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Fluorine in PDB 6o3f: Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand

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

All present enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6o3f 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) 45.55 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.490, 57.280, 138.190, 90.00, 95.19, 90.00
R / Rfree (%) 16.3 / 20.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand (pdb code 6o3f). 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand, PDB code: 6o3f:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 1 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:32.7
occ:1.00
 F2 A:FYB701 0.0 32.7 1.0
C13 A:FYB701 1.4 36.8 1.0
C12 A:FYB701 2.3 33.2 1.0
C14 A:FYB701 2.4 30.0 1.0
CB A:GLU273 3.2 45.5 1.0
O A:ARG271 3.4 38.1 1.0
CB A:ARG271 3.5 32.9 1.0
C11 A:FYB701 3.6 30.9 1.0
C15 A:FYB701 3.6 27.2 1.0
C A:ARG271 4.0 39.6 1.0
C16 A:FYB701 4.1 34.3 1.0
OE2 A:GLU273 4.2 71.7 1.0
CD2 A:HIS279 4.2 34.1 1.0
CG A:GLU273 4.2 60.6 1.0
N A:GLU273 4.2 42.4 1.0
CA A:GLU273 4.2 40.8 1.0
O A:GLY274 4.3 50.6 1.0
CA A:ARG271 4.3 35.6 1.0
CA A:PRO281 4.4 35.0 1.0
O A:ASN280 4.4 36.3 1.0
CB A:HIS279 4.4 34.9 1.0
CD A:GLU273 4.5 67.9 1.0
CG A:ARG271 4.6 34.4 1.0
C A:GLU273 4.7 41.7 1.0
C A:ASN280 4.7 35.3 1.0
CG A:HIS279 4.7 37.7 1.0
N A:PRO281 4.7 31.8 1.0
C10 A:FYB701 4.8 32.5 1.0
N A:ARG271 4.9 31.1 1.0
CD A:ARG271 4.9 31.5 1.0
CE1 A:PHE283 5.0 33.2 1.0

Fluorine binding site 2 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 2 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:42.4
occ:1.00
 F A:FYB701 0.0 42.4 1.0
C3 A:FYB701 1.4 41.4 1.0
F1 A:FYB701 2.2 39.9 1.0
C4 A:FYB701 2.3 33.0 1.0
C2 A:FYB701 2.3 38.4 1.0
C1 A:FYB701 2.9 37.4 1.0
C5 A:FYB701 2.9 33.4 1.0
N A:ILE494 3.0 26.6 1.0
C A:GLY493 3.0 25.8 1.0
C A:ILE494 3.1 28.8 1.0
N A:GLY495 3.2 30.1 1.0
O A:GLY493 3.3 28.1 1.0
CA A:ILE494 3.3 28.2 1.0
C A:FYB701 3.5 38.4 1.0
O A:ILE494 3.6 26.8 1.0
CA A:GLY493 3.6 25.6 1.0
CE A:MET285 3.7 34.7 1.0
CA A:GLY495 4.0 22.6 1.0
CB A:MET285 4.1 29.9 1.0
O A:FYB701 4.4 40.3 1.0
SD A:MET285 4.4 42.0 1.0
O A:LEU439 4.6 27.7 1.0
C6 A:FYB701 4.6 33.1 1.0
O A:ILE286 4.6 26.8 1.0
N A:GLY493 4.8 33.1 1.0
CG A:MET285 4.9 37.0 1.0
CB A:ILE494 4.9 28.5 1.0

Fluorine binding site 3 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 3 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:39.9
occ:1.00
 F1 A:FYB701 0.0 39.9 1.0
C3 A:FYB701 1.4 41.4 1.0
F A:FYB701 2.2 42.4 1.0
C4 A:FYB701 2.3 33.0 1.0
C2 A:FYB701 2.3 38.4 1.0
CB A:LYS720 3.1 21.2 1.0
OXT A:LYS720 3.1 34.6 1.0
CE A:MET285 3.1 34.7 1.0
C A:LYS720 3.1 29.1 1.0
O A:LYS720 3.4 28.5 1.0
CA A:GLY493 3.5 25.6 1.0
C1 A:FYB701 3.7 37.4 1.0
C A:GLY493 3.7 25.8 1.0
CA A:LYS720 3.7 26.7 1.0
C5 A:FYB701 3.7 33.4 1.0
O A:GLY493 3.8 28.1 1.0
C A:FYB701 4.1 38.4 1.0
CB A:ASN441 4.3 27.6 1.0
N A:ILE494 4.3 26.6 1.0
CG A:LYS720 4.4 22.7 1.0
O A:FYB701 4.4 40.3 1.0
N A:GLY493 4.4 33.1 1.0
SD A:MET285 4.4 42.0 1.0
O A:HOH864 4.5 37.2 1.0
N A:LYS720 4.5 29.5 1.0
N A:ASN441 4.9 27.5 1.0
OE2 A:GLU287 4.9 34.7 1.0
O A:ASN441 5.0 31.3 1.0
NH2 A:ARG271 5.0 28.8 1.0
ND2 A:ASN441 5.0 19.9 1.0

Fluorine binding site 4 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 4 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F702

b:36.1
occ:1.00
 F2 B:FYB702 0.0 36.1 1.0
C13 B:FYB702 1.4 35.6 1.0
C12 B:FYB702 2.3 36.2 1.0
C14 B:FYB702 2.3 30.8 1.0
O B:ARG271 3.2 34.7 1.0
CB B:GLU273 3.4 43.0 1.0
C15 B:FYB702 3.6 29.6 1.0
C11 B:FYB702 3.6 31.5 1.0
CB B:ARG271 3.7 27.1 1.0
C B:ARG271 4.0 35.3 1.0
CA B:PRO281 4.1 33.5 1.0
C16 B:FYB702 4.1 35.6 1.0
N B:GLU273 4.1 40.8 1.0
OE1 B:GLU273 4.1 60.9 1.0
O B:GLY274 4.1 48.1 1.0
CA B:GLU273 4.2 39.9 1.0
O B:ASN280 4.3 32.5 1.0
CA B:ARG271 4.4 37.9 1.0
O1 B:EDO708 4.4 71.8 1.0
CD2 B:HIS279 4.4 35.1 1.0
C B:GLU273 4.4 42.5 1.0
CG B:GLU273 4.6 50.3 1.0
N B:PRO281 4.6 31.1 1.0
CB B:HIS279 4.6 30.8 1.0
C B:ASN280 4.6 30.6 1.0
CD B:GLU273 4.6 56.7 1.0
O B:GLU273 4.8 43.1 1.0
O B:PRO281 4.8 34.2 1.0
N B:GLY274 4.8 47.7 1.0
C10 B:FYB702 4.8 34.8 1.0
CB B:PRO281 4.9 36.1 1.0
CG B:HIS279 4.9 37.9 1.0
CG B:ARG271 4.9 27.5 1.0
N B:ARG271 4.9 35.5 1.0
C B:PRO281 4.9 30.8 1.0
CG B:PRO281 5.0 33.3 1.0

Fluorine binding site 5 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 5 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F702

b:40.9
occ:1.00
 F B:FYB702 0.0 40.9 1.0
C3 B:FYB702 1.4 42.2 1.0
F1 B:FYB702 2.2 42.4 1.0
C2 B:FYB702 2.3 37.3 1.0
C4 B:FYB702 2.3 37.4 1.0
C1 B:FYB702 2.8 37.1 1.0
C5 B:FYB702 2.8 37.0 1.0
N B:ILE494 3.0 29.9 1.0
C B:GLY493 3.0 31.5 1.0
C B:ILE494 3.1 33.1 1.0
N B:GLY495 3.2 30.3 1.0
CA B:ILE494 3.3 28.0 1.0
O B:GLY493 3.3 32.7 1.0
C B:FYB702 3.4 38.9 1.0
O B:ILE494 3.6 35.9 1.0
CA B:GLY493 3.7 23.6 1.0
CE B:MET285 3.7 38.0 1.0
CA B:GLY495 4.0 28.9 1.0
O B:FYB702 4.3 37.7 1.0
CB B:MET285 4.3 35.6 1.0
O B:LEU439 4.4 37.8 1.0
SD B:MET285 4.5 38.7 1.0
C6 B:FYB702 4.6 34.4 1.0
O B:ILE286 4.7 31.8 1.0
CB B:ILE494 4.8 29.5 1.0
N B:GLY493 4.9 31.6 1.0
N B:ASN441 5.0 31.6 1.0

Fluorine binding site 6 out of 6 in 6o3f

Go back to Fluorine Binding Sites List in 6o3f
Fluorine binding site 6 out of 6 in the Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with 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 Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F702

b:42.4
occ:1.00
 F1 B:FYB702 0.0 42.4 1.0
C3 B:FYB702 1.4 42.2 1.0
F B:FYB702 2.2 40.9 1.0
C4 B:FYB702 2.3 37.4 1.0
C2 B:FYB702 2.3 37.3 1.0
CE B:MET285 3.1 38.0 1.0
CB B:LYS724 3.1 29.7 1.0
C B:LYS724 3.2 33.0 1.0
O B:LYS724 3.3 29.9 1.0
OXT B:LYS724 3.4 31.6 1.0
CA B:GLY493 3.6 23.6 1.0
C1 B:FYB702 3.6 37.1 1.0
C5 B:FYB702 3.7 37.0 1.0
C B:GLY493 3.7 31.5 1.0
CA B:LYS724 3.8 33.7 1.0
O B:GLY493 3.9 32.7 1.0
O B:HOH831 4.1 38.1 1.0
C B:FYB702 4.1 38.9 1.0
CB B:ASN441 4.2 29.7 1.0
N B:ILE494 4.3 29.9 1.0
O B:FYB702 4.3 37.7 1.0
SD B:MET285 4.4 38.7 1.0
CG B:LYS724 4.4 29.2 1.0
N B:GLY493 4.4 31.6 1.0
N B:ASN441 4.8 31.6 1.0
N B:LYS724 4.8 33.5 1.0
NH2 B:ARG271 4.9 34.0 1.0
OE2 B:GLU287 5.0 36.8 1.0
O B:ASN441 5.0 33.2 1.0

Reference:

D.M.Dranow, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Lysyl-Trna Synthetase From Chlamydia Trachomatis with Complexed with L-Lysine and A Difluoro Cyclohexyl Chromone Ligand To Be Published.
Page generated: Tue Jul 15 13:56:27 2025

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