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Fluorine in PDB 6dnp: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid, PDB code: 6dnp was solved by I.V.Krieger, J.C.Sacchettini, Tb Structural Genomics Consortium(Tbsgc), Mycobacterium Tuberculosis Structural Proteomics Project(Xmtb), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.62 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.737, 79.737, 227.288, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Other elements in 6dnp:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid (pdb code 6dnp). 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-F-3-Methyl-6-F-Phenyldiketoacid, PDB code: 6dnp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6dnp

Go back to Fluorine Binding Sites List in 6dnp
Fluorine binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-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-F-3-Methyl-6-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:31.5
occ:1.00
 F06 A:GZV803 0.0 31.5 1.0
C05 A:GZV803 1.3 31.4 1.0
C04 A:GZV803 2.4 29.9 1.0
C07 A:GZV803 2.4 28.8 1.0
C08 A:GZV803 2.9 29.2 1.0
C10 A:GZV803 3.1 27.7 1.0
CD1 A:LEU461 3.1 31.6 1.0
OD1 A:ASP633 3.2 29.5 1.0
C03 A:GZV803 3.6 30.6 1.0
C16 A:GZV803 3.6 32.7 1.0
CG A:ASP633 3.8 29.2 1.0
O09 A:GZV803 3.9 30.3 1.0
CG2 A:THR636 4.0 34.6 1.0
OD2 A:ASP633 4.1 29.6 1.0
C02 A:GZV803 4.1 32.8 1.0
C11 A:GZV803 4.1 29.6 1.0
CB A:ALA635 4.1 27.5 1.0
CG A:LEU461 4.3 27.5 1.0
CB A:LEU461 4.4 24.1 1.0
C13 A:GZV803 4.5 26.5 1.0
O15 A:GZV803 4.5 26.1 1.0
CB A:MET515 4.7 27.2 1.0
F17 A:GZV803 4.7 31.1 1.0
N A:THR636 4.8 29.3 1.0
CG A:MET515 4.8 28.1 1.0
CG2 A:THR517 4.8 33.4 1.0
CB A:ASP633 5.0 30.8 1.0

Fluorine binding site 2 out of 2 in 6dnp

Go back to Fluorine Binding Sites List in 6dnp
Fluorine binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-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-F-3-Methyl-6-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:31.1
occ:1.00
 F17 A:GZV803 0.0 31.1 1.0
C16 A:GZV803 1.3 32.7 1.0
C07 A:GZV803 2.4 28.8 1.0
C02 A:GZV803 2.4 32.8 1.0
C08 A:GZV803 2.8 29.2 1.0
C01 A:GZV803 2.8 37.8 1.0
O09 A:GZV803 2.8 30.3 1.0
OD2 A:ASP633 3.5 29.6 1.0
NH2 A:ARG339 3.5 25.1 1.0
CG1 A:VAL118 3.5 28.0 1.0
C05 A:GZV803 3.6 31.4 1.0
C03 A:GZV803 3.6 30.6 1.0
CE A:MET515 3.9 25.5 1.0
C10 A:GZV803 4.0 27.7 1.0
CB A:VAL118 4.0 30.3 1.0
C04 A:GZV803 4.1 29.9 1.0
CZ3 A:TRP541 4.3 27.6 1.0
CE3 A:TRP541 4.5 27.9 1.0
CZ A:ARG339 4.5 29.1 1.0
CG A:ASP633 4.5 29.2 1.0
CG2 A:VAL118 4.6 32.7 1.0
OD2 A:ASP271 4.6 27.0 1.0
F06 A:GZV803 4.7 31.5 1.0
CB A:SER275 4.8 30.0 1.0
NH1 A:ARG339 4.8 29.3 1.0
C11 A:GZV803 5.0 29.6 1.0

Reference:

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
Page generated: Tue Jul 15 10:50:18 2025

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