Fluorine in PDB 8oqq: Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79

Enzymatic activity of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79:
1.1.1.35;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79, PDB code: 8oqq 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) 50.27 / 2.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 250.339, 134.016, 119.745, 90, 110.53, 90
R / Rfree (%) 19.1 / 23

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79 (pdb code 8oqq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79, PDB code: 8oqq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8oqq

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Fluorine binding site 1 out of 4 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79


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-79 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F805

b:100.4
occ:1.00
 F A:VWE805 0.0 100.4 1.0
C2 A:VWE805 1.4 94.4 1.0
C1 A:VWE805 2.3 84.9 1.0
C3 A:VWE805 2.4 90.8 1.0
O4 A:VWE805 2.5 102.1 1.0
C6 A:VWE805 2.9 98.6 1.0
C A:VWE805 3.6 86.1 1.0
C4 A:VWE805 3.6 86.6 1.0
NH2 A:ARG175 3.7 60.7 1.0
O A:HOH924 4.0 60.5 1.0
O3 A:VWE805 4.1 108.0 1.0
C5 A:VWE805 4.1 80.8 1.0
O A:PHE303 4.1 57.4 1.0
CD2 A:LEU144 4.7 53.5 1.0
CG A:LEU144 4.9 48.0 1.0
CD1 A:LEU144 4.9 62.8 1.0
CD1 A:PHE304 5.0 73.5 1.0
CZ A:ARG175 5.0 66.0 1.0

Fluorine binding site 2 out of 4 in 8oqq

Go back to Fluorine Binding Sites List in 8oqq
Fluorine binding site 2 out of 4 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79


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-79 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F806

b:89.7
occ:1.00
 F A:VWE806 0.0 89.7 1.0
C2 A:VWE806 1.4 89.5 1.0
C1 A:VWE806 2.3 84.6 1.0
C3 A:VWE806 2.4 87.7 1.0
O3 A:VWE806 2.8 92.1 1.0
C6 A:VWE806 2.9 86.5 1.0
O A:LEU599 3.4 75.0 1.0
C A:VWE806 3.6 93.9 1.0
C4 A:VWE806 3.6 91.8 1.0
O4 A:VWE806 4.0 73.4 1.0
CA A:LYS600 4.0 63.7 1.0
C5 A:VWE806 4.1 105.0 1.0
C A:LEU599 4.3 76.8 1.0
O A:LYS600 4.4 82.9 1.0
N A:LYS600 4.6 73.1 1.0
C A:LYS600 4.6 66.9 1.0
CB A:LYS600 5.0 67.3 1.0

Fluorine binding site 3 out of 4 in 8oqq

Go back to Fluorine Binding Sites List in 8oqq
Fluorine binding site 3 out of 4 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79


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-79 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F808

b:97.4
occ:1.00
 F B:VWE808 0.0 97.4 1.0
C2 B:VWE808 1.4 90.5 1.0
C1 B:VWE808 2.3 75.7 1.0
C3 B:VWE808 2.4 96.0 1.0
O3 B:VWE808 2.7 91.9 1.0
C6 B:VWE808 2.9 96.7 1.0
C B:VWE808 3.6 95.4 1.0
C4 B:VWE808 3.6 104.5 1.0
O B:PHE303 3.8 50.2 1.0
NH2 B:ARG175 4.0 64.6 1.0
O4 B:VWE808 4.1 100.0 1.0
C5 B:VWE808 4.1 108.3 1.0
CD2 B:LEU144 4.5 41.0 1.0
C B:PHE303 4.9 34.3 1.0
CG B:LEU144 4.9 55.3 1.0
CD1 B:PHE304 5.0 57.2 1.0
CD1 B:LEU144 5.0 43.2 1.0

Fluorine binding site 4 out of 4 in 8oqq

Go back to Fluorine Binding Sites List in 8oqq
Fluorine binding site 4 out of 4 in the Structure of Mycobacterium Tuberculosis Beta-Oxidation Trifunctional Enzyme in Complex with Fragment-M-79


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-79 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:109.6
occ:1.00
 F B:VWE809 0.0 109.6 1.0
C2 B:VWE809 1.4 105.3 1.0
C1 B:VWE809 2.3 93.1 1.0
C3 B:VWE809 2.4 96.9 1.0
O3 B:VWE809 2.7 87.8 1.0
C6 B:VWE809 2.9 87.2 1.0
C B:VWE809 3.6 90.9 1.0
C4 B:VWE809 3.6 97.6 1.0
O B:LEU599 3.9 68.1 1.0
O4 B:VWE809 4.1 84.8 1.0
C5 B:VWE809 4.1 102.4 1.0
CA B:LYS600 4.3 69.7 1.0
O B:LYS600 4.3 79.2 1.0
C B:LYS600 4.7 67.2 1.0
C B:LEU599 4.7 73.7 1.0
N B:LYS600 4.9 74.8 1.0

Reference:

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
Page generated: Fri Aug 2 21:12:23 2024

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