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Fluorine in PDB 4wx2: Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site

Enzymatic activity of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site

All present enzymatic activity of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site, PDB code: 4wx2 was solved by E.Hilario, B.G.Caulkins, R.P.Young, D.Niks, M.F.Dunn, L.J.Mueller, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.95 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.809, 58.890, 67.270, 90.00, 95.21, 90.00
R / Rfree (%) 15.8 / 18.9

Other elements in 4wx2:

The structure of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site (pdb code 4wx2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site, PDB code: 4wx2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4wx2

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Fluorine binding site 1 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


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 Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:31.5
occ:0.85
 F9 A:F6F301 0.0 31.5 0.8
C8 A:F6F301 1.3 35.4 0.8
O7 A:F6F301 2.2 30.1 0.8
F11 A:F6F301 2.2 36.6 0.8
F10 A:F6F301 2.2 34.7 0.8
CB A:ALA59 3.1 34.7 1.0
O A:ALA129 3.2 19.3 1.0
CB B:PRO18 3.4 20.9 1.0
C1 A:F6F301 3.5 28.3 0.8
CB A:ALA129 3.6 18.4 1.0
O A:HOH437 3.7 18.0 1.0
CG B:PRO18 3.8 21.7 1.0
O B:HOH626 3.8 29.0 0.5
C A:ALA129 3.8 17.9 1.0
O B:HOH626 3.9 10.8 0.5
CA A:ALA129 3.9 17.9 1.0
C6 A:F6F302 4.1 43.5 0.8
C5 A:F6F302 4.2 46.8 0.8
C6 A:F6F301 4.2 26.3 0.8
CA B:PRO18 4.4 19.7 1.0
C2 A:F6F301 4.5 26.4 0.8
CA A:ALA59 4.6 34.5 1.0
O A:ALA59 4.9 36.1 1.0
N A:ASP130 5.0 17.2 1.0

Fluorine binding site 2 out of 9 in 4wx2

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Fluorine binding site 2 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


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 Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:34.7
occ:0.85
 F10 A:F6F301 0.0 34.7 0.8
C8 A:F6F301 1.4 35.4 0.8
F11 A:F6F301 2.2 36.6 0.8
F9 A:F6F301 2.2 31.5 0.8
O7 A:F6F301 2.3 30.1 0.8
C6 A:F6F301 3.0 26.3 0.8
C1 A:F6F301 3.0 28.3 0.8
CA A:ALA129 3.4 17.9 1.0
CG1 A:ILE153 3.5 25.3 1.0
O A:HOH437 3.5 18.0 1.0
CB A:ALA129 3.6 18.4 1.0
O A:ALA129 3.7 19.3 1.0
CD2 A:LEU127 3.7 21.2 1.0
CD1 A:ILE153 4.0 26.9 0.8
C A:ALA129 4.0 17.9 1.0
C5 A:F6F301 4.3 26.2 0.8
C2 A:F6F301 4.4 26.4 0.8
CD2 A:LEU100 4.5 24.4 1.0
O B:HOH626 4.5 10.8 0.5
CD1 A:LEU127 4.5 22.2 1.0
O B:HOH626 4.6 29.0 0.5
N A:ALA129 4.6 17.5 1.0
CG A:LEU127 4.7 21.5 1.0
O A:HOH440 4.8 20.1 1.0
CB A:ILE153 4.8 23.6 1.0
CB A:ALA59 4.9 34.7 1.0

Fluorine binding site 3 out of 9 in 4wx2

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Fluorine binding site 3 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


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 Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:36.6
occ:0.85
 F11 A:F6F301 0.0 36.6 0.8
C8 A:F6F301 1.3 35.4 0.8
F10 A:F6F301 2.2 34.7 0.8
F9 A:F6F301 2.2 31.5 0.8
O7 A:F6F301 2.2 30.1 0.8
O B:HOH626 2.7 29.0 0.5
C1 A:F6F301 2.8 28.3 0.8
C6 A:F6F301 3.1 26.3 0.8
CZ A:PHE212 3.6 33.3 0.7
O B:HOH626 3.7 10.8 0.5
CG1 A:ILE153 3.8 25.3 1.0
C2 A:F6F301 3.8 26.4 0.8
C5 A:F6F302 3.9 46.8 0.8
CD1 A:ILE153 3.9 26.9 0.8
C5 A:F6F301 4.2 26.2 0.8
C6 A:F6F302 4.3 43.5 0.8
CE1 A:PHE212 4.3 31.1 0.7
O A:HOH437 4.3 18.0 1.0
O14 A:F6F302 4.4 54.6 0.8
CB A:ALA59 4.5 34.7 1.0
CE2 A:PHE212 4.5 34.0 0.7
C3 A:F6F301 4.8 28.1 0.8
CB A:ILE153 4.9 23.6 1.0
CG2 A:ILE153 4.9 26.5 1.0
C4 A:F6F301 5.0 26.1 0.8
O A:ALA59 5.0 36.1 1.0

Fluorine binding site 4 out of 9 in 4wx2

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Fluorine binding site 4 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


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 Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:44.5
occ:0.80
 F9 A:F6F302 0.0 44.5 0.8
C8 A:F6F302 1.3 48.1 0.8
F11 A:F6F302 2.1 48.0 0.8
F10 A:F6F302 2.2 51.2 0.8
O7 A:F6F302 2.3 48.0 0.8
C1 A:F6F302 2.8 46.6 0.8
CG A:LEU58 3.0 42.6 1.0
CD1 A:LEU58 3.4 46.4 1.0
CA A:ALA59 3.4 34.5 1.0
C6 A:F6F302 3.4 43.5 0.8
CD2 A:LEU58 3.5 42.3 1.0
O A:LEU58 3.5 32.9 1.0
CG B:PRO18 3.5 21.7 1.0
C2 A:F6F302 3.5 47.1 0.8
C A:LEU58 3.7 35.5 1.0
N A:ALA59 3.7 32.9 1.0
CB A:ALA59 3.8 34.7 1.0
CD B:PRO18 4.2 20.2 1.0
CB A:LEU58 4.2 37.4 1.0
CB B:PRO18 4.3 20.9 1.0
C5 A:F6F302 4.5 46.8 0.8
C3 A:F6F302 4.6 51.0 0.8
CA A:LEU58 4.6 36.0 1.0
C A:ALA59 4.7 35.5 1.0
CG B:ARG175 4.7 35.3 1.0
O A:HOH602 4.8 46.2 0.7
CD1 B:LEU21 4.9 26.8 1.0
C4 A:F6F302 5.0 50.8 0.8

Fluorine binding site 5 out of 9 in 4wx2

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Fluorine binding site 5 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


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 Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:51.2
occ:0.80
 F10 A:F6F302 0.0 51.2 0.8
C8 A:F6F302 1.3 48.1 0.8
F11 A:F6F302 2.1 48.0 0.8
F9 A:F6F302 2.2 44.5 0.8
O7 A:F6F302 2.2 48.0 0.8
CD1 B:LEU21 2.8 26.8 1.0
CG B:LEU21 3.4 24.5 1.0
C1 A:F6F302 3.4 46.6 0.8
CG B:PRO18 3.7 21.7 1.0
CD B:PRO18 3.8 20.2 1.0
CD2 A:LEU58 4.0 42.3 1.0
CB B:PRO18 4.1 20.9 1.0
CB B:SER178 4.1 27.8 1.0
CG A:LEU58 4.2 42.6 1.0
C6 A:F6F302 4.3 43.5 0.8
C2 A:F6F302 4.3 47.1 0.8
CB B:LEU21 4.3 22.6 1.0
O B:LEU174 4.3 27.4 1.0
CD1 A:LEU58 4.4 46.4 1.0
CD2 B:LEU21 4.5 24.6 1.0
OG B:SER178 4.6 28.9 1.0
C B:LEU174 4.7 26.2 1.0
N B:PRO18 4.8 19.3 1.0
CB B:LEU174 4.8 26.4 1.0
CG1 B:ILE20 4.8 25.1 1.0
CD1 B:ILE20 4.9 27.4 0.7

Fluorine binding site 6 out of 9 in 4wx2

Go back to Fluorine Binding Sites List in 4wx2
Fluorine binding site 6 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:48.0
occ:0.80
 F11 A:F6F302 0.0 48.0 0.8
C8 A:F6F302 1.3 48.1 0.8
F9 A:F6F302 2.1 44.5 0.8
F10 A:F6F302 2.1 51.2 0.8
O7 A:F6F302 2.2 48.0 0.8
C1 A:F6F302 2.9 46.6 0.8
C2 A:F6F302 3.0 47.1 0.8
CA B:ARG175 3.3 29.9 1.0
N B:ARG175 3.6 28.6 1.0
O B:LEU174 3.6 27.4 1.0
CG B:ARG175 3.7 35.3 1.0
OG B:SER178 3.7 28.9 1.0
C B:LEU174 3.8 26.2 1.0
CD1 A:LEU58 3.8 46.4 1.0
CB B:SER178 3.9 27.8 1.0
CB B:ARG175 4.0 33.0 1.0
C6 A:F6F302 4.1 43.5 0.8
CG A:LEU58 4.2 42.6 1.0
O A:LEU58 4.3 32.9 1.0
C3 A:F6F302 4.3 51.0 0.8
C B:ARG175 4.3 30.0 1.0
CD1 B:LEU21 4.4 26.8 1.0
O B:ARG175 4.5 26.4 1.0
CD2 A:LEU58 4.6 42.3 1.0
CB B:LEU174 4.6 26.4 1.0
O A:HOH602 4.8 46.2 0.7
CG B:LEU21 4.9 24.5 1.0
CA B:LEU174 4.9 26.4 1.0
C A:LEU58 5.0 35.5 1.0

Fluorine binding site 7 out of 9 in 4wx2

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Fluorine binding site 7 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:26.2
occ:0.95
 F9 B:F6F404 0.0 26.2 0.9
C8 B:F6F404 1.3 26.8 0.9
F10 B:F6F404 2.1 27.9 0.9
O7 B:F6F404 2.2 25.1 0.9
F11 B:F6F404 2.2 25.6 0.9
O B:PHE280 2.9 18.7 1.0
C B:PHE280 3.2 18.1 1.0
CA B:PHE280 3.4 19.8 1.0
C1 B:F6F404 3.5 25.1 0.9
CD B:PRO194 3.6 15.6 1.0
CD1 B:LEU174 3.7 29.7 1.0
CB B:PHE280 3.8 20.9 1.0
N B:GLY281 4.0 16.4 1.0
CA B:GLY193 4.0 14.4 1.0
O B:HOH894 4.1 32.6 0.5
C2 B:F6F404 4.2 23.7 0.9
C6 B:F6F404 4.4 24.5 0.9
O B:HOH879 4.6 46.1 1.0
N B:PRO194 4.6 15.6 1.0
CA B:GLY281 4.6 15.7 1.0
CG B:LEU174 4.6 27.5 1.0
CD1 B:PHE280 4.7 23.5 1.0
CD1 B:LEU188 4.7 20.7 1.0
CG B:PRO194 4.7 15.3 1.0
CD2 B:LEU174 4.8 28.4 1.0
N B:PHE280 4.8 18.6 1.0
CG B:PHE280 4.8 22.1 1.0
C B:GLY193 4.9 15.2 1.0

Fluorine binding site 8 out of 9 in 4wx2

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Fluorine binding site 8 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:27.9
occ:0.95
 F10 B:F6F404 0.0 27.9 0.9
C8 B:F6F404 1.3 26.8 0.9
F11 B:F6F404 2.1 25.6 0.9
F9 B:F6F404 2.1 26.2 0.9
O7 B:F6F404 2.2 25.1 0.9
C1 B:F6F404 2.8 25.1 0.9
C2 B:F6F404 3.1 23.7 0.9
O B:HOH894 3.3 32.6 0.5
CB B:CYS170 3.5 31.2 1.0
CD1 B:PHE280 3.6 23.5 1.0
C6 B:F6F404 3.9 24.5 0.9
SG B:CYS170 3.9 32.7 1.0
CD1 B:LEU174 4.0 29.7 1.0
CA B:PHE280 4.0 19.8 1.0
CB B:PHE280 4.0 20.9 1.0
CG B:PHE280 4.3 22.1 1.0
C3 B:F6F404 4.4 25.7 0.9
O B:PHE280 4.4 18.7 1.0
C B:PHE280 4.5 18.1 1.0
CA B:CYS170 4.5 29.6 1.0
CE1 B:PHE280 4.6 24.2 1.0
OH B:TYR186 4.7 22.2 1.0
CG B:LEU174 4.7 27.5 1.0
C B:CYS170 4.7 29.7 1.0
O B:CYS170 4.8 28.1 1.0
O B:HOH879 4.9 46.1 1.0
C5 B:F6F404 4.9 26.4 0.9

Fluorine binding site 9 out of 9 in 4wx2

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Fluorine binding site 9 out of 9 in the Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Tryptophan Synthase From Salmonella Typhimurium in Complex with Two F6F Molecules in the Alpha-Site and One F6F Molecule in the Beta-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:25.6
occ:0.95
 F11 B:F6F404 0.0 25.6 0.9
C8 B:F6F404 1.3 26.8 0.9
F10 B:F6F404 2.1 27.9 0.9
F9 B:F6F404 2.2 26.2 0.9
O7 B:F6F404 2.2 25.1 0.9
C1 B:F6F404 2.9 25.1 0.9
C2 B:F6F404 2.9 23.7 0.9
OH B:TYR186 3.3 22.2 1.0
CE2 B:TYR186 3.5 20.1 1.0
CD1 B:LEU188 3.7 20.7 1.0
CD1 B:LEU174 3.8 29.7 1.0
CZ B:TYR186 3.9 19.9 1.0
CG B:LEU174 4.0 27.5 1.0
CG B:LEU188 4.0 19.2 1.0
CD2 B:LEU174 4.1 28.4 1.0
C6 B:F6F404 4.2 24.5 0.9
C3 B:F6F404 4.2 25.7 0.9
CB B:CYS170 4.5 31.2 1.0
CD B:PRO194 4.7 15.6 1.0
CD2 B:TYR186 4.7 18.4 1.0
CD2 B:LEU188 4.8 20.4 1.0
SG B:CYS170 4.9 32.7 1.0
O B:HOH894 4.9 32.6 0.5
O B:CYS170 4.9 28.1 1.0
O B:PHE280 4.9 18.7 1.0
CA B:GLY193 5.0 14.4 1.0

Reference:

E.Hilario, B.G.Caulkins, Y.M.Huang, W.You, C.E.Chang, L.J.Mueller, M.F.Dunn, L.Fan. Visualizing the Tunnel in Tryptophan Synthase with Crystallography: Insights Into A Selective Filter For Accommodating Indole and Rejecting Water. Biochim.Biophys.Acta V.1864 268 2016.
ISSN: ISSN 0006-3002
PubMed: 26708480
DOI: 10.1016/J.BBAPAP.2015.12.006
Page generated: Thu Aug 1 06:35:26 2024

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