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Fluorine in PDB 4wi1: Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506

Enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506

All present enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506, PDB code: 4wi1 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.29 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.180, 91.340, 110.910, 90.00, 129.53, 90.00
R / Rfree (%) 16.2 / 18.8

Other elements in 4wi1:

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 (pdb code 4wi1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506, PDB code: 4wi1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 4wi1

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Fluorine binding site 1 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:57.0
occ:1.00
 F10 A:3O6801 0.0 57.0 1.0
C09 A:3O6801 1.4 50.4 1.0
C08 A:3O6801 2.4 43.0 1.0
C11 A:3O6801 2.4 48.1 1.0
CD1 A:ILE474 3.0 30.4 0.2
CD1 A:ILE474 3.1 39.3 0.8
CG1 A:ILE518 3.5 19.3 1.0
C07 A:3O6801 3.6 40.5 1.0
C12 A:3O6801 3.6 34.6 1.0
CG2 A:ILE474 3.7 34.1 0.2
CG1 A:ILE474 3.8 33.8 0.8
CG1 A:ILE474 3.9 31.0 0.2
SD A:MET521 4.1 30.7 1.0
C06 A:3O6801 4.1 38.3 1.0
CG A:ARG514 4.2 33.4 1.0
CG2 A:ILE474 4.2 27.6 0.8
CB A:ILE474 4.3 31.5 0.8
CB A:ILE474 4.3 31.2 0.2
N A:ILE518 4.3 19.5 1.0
CD1 A:ILE518 4.4 19.8 1.0
CA A:ILE518 4.5 17.5 1.0
CE A:MET521 4.5 36.5 1.0
O A:ARG514 4.6 20.1 1.0
CB A:ILE518 4.6 18.0 1.0
C A:GLY517 4.7 20.4 1.0
CE1 A:TYR746 4.7 45.2 1.0
CD1 A:TYR746 4.7 49.5 1.0
CD A:ARG514 4.7 36.6 1.0
NE A:ARG514 5.0 37.2 1.0
CZ A:TYR746 5.0 43.5 1.0
CG A:TYR746 5.0 52.4 1.0

Fluorine binding site 2 out of 10 in 4wi1

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Fluorine binding site 2 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:36.0
occ:1.00
 F22 A:3O6801 0.0 36.0 1.0
C21 A:3O6801 1.4 38.8 1.0
C20 A:3O6801 2.4 32.4 1.0
C23 A:3O6801 2.4 35.3 1.0
CB A:ALA291 2.9 24.8 1.0
CG2 A:ILE516 3.4 24.3 1.0
CA A:ALA291 3.4 21.1 1.0
C19 A:3O6801 3.6 34.1 1.0
C24 A:3O6801 3.6 27.3 1.0
CD1 A:ILE516 3.7 25.8 1.0
O A:ALA291 4.0 19.9 1.0
C A:ALA291 4.0 18.3 1.0
CB A:ILE516 4.1 22.3 1.0
C18 A:3O6801 4.1 26.6 1.0
CD2 A:LEU275 4.5 32.8 1.0
CG1 A:ILE516 4.5 24.6 1.0
CB A:LEU275 4.5 25.1 1.0
CG2 A:ILE276 4.7 32.9 1.0
N A:ALA291 4.7 21.2 1.0
CD1 A:LEU275 4.7 29.4 1.0
CD1 A:ILE294 4.7 24.7 1.0
CD2 A:LEU287 4.8 31.2 1.0
CG A:LEU275 4.8 32.0 1.0
CD1 A:ILE520 5.0 31.8 1.0

Fluorine binding site 3 out of 10 in 4wi1

Go back to Fluorine Binding Sites List in 4wi1
Fluorine binding site 3 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:55.1
occ:1.00
 F26 A:3O6801 0.0 55.1 1.0
C25 A:3O6801 1.4 49.2 1.0
F28 A:3O6801 2.2 51.5 1.0
F27 A:3O6801 2.2 48.5 1.0
C04 A:3O6801 2.3 40.6 1.0
N03 A:3O6801 2.7 38.5 1.0
C05 A:3O6801 3.7 35.5 1.0
N02 A:3O6801 4.0 42.1 1.0
O A:HOH1197 4.3 59.6 1.0
C13 A:3O6801 4.5 34.9 1.0
C06 A:3O6801 4.5 38.3 1.0
CD2 A:TYR266 4.5 25.6 1.0
CE2 A:TYR266 4.6 24.8 1.0
C12 A:3O6801 4.7 34.6 1.0
NH1 A:ARG403 4.9 79.7 1.0

Fluorine binding site 4 out of 10 in 4wi1

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Fluorine binding site 4 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:48.5
occ:1.00
 F27 A:3O6801 0.0 48.5 1.0
C25 A:3O6801 1.4 49.2 1.0
F26 A:3O6801 2.2 55.1 1.0
F28 A:3O6801 2.2 51.5 1.0
C04 A:3O6801 2.3 40.6 1.0
C05 A:3O6801 3.0 35.5 1.0
C06 A:3O6801 3.1 38.3 1.0
CE A:MET521 3.2 36.5 1.0
C12 A:3O6801 3.3 34.6 1.0
O A:HOH1197 3.5 59.6 1.0
N03 A:3O6801 3.5 38.5 1.0
CD2 A:TYR266 3.8 25.6 1.0
CE2 A:TYR266 3.8 24.8 1.0
C07 A:3O6801 3.9 40.5 1.0
C11 A:3O6801 4.2 48.1 1.0
C13 A:3O6801 4.2 34.9 1.0
OH A:TYR746 4.3 49.5 1.0
CE2 A:TYR746 4.4 47.7 1.0
N02 A:3O6801 4.4 42.1 1.0
C08 A:3O6801 4.6 43.0 1.0
CG A:TYR266 4.7 20.3 1.0
CZ A:TYR266 4.7 26.7 1.0
CZ A:TYR746 4.7 43.5 1.0
C09 A:3O6801 4.8 50.4 1.0
SD A:MET521 4.9 30.7 1.0

Fluorine binding site 5 out of 10 in 4wi1

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Fluorine binding site 5 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:51.5
occ:1.00
 F28 A:3O6801 0.0 51.5 1.0
C25 A:3O6801 1.4 49.2 1.0
F26 A:3O6801 2.2 55.1 1.0
F27 A:3O6801 2.2 48.5 1.0
C04 A:3O6801 2.3 40.6 1.0
C12 A:3O6801 3.1 34.6 1.0
C05 A:3O6801 3.1 35.5 1.0
N03 A:3O6801 3.3 38.5 1.0
NH1 A:ARG403 3.4 79.7 1.0
C06 A:3O6801 3.5 38.3 1.0
CZ A:ARG403 3.7 80.4 1.0
NE A:ARG403 4.0 77.2 1.0
CE2 A:TYR746 4.1 47.7 1.0
NH2 A:ARG403 4.2 82.2 1.0
C11 A:3O6801 4.2 48.1 1.0
C13 A:3O6801 4.3 34.9 1.0
CD A:ARG403 4.3 72.6 1.0
N02 A:3O6801 4.3 42.1 1.0
O A:HOH1197 4.4 59.6 1.0
CD2 A:TYR746 4.6 48.3 1.0
C07 A:3O6801 4.7 40.5 1.0

Fluorine binding site 6 out of 10 in 4wi1

Go back to Fluorine Binding Sites List in 4wi1
Fluorine binding site 6 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:55.2
occ:1.00
 F10 B:3O6801 0.0 55.2 1.0
C09 B:3O6801 1.4 50.3 1.0
C08 B:3O6801 2.3 36.8 1.0
C11 B:3O6801 2.4 43.1 1.0
CD1 B:ILE474 2.8 29.8 0.4
CD1 B:ILE474 3.2 35.8 0.6
CG1 B:ILE518 3.4 18.1 1.0
C07 B:3O6801 3.6 34.9 1.0
C12 B:3O6801 3.6 40.5 1.0
CG2 B:ILE474 3.7 33.8 0.4
CG1 B:ILE474 3.8 33.9 0.6
CG1 B:ILE474 3.8 24.9 0.4
SD B:MET521 3.9 26.8 1.0
CG B:ARG514 4.1 25.5 1.0
C06 B:3O6801 4.1 34.5 1.0
CB B:ILE474 4.2 27.1 0.6
CG2 B:ILE474 4.3 22.9 0.6
N B:ILE518 4.3 19.1 1.0
CD1 B:ILE518 4.3 18.5 1.0
CB B:ILE474 4.3 27.7 0.4
CA B:ILE518 4.3 19.2 1.0
CE B:MET521 4.5 33.4 1.0
CB B:ILE518 4.5 18.2 1.0
CD B:ARG514 4.6 32.8 1.0
O B:ARG514 4.6 18.6 1.0
C B:GLY517 4.6 18.9 1.0
CE1 B:TYR746 4.7 42.6 1.0
CD1 B:TYR746 4.9 41.0 1.0
CZ B:TYR746 4.9 39.2 1.0

Fluorine binding site 7 out of 10 in 4wi1

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Fluorine binding site 7 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:29.4
occ:1.00
 F22 B:3O6801 0.0 29.4 1.0
C21 B:3O6801 1.4 26.5 1.0
C20 B:3O6801 2.4 27.1 1.0
C23 B:3O6801 2.4 24.9 1.0
CB B:ALA291 3.0 17.5 1.0
CG2 B:ILE516 3.4 20.8 1.0
C19 B:3O6801 3.6 32.6 1.0
C24 B:3O6801 3.6 24.1 1.0
CA B:ALA291 3.7 15.9 1.0
CB B:LEU275 3.9 14.2 1.0
CD2 B:LEU275 3.9 18.5 1.0
C18 B:3O6801 4.1 21.8 1.0
CD1 B:LEU275 4.2 20.3 1.0
CG2 B:ILE276 4.2 18.6 1.0
CG B:LEU275 4.2 17.3 1.0
CD2 B:LEU287 4.2 18.9 0.5
CB B:ILE516 4.4 17.7 1.0
CD1 B:ILE516 4.5 23.5 1.0
CD1 B:ILE520 4.5 22.3 1.0
C B:ALA291 4.6 15.7 1.0
O B:ALA291 4.7 16.8 1.0
O B:LEU275 4.8 17.1 1.0
CA B:LEU275 4.8 14.8 1.0
N B:ALA291 4.8 14.9 1.0
C B:LEU275 4.9 16.8 1.0

Fluorine binding site 8 out of 10 in 4wi1

Go back to Fluorine Binding Sites List in 4wi1
Fluorine binding site 8 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:47.0
occ:1.00
 F26 B:3O6801 0.0 47.0 1.0
C25 B:3O6801 1.4 35.0 1.0
F28 B:3O6801 2.2 37.2 1.0
F27 B:3O6801 2.2 37.1 1.0
C04 B:3O6801 2.3 36.7 1.0
N03 B:3O6801 2.6 35.8 1.0
C05 B:3O6801 3.6 36.6 1.0
C2 B:EDO804 3.6 51.1 1.0
C1 B:EDO804 3.7 55.5 1.0
O2 B:EDO804 3.9 48.6 1.0
NH2 B:ARG403 3.9 86.6 1.0
N02 B:3O6801 3.9 37.5 1.0
CZ B:ARG403 4.0 82.8 1.0
O B:HOH1028 4.1 30.5 1.0
NE B:ARG403 4.2 75.3 1.0
C13 B:3O6801 4.4 34.0 1.0
C06 B:3O6801 4.4 34.5 1.0
NH1 B:ARG403 4.5 83.1 1.0
C12 B:3O6801 4.6 40.5 1.0
O1 B:EDO804 4.8 49.2 1.0

Fluorine binding site 9 out of 10 in 4wi1

Go back to Fluorine Binding Sites List in 4wi1
Fluorine binding site 9 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:37.1
occ:1.00
 F27 B:3O6801 0.0 37.1 1.0
C25 B:3O6801 1.4 35.0 1.0
F26 B:3O6801 2.2 47.0 1.0
F28 B:3O6801 2.3 37.2 1.0
C04 B:3O6801 2.3 36.7 1.0
C05 B:3O6801 3.0 36.6 1.0
C06 B:3O6801 3.1 34.5 1.0
O2 B:EDO804 3.1 48.6 1.0
C1 B:EDO804 3.2 55.5 1.0
C12 B:3O6801 3.2 40.5 1.0
N03 B:3O6801 3.4 35.8 1.0
CE B:MET521 3.5 33.4 1.0
C2 B:EDO804 3.5 51.1 1.0
O1 B:EDO804 3.6 49.2 1.0
C07 B:3O6801 3.8 34.9 1.0
CE2 B:TYR746 4.1 36.2 1.0
C11 B:3O6801 4.1 43.1 1.0
C13 B:3O6801 4.2 34.0 1.0
CE2 B:TYR266 4.3 17.6 1.0
OH B:TYR746 4.3 41.1 1.0
CD2 B:TYR266 4.4 18.6 1.0
N02 B:3O6801 4.4 37.5 1.0
C08 B:3O6801 4.6 36.8 1.0
CZ B:TYR746 4.6 39.2 1.0
O B:HOH1028 4.6 30.5 1.0
C09 B:3O6801 4.7 50.3 1.0
CD2 B:TYR746 5.0 34.1 1.0

Fluorine binding site 10 out of 10 in 4wi1

Go back to Fluorine Binding Sites List in 4wi1
Fluorine binding site 10 out of 10 in the Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Prolyl-Trna Synthetase (Prors, Proline--Trna Ligase) From Plasmodium Falciparum in Complex with Tcmdc-124506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:37.2
occ:1.00
 F28 B:3O6801 0.0 37.2 1.0
C25 B:3O6801 1.4 35.0 1.0
F26 B:3O6801 2.2 47.0 1.0
F27 B:3O6801 2.3 37.1 1.0
C04 B:3O6801 2.3 36.7 1.0
NH1 B:ARG403 2.8 83.1 1.0
CZ B:ARG403 3.0 82.8 1.0
C12 B:3O6801 3.0 40.5 1.0
C05 B:3O6801 3.1 36.6 1.0
N03 B:3O6801 3.3 35.8 1.0
NH2 B:ARG403 3.3 86.6 1.0
C06 B:3O6801 3.4 34.5 1.0
NE B:ARG403 3.5 75.3 1.0
CE2 B:TYR746 3.9 36.2 1.0
C1 B:EDO804 4.0 55.5 1.0
CD B:ARG403 4.1 61.3 1.0
C11 B:3O6801 4.1 43.1 1.0
CD2 B:TYR746 4.3 34.1 1.0
C13 B:3O6801 4.3 34.0 1.0
O B:HOH1239 4.3 53.7 1.0
N02 B:3O6801 4.3 37.5 1.0
C2 B:EDO804 4.7 51.1 1.0
O1 B:EDO804 4.7 49.2 1.0
C07 B:3O6801 4.7 34.9 1.0
O2 B:EDO804 4.9 48.6 1.0

Reference:

S.Nakazawa Hewitt, D.M.Dranow, B.G.Horst, J.A.Abendroth, B.Forte, I.Hallyburton, C.Jansen, B.Baragana, R.Choi, K.L.Rivas, M.A.Hulverson, M.Dumais, T.E.Edwards, D.D.Lorimer, A.H.Fairlamb, D.W.Gray, K.D.Read, A.M.Lehane, K.Kirk, P.J.Myler, A.Wernimont, C.S.Walpole, R.Stacy, L.K.Barrett, I.H.Gilbert, W.C.Van Voorhis. Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium Falciparum Drug Target, Prolyl-Trna-Synthetase. Acs Infect Dis. 2016.
ISSN: ESSN 2373-8227
PubMed: 27798837
DOI: 10.1021/ACSINFECDIS.6B00078
Page generated: Thu Aug 1 06:28:06 2024

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