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Fluorine in PDB 6hcu: Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand

Enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand

All present enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6hcu was solved by J.Tamjar, D.A.Robinson, B.Baragana, N.Norcross, B.Forte, C.Walpole, I.H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.74 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.137, 95.344, 166.517, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand (pdb code 6hcu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6hcu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hcu

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Fluorine binding site 1 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:18.6
occ:1.00
 F2 A:FYB601 0.0 18.6 1.0
C13 A:FYB601 1.3 14.9 1.0
C12 A:FYB601 2.3 14.3 1.0
C14 A:FYB601 2.4 15.6 1.0
CB A:ARG330 3.2 18.9 1.0
O A:HOH973 3.4 16.3 1.0
C11 A:FYB601 3.6 14.4 1.0
C15 A:FYB601 3.6 16.7 1.0
CB A:GLU332 3.7 19.7 1.0
O A:GLY333 3.8 20.6 1.0
O A:ARG330 3.8 14.0 1.0
OE1 A:GLU332 3.9 38.4 1.0
CG A:ARG330 3.9 20.2 1.0
O A:ASN339 4.1 15.6 1.0
C16 A:FYB601 4.1 15.3 1.0
CB A:HIS338 4.2 14.5 1.0
O A:HOH966 4.2 34.9 1.0
CD2 A:HIS338 4.3 18.0 1.0
C A:ARG330 4.4 13.0 1.0
CA A:ARG330 4.4 15.4 1.0
O A:HOH712 4.4 35.8 1.0
CG A:GLU332 4.4 23.4 1.0
CD A:GLU332 4.5 30.3 1.0
N A:GLY333 4.6 17.9 1.0
CA A:GLU332 4.6 17.4 1.0
CG A:HIS338 4.6 14.2 1.0
C A:ASN339 4.6 12.8 1.0
N A:GLU332 4.7 17.0 1.0
CA A:PRO340 4.8 14.5 1.0
C A:GLU332 4.8 17.3 1.0
C10 A:FYB601 4.9 13.6 1.0
C A:GLY333 4.9 19.3 1.0
N A:ASN339 5.0 14.2 1.0

Fluorine binding site 2 out of 6 in 6hcu

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Fluorine binding site 2 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:22.1
occ:1.00
 F A:FYB601 0.0 22.1 1.0
C3 A:FYB601 1.4 20.4 1.0
F1 A:FYB601 2.1 17.2 1.0
C2 A:FYB601 2.3 16.6 1.0
C4 A:FYB601 2.4 20.1 1.0
C1 A:FYB601 2.9 18.8 1.0
N A:LEU555 3.0 11.9 1.0
C A:GLY554 3.1 12.6 1.0
C5 A:FYB601 3.1 19.1 1.0
C A:LEU555 3.2 13.3 1.0
O A:LEU555 3.2 13.0 1.0
CA A:GLY554 3.5 11.0 1.0
O A:GLY554 3.6 12.8 1.0
CA A:LEU555 3.6 12.8 1.0
C A:FYB601 3.6 17.9 1.0
N A:GLY556 3.7 10.7 1.0
CB A:SER344 4.0 14.6 1.0
O A:FYB601 4.4 18.6 1.0
CA A:GLY556 4.4 12.1 1.0
O A:CYS345 4.4 13.3 1.0
O A:HOH786 4.6 34.9 1.0
N A:GLY554 4.7 9.5 1.0
CA A:SER344 4.8 11.7 1.0
C6 A:FYB601 4.8 19.2 1.0
CG A:GLU346 4.8 18.6 1.0
OG A:SER344 5.0 14.7 1.0

Fluorine binding site 3 out of 6 in 6hcu

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Fluorine binding site 3 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:17.2
occ:1.00
 F1 A:FYB601 0.0 17.2 1.0
C3 A:FYB601 1.3 20.4 1.0
F A:FYB601 2.1 22.1 1.0
C4 A:FYB601 2.4 20.1 1.0
C2 A:FYB601 2.4 16.6 1.0
C2 A:TRS606 3.2 31.7 0.9
CA A:GLY554 3.5 11.0 1.0
C3 A:TRS606 3.6 26.8 0.9
O A:HOH906 3.6 24.8 1.0
O A:HOH786 3.6 34.9 1.0
C1 A:FYB601 3.8 18.8 1.0
C5 A:FYB601 3.8 19.1 1.0
C A:TRS606 3.8 28.5 0.9
O3 A:TRS606 3.8 26.8 0.9
C A:GLY554 3.8 12.6 1.0
C1 A:TRS606 4.0 28.7 0.9
CG A:GLU346 4.1 18.6 1.0
CD A:GLU346 4.2 22.2 1.0
O A:GLY554 4.2 12.8 1.0
N A:GLY554 4.3 9.5 1.0
C A:FYB601 4.3 17.9 1.0
O2 A:TRS606 4.4 47.0 0.9
N A:LEU555 4.4 11.9 1.0
OE2 A:GLU346 4.4 25.9 1.0
O A:FYB601 4.5 18.6 1.0
OE1 A:GLU346 4.5 20.3 1.0
O A:HOH1111 4.8 45.8 1.0
CB A:SER344 4.8 14.6 1.0
O1 A:TRS606 4.9 25.1 0.9

Fluorine binding site 4 out of 6 in 6hcu

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Fluorine binding site 4 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:19.5
occ:1.00
 F2 B:FYB601 0.0 19.5 1.0
C13 B:FYB601 1.4 15.8 1.0
C12 B:FYB601 2.3 15.4 1.0
C14 B:FYB601 2.4 16.0 1.0
O B:HOH745 2.9 44.4 1.0
C11 B:FYB601 3.6 14.9 1.0
CB B:ARG330 3.6 16.7 1.0
C15 B:FYB601 3.7 15.6 1.0
O B:HOH1133 3.7 26.4 1.0
O B:HOH918 3.8 28.5 1.0
O B:ARG330 3.8 16.8 1.0
CB B:GLU332 4.0 24.2 1.0
C16 B:FYB601 4.1 16.5 1.0
O B:ASN339 4.2 15.8 1.0
O B:HOH798 4.3 28.4 1.0
CA B:PRO340 4.3 14.4 1.0
CB B:HIS338 4.4 15.4 1.0
CD2 B:HIS338 4.4 18.2 1.0
C B:ARG330 4.4 13.4 1.0
O B:GLY333 4.5 22.8 1.0
C B:ASN339 4.5 17.4 1.0
CA B:ARG330 4.5 15.4 1.0
CG B:GLU332 4.7 25.0 1.0
N B:PRO340 4.7 18.5 1.0
CG B:ARG330 4.8 19.7 1.0
CG B:HIS338 4.8 16.2 1.0
C10 B:FYB601 4.8 15.1 1.0
CD B:ARG330 4.8 23.3 1.0
CA B:GLU332 4.9 20.2 1.0
N B:GLU332 4.9 16.3 1.0
CE1 B:PHE342 4.9 16.7 1.0
N B:ASN339 4.9 13.8 1.0

Fluorine binding site 5 out of 6 in 6hcu

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Fluorine binding site 5 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:23.6
occ:1.00
 F B:FYB601 0.0 23.6 1.0
C3 B:FYB601 1.4 19.9 1.0
F1 B:FYB601 2.1 19.5 1.0
C4 B:FYB601 2.3 20.7 1.0
C2 B:FYB601 2.3 17.0 1.0
C1 B:FYB601 2.7 21.0 1.0
C5 B:FYB601 2.9 19.5 1.0
C B:GLY554 3.1 8.9 1.0
N B:LEU555 3.1 8.8 1.0
C B:LEU555 3.2 12.2 1.0
O B:LEU555 3.2 10.6 1.0
C B:FYB601 3.3 18.5 1.0
CA B:GLY554 3.5 10.1 1.0
CA B:LEU555 3.6 11.6 1.0
O B:GLY554 3.6 10.5 1.0
N B:GLY556 3.7 11.0 1.0
CB B:SER344 4.1 11.4 1.0
O B:FYB601 4.1 20.3 1.0
CA B:GLY556 4.4 12.9 1.0
O B:CYS345 4.5 10.8 1.0
C6 B:FYB601 4.6 18.1 1.0
O B:HOH921 4.6 32.6 1.0
N B:GLY554 4.7 9.3 1.0
CG B:GLU346 4.9 12.6 1.0
CA B:SER344 4.9 10.2 1.0

Fluorine binding site 6 out of 6 in 6hcu

Go back to Fluorine Binding Sites List in 6hcu
Fluorine binding site 6 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand


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 Lysyl-Trna Synthetase From Plasmodium Falciparum Bound to A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:19.5
occ:1.00
 F1 B:FYB601 0.0 19.5 1.0
C3 B:FYB601 1.3 19.9 1.0
F B:FYB601 2.1 23.6 1.0
C4 B:FYB601 2.3 20.7 1.0
C2 B:FYB601 2.4 17.0 1.0
C1 B:TRS603 3.4 27.8 1.0
CA B:GLY554 3.4 10.1 1.0
O B:HOH719 3.4 30.5 1.0
O B:HOH921 3.5 32.6 1.0
C1 B:FYB601 3.7 21.0 1.0
C5 B:FYB601 3.7 19.5 1.0
C B:GLY554 3.9 8.9 1.0
O3 B:TRS603 3.9 35.2 1.0
O1 B:TRS603 3.9 27.6 1.0
C B:FYB601 4.1 18.5 1.0
C2 B:TRS603 4.1 28.4 1.0
CD B:GLU346 4.2 18.8 1.0
CG B:GLU346 4.2 12.6 1.0
C B:TRS603 4.2 32.3 1.0
O B:FYB601 4.3 20.3 1.0
O B:GLY554 4.3 10.5 1.0
N B:LEU555 4.4 8.8 1.0
OE2 B:GLU346 4.4 23.2 1.0
N B:GLY554 4.4 9.3 1.0
OE1 B:GLU346 4.5 18.1 1.0
C3 B:TRS603 4.6 32.3 1.0
O B:HOH1013 4.8 44.3 1.0
CB B:SER344 4.9 11.4 1.0

Reference:

B.Baragana, B.Forte, R.Choi, S.Nakazawa Hewitt, J.A.Bueren-Calabuig, J.P.Pisco, C.Peet, D.M.Dranow, D.A.Robinson, C.Jansen, N.R.Norcross, S.Vinayak, M.Anderson, C.F.Brooks, C.A.Cooper, S.Damerow, M.Delves, K.Dowers, J.Duffy, T.E.Edwards, I.Hallyburton, B.G.Horst, M.A.Hulverson, L.Ferguson, M.B.Jimenez-Diaz, R.S.Jumani, D.D.Lorimer, M.S.Love, S.Maher, H.Matthews, C.W.Mcnamara, P.Miller, S.O'neill, K.K.Ojo, M.Osuna-Cabello, E.Pinto, J.Post, J.Riley, M.Rottmann, L.M.Sanz, P.Scullion, A.Sharma, S.M.Shepherd, Y.Shishikura, F.R.C.Simeons, E.E.Stebbins, L.Stojanovski, U.Straschil, F.K.Tamaki, J.Tamjar, L.S.Torrie, A.Vantaux, B.Witkowski, S.Wittlin, M.Yogavel, F.Zuccotto, I.Angulo-Barturen, R.Sinden, J.Baum, F.J.Gamo, P.Maser, D.E.Kyle, E.A.Winzeler, P.J.Myler, P.G.Wyatt, D.Floyd, D.Matthews, A.Sharma, B.Striepen, C.D.Huston, D.W.Gray, A.H.Fairlamb, A.V.Pisliakov, C.Walpole, K.D.Read, W.C.Van Voorhis, I.H.Gilbert. Lysyl-Trna Synthetase As A Drug Target in Malaria and Cryptosporidiosis. Proc.Natl.Acad.Sci.Usa V. 116 7015 2019.
ISSN: ESSN 1091-6490
PubMed: 30894487
DOI: 10.1073/PNAS.1814685116
Page generated: Thu Aug 1 21:00:42 2024

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