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Fluorine in PDB 5jnl: Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese

Enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese

All present enzymatic activity of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese:
1.1.1.267;

Protein crystallography data

The structure of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese, PDB code: 5jnl was solved by S.Sooriyaarachchi, T.Bergfors, T.A.Jones, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.473, 56.035, 86.041, 103.10, 102.89, 100.90
R / Rfree (%) 17.8 / 19.9

Other elements in 5jnl:

The structure of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese (pdb code 5jnl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese, PDB code: 5jnl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5jnl

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Fluorine binding site 1 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:55.7
occ:1.00
 F25 A:L54501 0.0 55.7 1.0
C22 A:L54501 1.3 52.7 1.0
F24 A:L54501 2.2 54.4 1.0
F23 A:L54501 2.2 54.6 1.0
C21 A:L54501 2.3 48.7 1.0
N A:ASP359 2.6 27.8 1.0
N A:MET360 2.6 26.7 1.0
C A:ASP359 2.7 28.8 1.0
C19 A:L54501 2.7 45.8 1.0
CA A:ASP359 3.0 28.9 1.0
C A:PRO358 3.1 26.3 1.0
CA A:MET360 3.3 27.0 1.0
O A:ASP359 3.4 29.9 1.0
C20 A:L54501 3.6 46.6 1.0
CG A:MET360 3.6 34.0 1.0
O A:HOH659 3.7 29.4 1.0
O A:PRO358 3.7 32.1 1.0
CA A:PRO358 3.8 23.5 1.0
SD A:MET360 3.8 42.6 1.0
CB A:MET360 4.0 30.5 1.0
C17 A:L54501 4.1 44.5 1.0
CB A:PRO358 4.4 23.2 1.0
CB A:ASP359 4.5 29.6 1.0
C18 A:L54501 4.7 45.3 1.0
C A:MET360 4.7 23.8 1.0
O A:TYR357 4.9 19.3 1.0
C16 A:L54501 4.9 42.9 1.0
C11 A:L54501 5.0 25.6 1.0

Fluorine binding site 2 out of 6 in 5jnl

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Fluorine binding site 2 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:54.6
occ:1.00
 F23 A:L54501 0.0 54.6 1.0
C22 A:L54501 1.4 52.7 1.0
F24 A:L54501 2.2 54.4 1.0
F25 A:L54501 2.2 55.7 1.0
C21 A:L54501 2.3 48.7 1.0
O A:HOH659 2.5 29.4 1.0
C20 A:L54501 2.7 46.6 1.0
N A:ASP359 3.1 27.8 1.0
CE1 A:HIS341 3.4 20.8 1.0
CA A:PRO358 3.4 23.5 1.0
C19 A:L54501 3.6 45.8 1.0
C A:PRO358 3.6 26.3 1.0
NE2 A:HIS341 3.7 21.1 1.0
C A:ASP359 3.9 28.8 1.0
ND1 A:HIS341 3.9 21.1 1.0
O A:ASP359 3.9 29.9 1.0
O A:TYR357 4.0 19.3 1.0
C18 A:L54501 4.1 45.3 1.0
CB A:SER232 4.1 18.2 1.0
CA A:ASP359 4.1 28.9 1.0
CB A:PRO358 4.2 23.2 1.0
O A:HOH727 4.3 25.0 1.0
N A:MET360 4.3 26.7 1.0
CD2 A:HIS341 4.4 20.0 1.0
CG A:HIS341 4.5 19.1 1.0
N A:PRO358 4.5 21.7 1.0
OG A:SER232 4.5 19.6 1.0
O A:PRO358 4.7 32.1 1.0
C A:TYR357 4.7 19.4 1.0
C17 A:L54501 4.7 44.5 1.0
CA A:MET360 4.8 27.0 1.0
SD A:MET360 4.8 42.6 1.0
O3 A:GOL503 4.8 30.4 1.0
CG A:PRO363 4.9 16.7 1.0
C16 A:L54501 4.9 42.9 1.0

Fluorine binding site 3 out of 6 in 5jnl

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Fluorine binding site 3 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:54.4
occ:1.00
 F24 A:L54501 0.0 54.4 1.0
C22 A:L54501 1.3 52.7 1.0
F25 A:L54501 2.2 55.7 1.0
F23 A:L54501 2.2 54.6 1.0
C21 A:L54501 2.3 48.7 1.0
SD A:MET360 2.8 42.6 1.0
CB A:SER232 2.9 18.2 1.0
C19 A:L54501 3.1 45.8 1.0
C20 A:L54501 3.2 46.6 1.0
OG A:SER232 3.4 19.6 1.0
CG A:MET360 3.6 34.0 1.0
C11 A:L54501 3.7 25.6 1.0
CA A:MET360 4.0 27.0 1.0
N A:MET360 4.0 26.7 1.0
O A:HOH659 4.2 29.4 1.0
CG A:PRO363 4.2 16.7 1.0
CA A:SER232 4.2 17.3 1.0
C A:ASP359 4.3 28.8 1.0
CE A:MET360 4.3 40.4 1.0
C17 A:L54501 4.4 44.5 1.0
CB A:MET360 4.4 30.5 1.0
C18 A:L54501 4.4 45.3 1.0
O A:ASP359 4.4 29.9 1.0
N A:ASP359 4.5 27.8 1.0
O A:HOH604 4.6 22.0 1.0
O10 A:L54501 4.7 22.9 1.0
N9 A:L54501 4.7 24.8 1.0
CD A:PRO363 4.8 16.6 1.0
N A:SER232 4.9 17.9 1.0
C16 A:L54501 4.9 42.9 1.0
CA A:ASP359 5.0 28.9 1.0

Fluorine binding site 4 out of 6 in 5jnl

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Fluorine binding site 4 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:44.7
occ:1.00
 F25 B:L54501 0.0 44.7 1.0
C22 B:L54501 1.3 41.5 1.0
F23 B:L54501 2.2 43.5 1.0
F24 B:L54501 2.2 42.4 1.0
C21 B:L54501 2.3 38.6 1.0
N B:ASP359 2.4 22.4 1.0
C B:PRO358 2.8 21.3 1.0
C B:ASP359 2.9 22.3 1.0
O B:HOH648 2.9 28.4 1.0
C19 B:L54501 3.0 36.4 1.0
CA B:ASP359 3.1 22.5 1.0
N B:MET360 3.1 20.5 1.0
CA B:PRO358 3.2 19.3 1.0
O B:ASP359 3.3 22.8 1.0
C20 B:L54501 3.4 37.2 1.0
O B:PRO358 3.7 26.1 1.0
CA B:MET360 3.8 21.1 1.0
O B:TYR357 4.0 15.7 1.0
CB B:PRO358 4.1 19.0 1.0
C17 B:L54501 4.3 35.8 1.0
O B:HOH654 4.4 43.8 1.0
N B:PRO358 4.4 17.6 1.0
CB B:ASP359 4.5 23.0 1.0
CB B:MET360 4.5 24.1 1.0
CE1 B:HIS341 4.5 17.1 1.0
C18 B:L54501 4.5 36.5 1.0
C B:TYR357 4.7 16.2 1.0
NE2 B:HIS341 4.7 17.0 1.0
C16 B:L54501 4.9 34.8 1.0
CB B:SER232 4.9 13.5 1.0

Fluorine binding site 5 out of 6 in 5jnl

Go back to Fluorine Binding Sites List in 5jnl
Fluorine binding site 5 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:43.5
occ:1.00
 F23 B:L54501 0.0 43.5 1.0
C22 B:L54501 1.4 41.5 1.0
F25 B:L54501 2.2 44.7 1.0
F24 B:L54501 2.2 42.4 1.0
C21 B:L54501 2.3 38.6 1.0
C20 B:L54501 2.7 37.2 1.0
O B:HOH648 3.2 28.4 1.0
CE1 B:HIS341 3.2 17.1 1.0
CB B:SER232 3.3 13.5 1.0
ND1 B:HIS341 3.4 17.8 1.0
OG B:SER232 3.6 14.2 1.0
C19 B:L54501 3.6 36.4 1.0
NE2 B:HIS341 3.7 17.0 1.0
O3 B:GOL503 3.9 23.6 1.0
CG B:HIS341 3.9 15.9 1.0
C18 B:L54501 4.1 36.5 1.0
CD2 B:HIS341 4.1 16.3 1.0
CA B:PRO358 4.2 19.3 1.0
N B:ASP359 4.2 22.4 1.0
O B:HOH721 4.4 20.8 1.0
C B:PRO358 4.6 21.3 1.0
O B:HOH662 4.6 15.3 1.0
O B:ASP359 4.7 22.8 1.0
C B:ASP359 4.7 22.3 1.0
O B:TYR357 4.7 15.7 1.0
CA B:SER232 4.7 13.0 1.0
CG B:PRO363 4.7 13.7 1.0
C17 B:L54501 4.7 35.8 1.0
C11 B:L54501 4.8 18.8 1.0
CB B:PRO358 4.8 19.0 1.0
CB B:HIS341 4.9 14.3 1.0
C16 B:L54501 4.9 34.8 1.0
C3 B:GOL503 4.9 23.4 1.0
N B:MET360 4.9 20.5 1.0

Fluorine binding site 6 out of 6 in 5jnl

Go back to Fluorine Binding Sites List in 5jnl
Fluorine binding site 6 out of 6 in the Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Plasmodium Falciparum Dxr in Complex with A Beta- Substituted Fosmidomycin Analogue, LC54 and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:42.4
occ:1.00
 F24 B:L54501 0.0 42.4 1.0
C22 B:L54501 1.4 41.5 1.0
F25 B:L54501 2.2 44.7 1.0
F23 B:L54501 2.2 43.5 1.0
C21 B:L54501 2.3 38.6 1.0
C19 B:L54501 2.9 36.4 1.0
CB B:SER232 3.2 13.5 1.0
C20 B:L54501 3.5 37.2 1.0
CA B:MET360 3.6 21.1 1.0
OG B:SER232 3.7 14.2 1.0
N B:MET360 3.7 20.5 1.0
CB B:MET360 3.8 24.1 1.0
C11 B:L54501 3.8 18.8 1.0
O2 B:EDO506 4.0 24.6 1.0
C B:ASP359 4.1 22.3 1.0
CG B:PRO363 4.2 13.7 1.0
C17 B:L54501 4.2 35.8 1.0
O B:HOH648 4.3 28.4 1.0
O B:ASP359 4.4 22.8 1.0
C2 B:EDO506 4.4 24.9 1.0
N B:ASP359 4.5 22.4 1.0
CA B:SER232 4.5 13.0 1.0
C18 B:L54501 4.6 36.5 1.0
O1 B:EDO506 4.6 24.4 1.0
O10 B:L54501 4.8 17.0 1.0
CD B:PRO363 4.8 13.5 1.0
N9 B:L54501 4.8 18.5 1.0
CA B:ASP359 4.9 22.5 1.0
C16 B:L54501 4.9 34.8 1.0
C B:MET360 4.9 18.8 1.0
C B:PRO358 4.9 21.3 1.0

Reference:

S.Sooriyaarachchi, R.Chofor, M.D.Risseeuw, T.Bergfors, J.Pouyez, C.S.Dowd, L.Maes, J.Wouters, T.A.Jones, S.Van Calenbergh, S.L.Mowbray. Targeting An Aromatic Hotspot in Plasmodium Falciparum 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase with Beta-Arylpropyl Analogues of Fosmidomycin. Chemmedchem V. 11 2024 2016.
ISSN: ESSN 1860-7187
PubMed: 27487410
DOI: 10.1002/CMDC.201600249
Page generated: Thu Aug 1 10:36:42 2024

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