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Fluorine in PDB 7ros: Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr

Enzymatic activity of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr

All present enzymatic activity of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr:
6.1.1.1;

Protein crystallography data

The structure of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr, PDB code: 7ros was solved by R.D.Metcalfe, S.C.Xie, C.J.Morton, L.Tilley, M.D.W.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.24 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.292, 46.529, 139.015, 90, 93.77, 90
R / Rfree (%) 20 / 23.1

Other elements in 7ros:

The structure of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr (pdb code 7ros). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr, PDB code: 7ros:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7ros

Go back to Fluorine Binding Sites List in 7ros
Fluorine binding site 1 out of 4 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:85.8
occ:1.00
 F11 A:66I401 0.0 85.8 1.0
C10 A:66I401 1.4 71.4 1.0
F12 A:66I401 2.1 79.3 1.0
O09 A:66I401 2.3 61.6 1.0
O A:HOH548 3.3 56.4 1.0
C08 A:66I401 3.4 56.5 1.0
O A:HOH550 3.7 67.8 1.0
N13 A:66I401 4.0 53.8 1.0
O A:LYS247 4.2 77.7 1.0
C07 A:66I401 4.5 57.8 1.0
O21 A:66I401 4.7 52.3 1.0
O A:HOH507 4.9 51.9 1.0
N01 A:66I401 5.0 58.2 1.0

Fluorine binding site 2 out of 4 in 7ros

Go back to Fluorine Binding Sites List in 7ros
Fluorine binding site 2 out of 4 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:79.3
occ:1.00
 F12 A:66I401 0.0 79.3 1.0
C10 A:66I401 1.3 71.4 1.0
F11 A:66I401 2.1 85.8 1.0
O09 A:66I401 2.2 61.6 1.0
O A:HOH550 3.3 67.8 1.0
C08 A:66I401 3.4 56.5 1.0
N13 A:66I401 3.8 53.8 1.0
NE2 A:GLN73 4.1 50.8 1.0
O A:HOH548 4.3 56.4 1.0
O A:HOH518 4.5 58.4 1.0
O21 A:66I401 4.6 52.3 1.0
CD A:GLN73 4.6 52.6 1.0
CB A:HIS70 4.7 56.3 1.0
C07 A:66I401 4.7 57.8 1.0
OE1 A:GLN73 4.9 60.9 1.0
CD2 A:HIS70 4.9 74.4 1.0

Fluorine binding site 3 out of 4 in 7ros

Go back to Fluorine Binding Sites List in 7ros
Fluorine binding site 3 out of 4 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:79.5
occ:1.00
 F11 B:66I401 0.0 79.5 1.0
C10 B:66I401 1.4 57.1 1.0
F12 B:66I401 2.1 69.5 1.0
O09 B:66I401 2.3 49.1 1.0
CD B:LYS247 3.3 60.2 1.0
OG B:SER249 3.3 71.8 1.0
CB B:SER249 3.3 67.1 1.0
C08 B:66I401 3.4 43.0 1.0
O B:HOH559 3.5 54.1 1.0
O B:HOH509 3.7 44.9 1.0
CG B:LYS247 3.8 57.5 1.0
O B:MET248 3.8 50.9 1.0
N13 B:66I401 4.0 44.8 1.0
CE B:LYS247 4.0 68.8 1.0
O B:HOH545 4.0 61.7 1.0
CA B:SER249 4.2 64.8 1.0
C07 B:66I401 4.6 45.9 1.0
C B:MET248 4.7 52.3 1.0
N B:SER249 4.9 58.8 1.0
NE2 B:HIS70 4.9 65.2 1.0
O21 B:66I401 5.0 41.6 1.0

Fluorine binding site 4 out of 4 in 7ros

Go back to Fluorine Binding Sites List in 7ros
Fluorine binding site 4 out of 4 in the Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum Tyrosyl-Trna Synthetase in Complex with ML901- Tyr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:69.5
occ:1.00
 F12 B:66I401 0.0 69.5 1.0
C10 B:66I401 1.3 57.1 1.0
F11 B:66I401 2.1 79.5 1.0
O09 B:66I401 2.2 49.1 1.0
O B:HOH545 2.3 61.7 1.0
NE2 B:HIS70 3.2 65.2 1.0
C08 B:66I401 3.4 43.0 1.0
OG B:SER249 3.5 71.8 1.0
CB B:SER249 3.7 67.1 1.0
O B:MET248 3.8 50.9 1.0
CA B:SER249 3.8 64.8 1.0
NE2 B:GLN73 3.8 46.5 1.0
N13 B:66I401 3.9 44.8 1.0
CE1 B:HIS70 4.0 51.6 1.0
O B:HOH559 4.2 54.1 1.0
CD2 B:HIS70 4.2 55.2 1.0
N B:LYS250 4.6 76.0 1.0
O B:HOH509 4.7 44.9 1.0
C07 B:66I401 4.7 45.9 1.0
C B:MET248 4.7 52.3 1.0
O21 B:66I401 4.7 41.6 1.0
N B:SER249 4.8 58.8 1.0
CD B:GLN73 4.8 51.1 1.0
C B:SER249 4.8 70.5 1.0

Reference:

S.C.Xie, R.D.Metcalfe, E.Dunn, C.J.Morton, S.C.Huang, T.Puhalovich, Y.Du, S.Wittlin, S.Nie, M.R.Luth, L.Ma, M.S.Kim, C.F.A.Pasaje, K.Kumpornsin, C.Giannangelo, F.J.Houghton, A.Churchyard, M.T.Famodimu, D.C.Barry, D.L.Gillett, S.Dey, C.C.Kosasih, W.Newman, J.C.Niles, M.C.S.Lee, J.Baum, S.Ottilie, E.A.Winzeler, D.J.Creek, N.Williamson, M.W.Parker, S.Brand, S.P.Langston, L.R.Dick, M.D.W.Griffin, A.E.Gould, L.Tilley. Reaction Hijacking of Tyrosine Trna Synthetase As A New Whole-of-Life-Cycle Antimalarial Strategy. Science V. 376 1074 2022.
ISSN: ESSN 1095-9203
PubMed: 35653481
DOI: 10.1126/SCIENCE.ABN0611
Page generated: Fri Aug 2 12:19:17 2024

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