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Fluorine in PDB 6hcw: Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand

Enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand

All present enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6hcw was solved by 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) 72.94 / 1.46
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.514, 142.650, 72.939, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand (pdb code 6hcw). 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6hcw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hcw

Go back to Fluorine Binding Sites List in 6hcw
Fluorine binding site 1 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:10.9
occ:1.00
 F2 A:FYB602 0.0 10.9 1.0
C13 A:FYB602 1.4 10.2 1.0
C12 A:FYB602 2.3 9.7 1.0
C14 A:FYB602 2.3 10.0 1.0
CG A:GLU297 2.9 13.3 0.5
O A:HOH701 3.1 30.6 1.0
CD A:GLU297 3.2 12.8 0.5
O A:ARG295 3.4 8.6 1.0
CB A:ARG295 3.5 7.7 1.0
C11 A:FYB602 3.6 9.1 1.0
C15 A:FYB602 3.6 9.1 1.0
O A:HOH854 3.7 19.2 1.0
OE2 A:GLU297 3.7 11.3 0.5
OE1 A:GLU297 3.7 13.1 0.5
O A:ASN304 3.9 7.9 1.0
CB A:GLU297 4.0 15.5 0.5
C A:ARG295 4.0 7.8 1.0
C16 A:FYB602 4.1 9.5 1.0
OE1 A:GLU297 4.2 21.2 0.5
O A:GLY298 4.2 20.5 1.0
CA A:ARG295 4.3 7.5 1.0
CB A:GLU297 4.3 14.1 0.5
CD2 A:HIS303 4.3 9.8 1.0
CG A:GLU297 4.4 15.3 0.5
CB A:HIS303 4.5 9.7 1.0
C A:ASN304 4.5 9.4 1.0
CA A:PRO305 4.6 9.5 1.0
N A:GLU297 4.6 12.4 1.0
CG A:ARG295 4.7 7.9 1.0
O A:HOH713 4.7 27.9 1.0
CA A:GLU297 4.8 14.4 0.5
CD A:GLU297 4.8 17.6 0.5
CG A:HIS303 4.8 9.7 1.0
CD A:ARG295 4.8 8.0 1.0
N A:ARG295 4.8 7.1 1.0
C10 A:FYB602 4.8 10.0 1.0
CE1 A:PHE307 4.9 9.8 1.0
CA A:GLU297 4.9 13.9 0.5
N A:PRO305 4.9 9.4 1.0
N A:ASN304 5.0 8.6 1.0

Fluorine binding site 2 out of 6 in 6hcw

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Fluorine binding site 2 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:8.1
occ:1.00
 F A:FYB602 0.0 8.1 1.0
C3 A:FYB602 1.4 7.9 1.0
F1 A:FYB602 2.2 9.6 1.0
C2 A:FYB602 2.3 7.7 1.0
C4 A:FYB602 2.3 8.3 1.0
C1 A:FYB602 2.9 8.0 1.0
C5 A:FYB602 2.9 7.8 1.0
N A:LEU519 3.0 7.2 1.0
C A:LEU519 3.0 7.5 1.0
C A:GLY518 3.2 6.4 1.0
O A:LEU519 3.2 7.5 1.0
N A:GLY520 3.4 6.9 1.0
CA A:LEU519 3.4 7.1 1.0
C A:FYB602 3.5 8.2 1.0
CA A:GLY518 3.6 6.1 1.0
CB A:ALA309 3.7 9.3 1.0
O A:GLY518 3.8 7.4 1.0
CA A:GLY520 4.1 7.4 1.0
O A:MET310 4.3 10.4 1.0
O A:HOH772 4.4 11.7 1.0
O A:FYB602 4.5 8.7 1.0
C6 A:FYB602 4.6 8.4 1.0
CA A:ALA309 4.7 8.4 1.0
O A:LEU465 4.7 8.1 1.0
CB A:LEU519 4.9 8.0 1.0
N A:MET310 4.9 8.9 1.0
N A:GLY518 4.9 6.9 1.0

Fluorine binding site 3 out of 6 in 6hcw

Go back to Fluorine Binding Sites List in 6hcw
Fluorine binding site 3 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:9.6
occ:1.00
 F1 A:FYB602 0.0 9.6 1.0
C3 A:FYB602 1.4 7.9 1.0
F A:FYB602 2.2 8.1 1.0
C2 A:FYB602 2.3 7.7 1.0
C4 A:FYB602 2.3 8.3 1.0
O A:HOH772 3.0 11.7 1.0
C A:LYS601 3.1 7.9 1.0
CB A:LYS601 3.1 7.2 1.0
O A:LYS601 3.2 8.5 1.0
OXT A:LYS601 3.4 8.1 1.0
CA A:GLY518 3.5 6.1 1.0
C1 A:FYB602 3.7 8.0 1.0
CA A:LYS601 3.7 7.5 1.0
C5 A:FYB602 3.7 7.8 1.0
C A:GLY518 3.9 6.4 1.0
OE2 A:GLU311 4.0 10.4 1.0
C A:FYB602 4.2 8.2 1.0
N A:LEU519 4.3 7.2 1.0
CG A:GLU311 4.4 10.1 1.0
O A:GLY518 4.4 7.4 1.0
N A:LYS601 4.4 7.9 1.0
CG A:LYS601 4.5 7.2 1.0
O A:FYB602 4.5 8.7 1.0
N A:GLY518 4.5 6.9 1.0
CD A:GLU311 4.5 10.0 1.0
CB A:ALA309 4.7 9.3 1.0
O A:HOH740 4.7 11.9 1.0
O A:MET310 4.9 10.4 1.0
NH2 A:ARG295 4.9 8.7 1.0

Fluorine binding site 4 out of 6 in 6hcw

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Fluorine binding site 4 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:11.3
occ:1.00
 F2 B:FYB602 0.0 11.3 1.0
C13 B:FYB602 1.4 8.8 1.0
C14 B:FYB602 2.3 9.6 1.0
C12 B:FYB602 2.3 9.3 1.0
O B:HOH702 3.1 42.6 1.0
O B:HOH879 3.2 17.3 1.0
O B:ARG295 3.5 8.8 1.0
CB B:ARG295 3.5 8.4 1.0
C15 B:FYB602 3.6 9.5 1.0
C11 B:FYB602 3.6 8.8 1.0
CB B:GLU297 3.7 14.8 1.0
O B:ASN304 3.9 10.6 1.0
OE1 B:GLU297 4.0 15.8 1.0
O B:GLY298 4.0 19.4 1.0
C B:ARG295 4.0 8.5 1.0
C16 B:FYB602 4.0 9.4 1.0
CD2 B:HIS303 4.3 9.3 1.0
CA B:ARG295 4.3 8.0 1.0
CG B:GLU297 4.4 16.4 1.0
O B:HOH977 4.5 24.8 1.0
N B:GLU297 4.5 11.5 1.0
CA B:GLU297 4.5 13.3 1.0
CB B:HIS303 4.5 8.9 1.0
C B:ASN304 4.6 9.9 1.0
CA B:PRO305 4.6 10.7 1.0
N B:GLY298 4.6 19.1 1.0
CG B:ARG295 4.7 8.6 1.0
CD B:GLU297 4.7 18.1 1.0
C B:GLU297 4.8 14.8 1.0
CG B:HIS303 4.8 9.5 1.0
CD B:ARG295 4.8 9.2 1.0
C10 B:FYB602 4.8 8.8 1.0
N B:ARG295 4.9 7.6 1.0
CE1 B:PHE307 4.9 9.4 1.0
O B:PRO305 4.9 10.3 1.0
N B:PRO305 5.0 10.3 1.0

Fluorine binding site 5 out of 6 in 6hcw

Go back to Fluorine Binding Sites List in 6hcw
Fluorine binding site 5 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:11.7
occ:1.00
 F B:FYB602 0.0 11.7 1.0
C3 B:FYB602 1.4 10.1 1.0
F1 B:FYB602 2.1 10.1 1.0
C2 B:FYB602 2.3 9.5 1.0
C4 B:FYB602 2.4 10.3 1.0
C1 B:FYB602 2.9 11.3 1.0
C5 B:FYB602 2.9 11.5 1.0
N B:LEU519 3.0 6.8 1.0
C B:LEU519 3.0 7.1 1.0
C B:GLY518 3.2 7.3 1.0
O B:LEU519 3.2 8.1 1.0
N B:GLY520 3.4 7.4 1.0
C B:FYB602 3.4 10.7 1.0
CA B:LEU519 3.4 7.1 1.0
CA B:GLY518 3.6 6.6 1.0
O B:GLY518 3.7 7.0 1.0
CB B:ALA309 3.8 9.5 1.0
CA B:GLY520 4.1 7.1 1.0
O B:MET310 4.4 10.3 1.0
O B:FYB602 4.4 12.5 1.0
O B:HOH804 4.5 12.2 1.0
C6 B:FYB602 4.5 11.2 1.0
CA B:ALA309 4.6 9.3 1.0
O B:LEU465 4.6 7.9 1.0
N B:MET310 4.9 7.9 1.0
CB B:LEU519 4.9 8.0 1.0
N B:GLY518 4.9 6.6 1.0

Fluorine binding site 6 out of 6 in 6hcw

Go back to Fluorine Binding Sites List in 6hcw
Fluorine binding site 6 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Cryptosporidium Parvum Complexed with L-Lysine and 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 Cryptosporidium Parvum Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:10.1
occ:1.00
 F1 B:FYB602 0.0 10.1 1.0
C3 B:FYB602 1.4 10.1 1.0
F B:FYB602 2.1 11.7 1.0
C2 B:FYB602 2.3 9.5 1.0
C4 B:FYB602 2.3 10.3 1.0
O B:HOH804 3.1 12.2 1.0
CB B:LYS601 3.2 7.8 1.0
C B:LYS601 3.4 10.0 1.0
CA B:GLY518 3.4 6.6 1.0
OXT B:LYS601 3.5 9.1 1.0
O B:LYS601 3.6 10.3 1.0
C1 B:FYB602 3.6 11.3 1.0
C5 B:FYB602 3.7 11.5 1.0
C B:GLY518 3.8 7.3 1.0
CA B:LYS601 3.9 7.9 1.0
OE2 B:GLU311 4.0 8.9 1.0
C B:FYB602 4.1 10.7 1.0
N B:LEU519 4.2 6.8 1.0
O B:GLY518 4.3 7.0 1.0
CG B:GLU311 4.4 8.8 1.0
O B:FYB602 4.4 12.5 1.0
N B:GLY518 4.4 6.6 1.0
CG B:LYS601 4.5 7.6 1.0
N B:LYS601 4.6 8.0 1.0
CB B:ALA309 4.6 9.5 1.0
CD B:GLU311 4.6 7.8 1.0
O B:HOH754 4.8 13.6 1.0
O B:MET310 4.9 10.3 1.0
C B:LEU519 5.0 7.1 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 21:00:41 2024

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