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Fluorine in PDB 5tci: Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form

Enzymatic activity of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form

All present enzymatic activity of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form, PDB code: 5tci was solved by K.Michalska, N.Maltseva, R.Jedrzejczak, S.Wellington, P.P.Nag, S.L.Fisher, S.L.Schreiber, D.T.Hung, A.Joachimiak, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.955, 158.335, 166.631, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form (pdb code 5tci). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form, PDB code: 5tci:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 5tci

Go back to Fluorine Binding Sites List in 5tci
Fluorine binding site 1 out of 5 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form


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 Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:43.0
occ:0.90
 F21 B:79V501 0.0 43.0 0.9
C04 B:79V501 1.3 40.2 0.9
C05 B:79V501 2.4 40.6 0.9
C03 B:79V501 2.4 39.5 0.9
C07 B:79V501 2.9 42.3 0.9
C12 B:79V501 3.1 45.6 0.9
C06 B:79V501 3.6 39.1 0.9
CZ3 B:TRP191 3.7 43.3 0.9
C02 B:79V501 3.7 38.5 0.9
CG B:PRO208 3.9 37.9 1.0
CD1 B:LEU34 3.9 44.7 1.0
C08 B:79V501 4.0 42.9 0.9
CD1 B:ILE38 4.1 41.1 1.0
C01 B:79V501 4.2 38.8 0.9
CD B:PRO208 4.2 37.0 1.0
C11 B:79V501 4.3 47.1 0.9
CG1 B:VAL30 4.4 39.3 1.0
CE3 B:TRP191 4.4 44.0 0.9
CD2 B:LEU34 4.6 43.5 1.0
CH2 B:TRP191 4.6 42.6 0.9
CG B:LEU34 4.6 44.3 1.0
CG1 B:ILE38 4.7 39.9 1.0
CB B:LEU34 4.9 42.7 1.0
CE2 B:TYR200 4.9 43.1 0.9

Fluorine binding site 2 out of 5 in 5tci

Go back to Fluorine Binding Sites List in 5tci
Fluorine binding site 2 out of 5 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form


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 Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F501

b:37.0
occ:0.20
 F21 H:79V501 0.0 37.0 0.2
F21 H:79V501 0.4 47.6 0.8
C04 H:79V501 1.3 36.4 0.2
C04 H:79V501 1.6 46.1 0.8
C03 H:79V501 2.4 36.3 0.2
C05 H:79V501 2.4 36.3 0.2
C03 H:79V501 2.5 45.6 0.8
C05 H:79V501 2.8 46.6 0.8
C08 H:79V501 2.9 36.2 0.2
C07 H:79V501 2.9 36.1 0.2
C07 H:79V501 3.3 47.4 0.8
CD1 H:LEU34 3.5 46.3 1.0
C06 H:79V501 3.7 36.2 0.2
C02 H:79V501 3.7 36.3 0.2
CZ3 H:TRP191 3.7 45.4 0.8
CZ3 H:TRP191 3.7 32.5 0.2
C12 H:79V501 3.8 46.8 0.8
C02 H:79V501 3.9 45.8 0.8
CE3 H:TRP191 3.9 46.2 0.8
C08 H:79V501 4.0 49.8 0.8
C06 H:79V501 4.0 46.1 0.8
CD1 H:ILE38 4.1 43.8 1.0
CG H:PRO208 4.1 33.7 1.0
C09 H:79V501 4.2 36.1 0.2
C01 H:79V501 4.2 36.3 0.2
C12 H:79V501 4.2 35.8 0.2
CD2 H:LEU34 4.3 45.3 1.0
CE3 H:TRP191 4.4 33.4 0.2
CE2 H:TYR200 4.4 39.9 0.2
CG H:LEU34 4.5 45.7 1.0
C01 H:79V501 4.5 46.4 0.8
CD H:PRO208 4.5 33.0 1.0
CG1 H:VAL30 4.5 39.3 1.0
CD2 H:TYR200 4.5 39.7 0.2
CH2 H:TRP191 4.7 31.8 0.2
CD2 H:TYR200 4.8 44.0 0.8
CE2 H:TYR200 4.8 44.5 0.8
CG1 H:ILE38 4.9 42.5 1.0
C11 H:79V501 4.9 47.9 0.8
CB H:PHE188 4.9 59.1 0.8
CH2 H:TRP191 5.0 44.8 0.8
CB H:LEU34 5.0 44.3 1.0

Fluorine binding site 3 out of 5 in 5tci

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Fluorine binding site 3 out of 5 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form


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 Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F501

b:47.6
occ:0.80
 F21 H:79V501 0.0 47.6 0.8
F21 H:79V501 0.4 37.0 0.2
C04 H:79V501 1.1 36.4 0.2
C04 H:79V501 1.3 46.1 0.8
C05 H:79V501 2.0 36.3 0.2
C03 H:79V501 2.3 36.3 0.2
C03 H:79V501 2.4 45.6 0.8
C05 H:79V501 2.4 46.6 0.8
C07 H:79V501 2.6 36.1 0.2
C08 H:79V501 2.7 36.2 0.2
C07 H:79V501 2.9 47.4 0.8
C06 H:79V501 3.3 36.2 0.2
C12 H:79V501 3.5 46.8 0.8
C02 H:79V501 3.5 36.3 0.2
C06 H:79V501 3.7 46.1 0.8
C02 H:79V501 3.7 45.8 0.8
C08 H:79V501 3.7 49.8 0.8
CD1 H:LEU34 3.7 46.3 1.0
C12 H:79V501 3.8 35.8 0.2
CG H:PRO208 3.9 33.7 1.0
C01 H:79V501 3.9 36.3 0.2
C09 H:79V501 4.0 36.1 0.2
CZ3 H:TRP191 4.1 45.4 0.8
CZ3 H:TRP191 4.1 32.5 0.2
C01 H:79V501 4.2 46.4 0.8
CD H:PRO208 4.2 33.0 1.0
CD1 H:ILE38 4.2 43.8 1.0
CG1 H:VAL30 4.3 39.3 1.0
CE3 H:TRP191 4.3 46.2 0.8
CE2 H:TYR200 4.5 39.9 0.2
C11 H:79V501 4.6 47.9 0.8
CD2 H:TYR200 4.7 39.7 0.2
CD2 H:LEU34 4.7 45.3 1.0
C09 H:79V501 4.7 50.4 0.8
CG H:LEU34 4.7 45.7 1.0
CE3 H:TRP191 4.8 33.4 0.2
C11 H:79V501 4.8 35.8 0.2
CE2 H:TYR200 4.9 44.5 0.8
CD2 H:TYR200 4.9 44.0 0.8
CB H:PHE188 4.9 59.1 0.8
C10 H:79V501 4.9 36.0 0.2

Fluorine binding site 4 out of 5 in 5tci

Go back to Fluorine Binding Sites List in 5tci
Fluorine binding site 4 out of 5 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form


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 Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F501

b:46.7
occ:1.00
 F21 F:79V501 0.0 46.7 1.0
C04 F:79V501 1.3 43.8 1.0
C03 F:79V501 2.4 43.4 1.0
C05 F:79V501 2.4 43.0 1.0
C07 F:79V501 2.9 42.9 1.0
CD1 F:LEU34 3.1 48.5 1.0
C12 F:79V501 3.2 42.2 1.0
C02 F:79V501 3.7 42.5 1.0
C06 F:79V501 3.7 42.6 1.0
CD1 F:PHE188 3.8 43.1 1.0
C08 F:79V501 4.1 43.4 1.0
CG F:PRO208 4.1 40.5 1.0
CZ3 F:TRP191 4.1 42.4 1.0
C01 F:79V501 4.1 43.3 1.0
CE3 F:TRP191 4.2 42.1 1.0
CD F:PRO208 4.2 39.6 1.0
C11 F:79V501 4.4 43.1 1.0
CG1 F:VAL30 4.5 44.3 1.0
CG F:LEU34 4.5 48.7 1.0
CD1 F:ILE38 4.5 46.6 1.0
CE1 F:PHE188 4.6 44.5 1.0
CB F:PHE188 4.8 41.3 1.0
CG F:PHE188 4.8 42.4 1.0
CD2 F:TYR200 4.8 41.1 1.0
CE2 F:TYR200 4.9 41.2 1.0

Fluorine binding site 5 out of 5 in 5tci

Go back to Fluorine Binding Sites List in 5tci
Fluorine binding site 5 out of 5 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form


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 Tryptophan Synthase From M. Tuberculosis - BRD4592-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:42.3
occ:1.00
 F21 D:79V501 0.0 42.3 1.0
C04 D:79V501 1.3 40.0 1.0
C03 D:79V501 2.4 39.0 1.0
C05 D:79V501 2.4 39.3 1.0
C07 D:79V501 2.9 38.5 1.0
C08 D:79V501 3.1 38.8 1.0
CD1 D:LEU34 3.2 40.8 1.0
C06 D:79V501 3.7 38.6 1.0
C02 D:79V501 3.7 39.2 1.0
CD1 D:PHE188 3.7 37.3 1.0
C12 D:79V501 4.0 38.7 1.0
CZ3 D:TRP191 4.1 36.1 1.0
C01 D:79V501 4.2 38.7 1.0
CG D:PRO208 4.2 35.5 1.0
CD D:PRO208 4.3 34.8 1.0
CE3 D:TRP191 4.3 36.1 1.0
CE1 D:PHE188 4.3 38.7 1.0
C09 D:79V501 4.3 39.4 1.0
CG D:LEU34 4.5 40.7 1.0
CG1 D:VAL30 4.5 36.6 1.0
CD2 D:TYR200 4.7 37.5 1.0
CG D:PHE188 4.7 37.3 1.0
CE2 D:TYR200 4.8 37.9 1.0
CD1 D:ILE38 4.8 40.8 1.0
CB D:PHE188 4.9 36.7 1.0
C11 D:79V501 5.0 39.5 1.0

Reference:

S.Wellington, P.P.Nag, K.Michalska, S.E.Johnston, R.P.Jedrzejczak, V.K.Kaushik, A.E.Clatworthy, N.Siddiqi, P.Mccarren, B.Bajrami, N.I.Maltseva, S.Combs, S.L.Fisher, A.Joachimiak, S.L.Schreiber, D.T.Hung. A Small-Molecule Allosteric Inhibitor of Mycobacterium Tuberculosis Tryptophan Synthase. Nat. Chem. Biol. V. 13 943 2017.
ISSN: ESSN 1552-4469
PubMed: 28671682
DOI: 10.1038/NCHEMBIO.2420
Page generated: Thu Aug 1 15:10:06 2024

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