zni). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine, PDB code: 5zni:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5zni

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Fluorine binding site 1 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:85.9
occ:1.00
 FAE A:YMZ302 0.0 85.9 1.0
CAZ A:YMZ302 1.3 83.6 1.0
FAF A:YMZ302 2.0 85.5 1.0
FAG A:YMZ302 2.1 97.3 1.0
CAT A:YMZ302 2.5 73.7 1.0
NAP A:YMZ302 2.5 61.5 1.0
CAV A:YMZ302 2.9 65.7 1.0
CAI A:YMZ302 3.7 65.2 1.0
CAR A:YMZ302 3.7 69.3 1.0
N A:PRO209 3.9 33.3 1.0
FAC A:YMZ302 4.0 89.3 1.0
CD A:PRO209 4.1 29.4 1.0
FAB A:YMZ302 4.1 89.6 1.0
CA A:PRO209 4.1 32.4 1.0
C A:CYS208 4.1 33.4 1.0
CB A:PRO209 4.2 29.2 1.0
CAY A:YMZ302 4.3 76.5 1.0
CAU A:YMZ302 4.3 62.0 1.0
N A:CYS208 4.5 30.0 1.0
CA A:GLY93 4.5 23.0 1.0
O A:CYS208 4.5 30.4 1.0
CA A:CYS208 4.7 31.5 1.0
CG A:PRO209 4.7 29.0 1.0
CAH A:YMZ302 4.8 65.6 1.0
C A:GLY207 4.9 29.6 1.0
CAK A:YMZ302 4.9 64.5 1.0

Fluorine binding site 2 out of 6 in 5zni

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Fluorine binding site 2 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:85.5
occ:1.00
 FAF A:YMZ302 0.0 85.5 1.0
CAZ A:YMZ302 1.3 83.6 1.0
FAE A:YMZ302 2.0 85.9 1.0
CAT A:YMZ302 2.2 73.7 1.0
FAG A:YMZ302 2.2 97.3 1.0
CAI A:YMZ302 2.6 65.2 1.0
N A:CYS208 3.4 30.0 1.0
CAV A:YMZ302 3.4 65.7 1.0
CA A:GLY207 3.4 29.6 1.0
C A:GLY207 3.5 29.6 1.0
NAP A:YMZ302 3.8 61.5 1.0
CAH A:YMZ302 4.0 65.6 1.0
C A:CYS208 4.0 33.4 1.0
CA A:CYS208 4.2 31.5 1.0
O A:CYS208 4.2 30.4 1.0
O A:GLY207 4.4 27.4 1.0
N A:GLY207 4.4 29.8 1.0
N A:PRO209 4.4 33.3 1.0
CAU A:YMZ302 4.5 62.0 1.0
CA A:GLY93 4.6 23.0 1.0
O A:ASP206 4.7 30.9 1.0
CAJ A:YMZ302 4.7 65.5 1.0
C A:ASP206 4.8 32.7 1.0
CD A:PRO209 4.9 29.4 1.0

Fluorine binding site 3 out of 6 in 5zni

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Fluorine binding site 3 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:97.3
occ:1.00
 FAG A:YMZ302 0.0 97.3 1.0
CAZ A:YMZ302 1.3 83.6 1.0
FAE A:YMZ302 2.1 85.9 1.0
CAT A:YMZ302 2.2 73.7 1.0
FAF A:YMZ302 2.2 85.5 1.0
CA A:GLY93 2.6 23.0 1.0
CAI A:YMZ302 3.0 65.2 1.0
CAV A:YMZ302 3.1 65.7 1.0
NAP A:YMZ302 3.2 61.5 1.0
C A:GLY207 3.3 29.6 1.0
N A:CYS208 3.3 30.0 1.0
CD A:PRO209 3.5 29.4 1.0
O A:GLY207 3.5 27.4 1.0
CA A:CYS208 3.5 31.5 1.0
N A:GLY93 3.6 23.4 1.0
N A:PRO209 3.6 33.3 1.0
C A:CYS208 3.7 33.4 1.0
C A:GLY93 3.8 23.7 1.0
CA A:GLY207 3.9 29.6 1.0
N A:SER94 4.1 20.6 1.0
CAH A:YMZ302 4.2 65.6 1.0
CAU A:YMZ302 4.3 62.0 1.0
CG1 A:VAL181 4.4 20.3 1.0
C A:CYS92 4.4 25.4 1.0
O A:CYS208 4.5 30.4 1.0
CAR A:YMZ302 4.5 69.3 1.0
CA A:PRO209 4.6 32.4 1.0
O A:CYS92 4.6 24.5 1.0
CG A:PRO209 4.6 29.0 1.0
N A:GLY207 4.6 29.8 1.0
CAJ A:YMZ302 4.7 65.5 1.0
CB A:PRO209 4.7 29.2 1.0
O A:GLY93 4.8 23.4 1.0
FAB A:YMZ302 4.9 89.6 1.0

Fluorine binding site 4 out of 6 in 5zni

Go back to Fluorine Binding Sites List in 5zni
Fluorine binding site 4 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:89.3
occ:1.00
 FAC A:YMZ302 0.0 89.3 1.0
CAY A:YMZ302 1.3 76.5 1.0
FAB A:YMZ302 2.0 89.6 1.0
FAD A:YMZ302 2.2 75.0 1.0
CAR A:YMZ302 2.3 69.3 1.0
NAP A:YMZ302 2.8 61.5 1.0
O A:HOH442 2.9 38.3 1.0
CD1 A:TYR160 3.2 31.7 1.0
CAK A:YMZ302 3.3 64.5 1.0
CE1 A:TYR160 3.6 31.9 1.0
O A:TYR160 3.7 21.2 1.0
CA A:TYR160 3.8 23.1 1.0
CG A:TYR160 4.0 26.9 1.0
FAE A:YMZ302 4.0 85.9 1.0
CAV A:YMZ302 4.1 65.7 1.0
O A:MET159 4.2 24.5 1.0
C A:TYR160 4.3 22.2 1.0
CB A:TYR160 4.4 23.1 1.0
CAS A:YMZ302 4.5 64.4 1.0
CZ A:TYR160 4.6 31.5 1.0
CAU A:YMZ302 4.8 62.0 1.0
N A:TYR160 4.9 21.9 1.0
CAZ A:YMZ302 4.9 83.6 1.0
CD2 A:TYR160 4.9 28.2 1.0
C A:MET159 5.0 20.7 1.0
CAT A:YMZ302 5.0 73.7 1.0

Fluorine binding site 5 out of 6 in 5zni

Go back to Fluorine Binding Sites List in 5zni
Fluorine binding site 5 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:75.0
occ:1.00
 FAD A:YMZ302 0.0 75.0 1.0
CAY A:YMZ302 1.3 76.5 1.0
FAB A:YMZ302 2.2 89.6 1.0
FAC A:YMZ302 2.2 89.3 1.0
CAR A:YMZ302 2.4 69.3 1.0
CAK A:YMZ302 2.7 64.5 1.0
NAP A:YMZ302 3.6 61.5 1.0
CD1 A:TYR160 3.9 31.7 1.0
O A:MET159 3.9 24.5 1.0
CG A:MET183 3.9 19.3 1.0
CG2 A:VAL181 4.0 20.9 1.0
CAS A:YMZ302 4.1 64.4 1.0
O A:GLU182 4.3 16.8 1.0
CA A:TYR160 4.3 23.1 1.0
O A:HOH442 4.3 38.3 1.0
SD A:MET183 4.4 21.1 1.0
OAA A:YMZ302 4.5 62.8 1.0
C A:GLU182 4.5 18.6 1.0
CE1 A:TYR160 4.6 31.9 1.0
O A:SER157 4.6 14.3 1.0
CA A:GLU182 4.6 19.2 1.0
C A:MET159 4.7 20.7 1.0
CAV A:YMZ302 4.7 65.7 1.0
CB A:TYR160 4.7 23.1 1.0
CG A:TYR160 4.7 26.9 1.0
CG1 A:VAL181 4.8 20.3 1.0
N A:GLU182 4.8 20.6 1.0
CAO A:YMZ302 4.9 61.5 1.0
CE A:MET183 4.9 22.5 1.0
CAU A:YMZ302 4.9 62.0 1.0
N A:TYR160 4.9 21.9 1.0
O A:VAL181 5.0 23.7 1.0
CAW A:YMZ302 5.0 60.0 1.0
CB A:SER157 5.0 14.9 1.0
C A:VAL181 5.0 22.1 1.0

Fluorine binding site 6 out of 6 in 5zni

Go back to Fluorine Binding Sites List in 5zni
Fluorine binding site 6 out of 6 in the Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Falciparum Purine Nucleoside Phosphorylase in Complex with Mefloquine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:89.6
occ:1.00
 FAB A:YMZ302 0.0 89.6 1.0
CAY A:YMZ302 1.3 76.5 1.0
FAC A:YMZ302 2.0 89.3 1.0
FAD A:YMZ302 2.2 75.0 1.0
CAR A:YMZ302 2.4 69.3 1.0
NAP A:YMZ302 2.9 61.5 1.0
CG2 A:VAL181 3.3 20.9 1.0
CG1 A:VAL181 3.3 20.3 1.0
O A:HOH442 3.4 38.3 1.0
CAK A:YMZ302 3.5 64.5 1.0
CB A:VAL181 4.0 20.4 1.0
FAE A:YMZ302 4.1 85.9 1.0
CAV A:YMZ302 4.2 65.7 1.0
CD1 A:LEU170 4.3 21.5 1.0
O A:VAL181 4.7 23.7 1.0
CAS A:YMZ302 4.7 64.4 1.0
O A:MET159 4.8 24.5 1.0
C A:VAL181 4.8 22.1 1.0
CAZ A:YMZ302 4.9 83.6 1.0
CD1 A:TYR160 4.9 31.7 1.0
FAG A:YMZ302 4.9 97.3 1.0
CAU A:YMZ302 5.0 62.0 1.0
CD2 A:LEU170 5.0 20.9 1.0

Reference:

J.M.Dziekan, H.Yu, D.Chen, L.Dai, G.Wirjanata, A.Larsson, N.Prabhu, R.M.Sobota, Z.Bozdech, P.Nordlund. Identifying Purine Nucleoside Phosphorylase As the Target of Quinine Using Cellular Thermal Shift Assay. Sci Transl Med V. 11 2019.
ISSN: ESSN 1946-6242
PubMed: 30602534
DOI: 10.1126/SCITRANSLMED.AAU3174
Page generated: Thu Aug 1 17:31:52 2024

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