Fluorine in PDB 6dko: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid:
2.3.3.9;

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid, PDB code: 6dko was solved by I.V.Krieger, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 1.56
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.016, 79.016, 225.961, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.3

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid (pdb code 6dko). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid, PDB code: 6dko:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:F804 b:26.5 occ:1.00 F11 A:GXG804 0.0 26.5 1.0 C10 A:GXG804 1.3 23.0 1.0 C12 A:GXG804 2.4 25.4 1.0 C09 A:GXG804 2.4 23.1 1.0 C07 A:GXG804 2.8 23.7 1.0 OD1 A:ASP633 3.0 25.3 1.0 C06 A:GXG804 3.1 24.3 1.0 CD1 A:LEU461 3.2 25.6 1.0 C13 A:GXG804 3.6 24.8 1.0 C15 A:GXG804 3.6 25.3 1.0 CB A:ALA635 3.7 22.9 1.0 O08 A:GXG804 3.7 24.2 1.0 CG A:ASP633 3.8 25.1 1.0 CG2 A:THR636 3.8 27.9 1.0 C04 A:GXG804 4.1 24.6 1.0 OD2 A:ASP633 4.1 26.5 1.0 C14 A:GXG804 4.1 26.4 1.0 CB A:LEU461 4.2 24.9 1.0 CG A:LEU461 4.3 26.1 1.0 N A:THR636 4.3 21.7 1.0 C02 A:GXG804 4.4 23.8 1.0 O01 A:GXG804 4.5 22.4 1.0 CA A:ALA635 4.7 24.3 1.0 F16 A:GXG804 4.7 25.7 1.0 N A:ALA635 4.8 23.4 1.0 C A:ALA635 4.8 24.4 1.0 O A:HOH933 4.8 25.0 1.0 CB A:THR636 4.9 25.1 1.0 CB A:ASP633 4.9 26.7 1.0 N A:ASP633 5.0 24.7 1.0 CG2 A:THR517 5.0 28.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:F804 b:25.7 occ:1.00 F16 A:GXG804 0.0 25.7 1.0 C15 A:GXG804 1.3 25.3 1.0 C09 A:GXG804 2.4 23.1 1.0 C14 A:GXG804 2.4 26.4 1.0 C07 A:GXG804 2.8 23.7 1.0 O08 A:GXG804 3.0 24.2 1.0 CE A:MET515 3.5 20.9 1.0 CG1 A:VAL118 3.6 25.5 1.0 OD2 A:ASP633 3.6 26.5 1.0 C13 A:GXG804 3.6 24.8 1.0 C10 A:GXG804 3.6 23.0 1.0 C06 A:GXG804 3.9 24.3 1.0 CB A:VAL118 3.9 21.1 1.0 NH2 A:ARG339 4.0 23.3 1.0 C12 A:GXG804 4.1 25.4 1.0 CZ3 A:TRP541 4.4 25.2 1.0 CG2 A:VAL118 4.4 24.2 1.0 CE3 A:TRP541 4.4 22.1 1.0 CG A:ASP633 4.5 25.1 1.0 F11 A:GXG804 4.7 26.5 1.0 CG A:MET515 4.8 22.8 1.0 SD A:MET515 4.9 24.9 1.0

J.F.Ellenbarger, I.V.Krieger, H.L.Huang, S.Gomez-Coca, T.R.Ioerger, J.C.Sacchettini, S.E.Wheeler, K.R.Dunbar. Anion-Pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase By Phenyl-Diketo Acids. J Chem Inf Model V. 58 2085 2018.
ISSN: ESSN 1549-960X
PubMed: 30137983
DOI: 10.1021/ACS.JCIM.8B00417