Fluorine in PDB 8pf8: Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72:
1.1.1.35;

The structure of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72, PDB code: 8pf8 was solved by S.Dalwani, R.K.Wierenga, R.Venkatesan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	112.42 / 2.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	250.961, 134.614, 119.974, 90, 110.44, 90
R / Rfree (%)	18.6 / 22.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Fluorine atom in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 (pdb code 8pf8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 54 binding sites of Fluorine where determined in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72, PDB code: 8pf8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:80.3 occ:1.00 F1 A:YMK806 0.0 80.3 1.0 C4 A:YMK806 1.3 92.9 1.0 F3 A:YMK806 2.1 70.9 1.0 F2 A:YMK806 2.1 98.4 1.0 C1 A:YMK806 2.3 99.7 1.0 NE A:ARG175 3.1 84.5 1.0 N2 A:YMK806 3.2 102.4 1.0 CD A:ARG175 3.2 60.1 1.0 C2 A:YMK806 3.3 85.2 1.0 CZ A:ARG175 3.4 97.8 1.0 NH1 A:ARG175 3.8 98.3 1.0 CB A:PRO140 4.0 46.5 1.0 CG A:ARG175 4.0 52.8 1.0 NH2 A:ARG175 4.1 89.8 1.0 CG A:PRO140 4.2 48.6 1.0 N1 A:YMK806 4.3 98.5 1.0 O A:JXL809 4.3 110.5 1.0 C3 A:YMK806 4.4 93.6 1.0 CD1 A:LEU114 4.8 49.2 1.0

Fluorine binding site 2 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:98.4 occ:1.00 F2 A:YMK806 0.0 98.4 1.0 C4 A:YMK806 1.3 92.9 1.0 F3 A:YMK806 2.1 70.9 1.0 F1 A:YMK806 2.1 80.3 1.0 C1 A:YMK806 2.3 99.7 1.0 O A:JXL809 2.7 110.5 1.0 N2 A:YMK806 2.7 102.4 1.0 CZ A:PHE303 3.5 75.7 1.0 C2 A:YMK806 3.6 85.2 1.0 B A:JXL809 3.8 93.5 1.0 CE1 A:PHE303 4.0 73.9 1.0 N1 A:YMK806 4.0 98.5 1.0 C1 A:JXL809 4.2 85.9 1.0 CE2 A:PHE303 4.3 77.5 1.0 C A:JXL809 4.4 91.2 1.0 C3 A:YMK806 4.5 93.6 1.0 NE A:ARG175 4.8 84.5 1.0 CZ A:ARG175 4.8 97.8 1.0 O1 A:JXL809 4.8 81.7 1.0 CD1 A:LEU114 4.9 49.2 1.0 NH2 A:ARG175 4.9 89.8 1.0

Fluorine binding site 3 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:70.9 occ:1.00 F3 A:YMK806 0.0 70.9 1.0 C4 A:YMK806 1.3 92.9 1.0 F2 A:YMK806 2.1 98.4 1.0 F1 A:YMK806 2.1 80.3 1.0 C1 A:YMK806 2.3 99.7 1.0 C2 A:YMK806 2.9 85.2 1.0 N2 A:YMK806 3.5 102.4 1.0 C1 A:JXL809 3.8 85.9 1.0 CB A:PRO140 3.8 46.5 1.0 CG A:PRO140 3.9 48.6 1.0 O A:JXL809 4.0 110.5 1.0 CZ A:PHE303 4.0 75.7 1.0 C3 A:YMK806 4.2 93.6 1.0 OG1 A:THR143 4.2 42.5 1.0 F2 A:JXL809 4.2 84.6 1.0 CE2 A:PHE303 4.4 77.5 1.0 N1 A:YMK806 4.4 98.5 1.0 CE1 A:PHE303 4.5 73.9 1.0 C A:JXL809 4.6 91.2 1.0 C2 A:JXL809 4.7 102.2 1.0 B A:JXL809 4.7 93.5 1.0 O A:PRO140 4.8 43.0 1.0

Fluorine binding site 4 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:76.6 occ:1.00 F4 A:YMK806 0.0 76.6 1.0 C9 A:YMK806 1.3 72.0 1.0 F6 A:YMK806 2.1 79.8 1.0 F5 A:YMK806 2.1 75.6 1.0 C6 A:YMK806 2.3 76.2 1.0 C7 A:YMK806 2.9 84.5 1.0 CD1 A:ILE664 3.4 48.7 1.0 CE A:MET668 3.5 53.0 1.0 N4 A:YMK806 3.5 76.5 1.0 CD2 A:LEU307 3.8 45.5 1.0 C8 A:YMK806 4.2 94.0 1.0 CB A:LEU307 4.4 47.8 1.0 CG A:LEU307 4.4 47.2 1.0 CG2 A:ILE664 4.4 48.4 1.0 CD1 A:LEU307 4.4 43.9 1.0 N3 A:YMK806 4.4 83.0 1.0 SD A:MET668 4.6 60.1 1.0 CG1 A:ILE664 4.6 48.2 1.0 CG A:MET668 4.7 46.0 1.0 O A:ALA302 4.8 58.4 1.0

Fluorine binding site 5 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:75.6 occ:1.00 F5 A:YMK806 0.0 75.6 1.0 C9 A:YMK806 1.3 72.0 1.0 F6 A:YMK806 2.1 79.8 1.0 F4 A:YMK806 2.1 76.6 1.0 C6 A:YMK806 2.3 76.2 1.0 N4 A:YMK806 3.1 76.5 1.0 C7 A:YMK806 3.3 84.5 1.0 CD1 A:ILE667 3.6 47.9 1.0 CD1 A:ILE664 3.8 48.7 1.0 CB A:ALA302 3.9 41.9 1.0 CG2 A:ILE667 4.0 47.7 1.0 N3 A:YMK806 4.2 83.0 1.0 C8 A:YMK806 4.4 94.0 1.0 CB A:ILE667 4.5 50.7 1.0 CG1 A:ILE667 4.6 44.7 1.0 C A:ALA302 4.8 49.2 1.0 O A:ALA302 4.9 58.4 1.0 CA A:ALA302 5.0 48.8 1.0

Fluorine binding site 6 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F806 b:79.8 occ:1.00 F6 A:YMK806 0.0 79.8 1.0 C9 A:YMK806 1.3 72.0 1.0 F4 A:YMK806 2.1 76.6 1.0 F5 A:YMK806 2.1 75.6 1.0 C6 A:YMK806 2.3 76.2 1.0 N4 A:YMK806 2.7 76.5 1.0 O A:ALA302 3.1 58.4 1.0 C A:ALA302 3.1 49.2 1.0 N A:PHE303 3.3 52.9 1.0 CD1 A:ILE664 3.3 48.7 1.0 CA A:PHE303 3.4 56.8 1.0 CB A:ALA302 3.4 41.9 1.0 C7 A:YMK806 3.6 84.5 1.0 CA A:ALA302 3.9 48.8 1.0 CB A:PHE303 3.9 49.0 1.0 N3 A:YMK806 4.0 83.0 1.0 CB A:LEU307 4.0 47.8 1.0 CD2 A:LEU307 4.2 45.5 1.0 C8 A:YMK806 4.5 94.0 1.0 CD1 A:PHE303 4.5 68.5 1.0 CG A:LEU307 4.7 47.2 1.0 C A:PHE303 4.7 57.5 1.0 CG A:PHE303 4.8 58.8 1.0 CG1 A:ILE664 4.8 48.2 1.0

Fluorine binding site 7 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:64.0 occ:1.00 F1 A:YLZ807 0.0 64.0 1.0 C4 A:YLZ807 1.3 63.3 1.0 F3 A:YLZ807 2.1 69.8 1.0 F2 A:YLZ807 2.1 66.0 1.0 C1 A:YLZ807 2.3 74.1 1.0 F2 A:JXL810 2.4 70.4 1.0 C2 A:YLZ807 3.1 80.9 1.0 N2 A:YLZ807 3.3 72.3 1.0 CG A:GLN172 3.5 53.5 1.0 C4 A:JXL810 3.7 75.8 1.0 CD A:GLN172 3.8 55.6 1.0 N A:JXL810 4.0 78.8 1.0 OE1 A:GLN172 4.0 64.0 1.0 F A:JXL810 4.1 74.9 1.0 CB A:GLN252 4.3 49.6 1.0 C3 A:YLZ807 4.3 78.7 1.0 CB A:ALA171 4.3 46.5 1.0 N1 A:YLZ807 4.3 74.8 1.0 C2 A:JXL810 4.3 89.8 1.0 F1 A:JXL810 4.5 74.7 1.0 NE2 A:GLN172 4.5 52.9 1.0 CG A:GLN252 4.7 59.5 1.0 O A:ALA171 4.7 53.4 1.0 CD1 A:LEU249 4.8 49.4 1.0 C A:ALA171 4.8 50.8 1.0 CB A:GLN172 4.9 46.4 1.0 CD2 A:LEU253 5.0 54.5 1.0 OE1 A:GLN252 5.0 81.8 1.0

Fluorine binding site 8 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:66.0 occ:1.00 F2 A:YLZ807 0.0 66.0 1.0 C4 A:YLZ807 1.3 63.3 1.0 F3 A:YLZ807 2.1 69.8 1.0 F1 A:YLZ807 2.1 64.0 1.0 C1 A:YLZ807 2.3 74.1 1.0 N2 A:YLZ807 2.7 72.3 1.0 O A:ALA171 3.4 53.4 1.0 F2 A:JXL810 3.6 70.4 1.0 C2 A:YLZ807 3.7 80.9 1.0 CD2 A:LEU253 3.9 54.5 1.0 C A:ALA171 4.0 50.8 1.0 CD1 A:LEU249 4.0 49.4 1.0 CB A:ALA171 4.0 46.5 1.0 N1 A:YLZ807 4.0 74.8 1.0 CG A:GLN172 4.1 53.5 1.0 CG A:PRO261 4.1 37.6 1.0 CB A:PRO261 4.2 38.5 1.0 CA A:ALA171 4.5 40.2 1.0 C3 A:YLZ807 4.5 78.7 1.0 CG A:LEU253 4.7 52.1 1.0 N A:GLN172 4.7 44.9 1.0 C4 A:JXL810 4.9 75.8 1.0 CD A:GLN172 5.0 55.6 1.0

Fluorine binding site 9 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:69.8 occ:1.00 F3 A:YLZ807 0.0 69.8 1.0 C4 A:YLZ807 1.3 63.3 1.0 F2 A:YLZ807 2.1 66.0 1.0 F1 A:YLZ807 2.1 64.0 1.0 C1 A:YLZ807 2.3 74.1 1.0 F2 A:JXL810 3.0 70.4 1.0 C2 A:YLZ807 3.1 80.9 1.0 CD2 A:LEU253 3.2 54.5 1.0 CB A:GLN252 3.3 49.6 1.0 N2 A:YLZ807 3.4 72.3 1.0 CD1 A:LEU249 3.5 49.4 1.0 CG A:LEU253 3.6 52.1 1.0 N A:LEU253 4.2 49.2 1.0 CG A:GLN252 4.2 59.5 1.0 C3 A:YLZ807 4.3 78.7 1.0 C4 A:JXL810 4.3 75.8 1.0 C A:GLN252 4.3 51.1 1.0 O A:LEU249 4.3 46.3 1.0 N1 A:YLZ807 4.4 74.8 1.0 CA A:GLN252 4.5 46.8 1.0 CD1 A:LEU253 4.5 49.5 1.0 F1 A:JXL810 4.5 74.7 1.0 CB A:LEU253 4.8 46.1 1.0 CG A:LEU249 4.8 48.2 1.0 CA A:LEU253 4.8 47.3 1.0 O A:GLN252 4.9 59.7 1.0 F A:JXL810 5.0 74.9 1.0

Fluorine binding site 10 out of 54 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-72 within 5.0Å range: probe atom residue distance (Å) B Occ A:F808 b:68.6 occ:1.00 F1 A:YLZ808 0.0 68.6 1.0 C4 A:YLZ808 1.3 65.3 1.0 F3 A:YLZ808 2.1 63.2 1.0 F2 A:YLZ808 2.1 65.6 1.0 C1 A:YLZ808 2.3 62.5 1.0 N2 A:YLZ808 3.0 63.5 1.0 C2 A:YLZ808 3.4 68.6 1.0 F4 A:YLN812 3.5 51.8 1.0 CG A:MET73 3.6 55.4 1.0 CG2 A:VAL84 4.0 33.8 1.0 CA A:MET73 4.1 50.2 1.0 CG2 A:THR72 4.1 65.0 1.0 N1 A:YLZ808 4.1 64.4 1.0 CG1 A:VAL84 4.2 35.6 1.0 F6 A:YLN812 4.2 61.4 1.0 CB A:MET73 4.3 55.7 1.0 CG1 A:VAL291 4.4 50.9 1.0 C3 A:YLZ808 4.4 64.3 1.0 N A:MET73 4.4 59.2 1.0 C9 A:YLN812 4.5 50.3 1.0 CB A:VAL84 4.5 38.4 1.0 C A:THR72 4.6 54.5 1.0 O A:THR72 4.7 49.7 1.0 CA A:VAL84 4.7 41.0 1.0 SD A:MET73 4.8 65.2 1.0 CB A:ALA76 4.9 47.5 1.0 CB A:THR72 5.0 59.1 1.0

S.Dalwani, A.Metz, F.U.Huschmann, M.S.Weiss, R.K.Wierenga, R.Venkatesan. Crystallographic Fragment Binding Studies of the Mycobacterium Tuberculosis Trifunctional Enzyme Suggest Binding Pockets For the Tails of the Acyl-Coa Substrates at Its Active Sites and A Potential Substrate Channeling Path Between Them Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.11.575214