Fluorine in PDB 7rud: Dahp Synthase Complex with Trifluoropyruvate Oxime

Enzymatic activity of Dahp Synthase Complex with Trifluoropyruvate Oxime

All present enzymatic activity of Dahp Synthase Complex with Trifluoropyruvate Oxime:
2.5.1.54;

Protein crystallography data

The structure of Dahp Synthase Complex with Trifluoropyruvate Oxime, PDB code: 7rud was solved by M.Heimhalt, P.Mukherjee, R.Grainger, R.Szabla, C.Brown, R.Turner, M.S.Junop, P.J.Berti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.55 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.789, 52.19, 149.8, 90, 115.82, 90
R / Rfree (%) 20 / 28.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dahp Synthase Complex with Trifluoropyruvate Oxime (pdb code 7rud). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Dahp Synthase Complex with Trifluoropyruvate Oxime, PDB code: 7rud:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 7rud

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Fluorine binding site 1 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.2
occ:0.81
 F1 B:7QE401 0.0 40.2 0.8
C3 B:7QE401 1.3 45.8 0.8
F3 B:7QE401 2.2 54.2 0.8
F2 B:7QE401 2.2 41.5 0.8
C2 B:7QE401 2.4 45.0 0.8
NH2 B:ARG234 3.0 43.1 1.0
C1 B:7QE401 3.1 43.5 0.8
CE B:LYS186 3.2 40.3 1.0
CD B:ARG234 3.3 37.6 1.0
N1 B:7QE401 3.3 49.4 0.8
ND1 B:HIS268 3.5 47.2 1.0
O1 B:7QE401 3.5 41.1 0.8
CD B:LYS186 3.6 38.9 1.0
CG B:HIS268 3.8 48.6 1.0
O3 B:7QE401 3.8 42.9 0.8
O2 B:7QE401 3.9 48.6 0.8
CZ B:ARG234 3.9 36.1 1.0
NE B:ARG234 4.0 32.3 1.0
CB B:HIS268 4.0 44.6 1.0
CE1 B:HIS268 4.0 49.2 1.0
CB B:ALA164 4.3 37.4 1.0
CB B:ARG234 4.3 41.7 1.0
CG B:ARG234 4.3 34.3 1.0
NZ B:LYS186 4.4 35.6 1.0
CD2 B:HIS268 4.4 46.8 1.0
NE2 B:HIS268 4.5 47.6 1.0
H31 B:7QE401 4.6 51.3 0.8
OD2 B:ASP265 4.6 46.0 1.0
CG B:LYS186 4.8 34.7 1.0
N B:ALA164 5.0 41.1 1.0

Fluorine binding site 2 out of 9 in 7rud

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Fluorine binding site 2 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:41.5
occ:0.81
 F2 B:7QE401 0.0 41.5 0.8
C3 B:7QE401 1.3 45.8 0.8
F3 B:7QE401 2.1 54.2 0.8
F1 B:7QE401 2.2 40.2 0.8
C2 B:7QE401 2.4 45.0 0.8
NH2 B:ARG234 2.8 43.1 1.0
O2 B:7QE401 2.8 48.6 0.8
C1 B:7QE401 2.8 43.5 0.8
N1 B:7QE401 3.6 49.4 0.8
O1 B:7QE401 3.8 41.1 0.8
NH2 B:ARG165 4.0 64.2 1.0
CZ B:ARG234 4.1 36.1 1.0
CB B:ALA164 4.3 37.4 1.0
O3 B:7QE401 4.3 42.9 0.8
NE B:ARG165 4.4 69.7 1.0
CD B:ARG234 4.5 37.6 1.0
CG B:HIS268 4.6 48.6 1.0
CZ B:ARG165 4.7 66.7 1.0
NE B:ARG234 4.8 32.3 1.0
CB B:HIS268 4.8 44.6 1.0
CD2 B:HIS268 4.8 46.8 1.0
ND1 B:HIS268 4.9 47.2 1.0
CE B:LYS186 5.0 40.3 1.0

Fluorine binding site 3 out of 9 in 7rud

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Fluorine binding site 3 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:54.2
occ:0.81
 F3 B:7QE401 0.0 54.2 0.8
C3 B:7QE401 1.3 45.8 0.8
F2 B:7QE401 2.1 41.5 0.8
F1 B:7QE401 2.2 40.2 0.8
C2 B:7QE401 2.4 45.0 0.8
CD2 B:HIS268 2.9 46.8 1.0
CG B:HIS268 2.9 48.6 1.0
O3 B:7QE401 2.9 42.9 0.8
N1 B:7QE401 3.0 49.4 0.8
NE2 B:HIS268 3.1 47.6 1.0
ND1 B:HIS268 3.1 47.2 1.0
CE1 B:HIS268 3.3 49.2 1.0
C1 B:7QE401 3.5 43.5 0.8
CB B:HIS268 3.6 44.6 1.0
H31 B:7QE401 3.8 51.3 0.8
O2 B:7QE401 4.0 48.6 0.8
NH2 B:ARG234 4.0 43.1 1.0
O1 B:7QE401 4.4 41.1 0.8
CE B:LYS186 4.7 40.3 1.0
OD2 B:ASP326 4.7 44.1 1.0
CA B:HIS268 4.9 47.1 1.0

Fluorine binding site 4 out of 9 in 7rud

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Fluorine binding site 4 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:62.3
occ:1.00
 F1 C:7QE401 0.0 62.3 1.0
C3 C:7QE401 1.3 63.9 1.0
F3 C:7QE401 2.1 61.2 1.0
F2 C:7QE401 2.1 64.2 1.0
C2 C:7QE401 2.4 60.1 1.0
C1 C:7QE401 2.7 55.5 1.0
NE C:ARG234 2.8 55.3 1.0
O1 C:7QE401 2.9 52.1 1.0
NH1 C:ARG234 3.4 54.1 1.0
O2 C:7QE401 3.4 52.4 1.0
CZ C:ARG234 3.5 51.8 1.0
N1 C:7QE401 3.7 57.9 1.0
CD C:ARG234 3.7 49.1 1.0
CB C:ALA164 3.8 43.3 1.0
NH2 C:ARG165 3.8 61.8 1.0
NZ C:LYS186 3.9 48.5 1.0
CD C:LYS186 4.0 44.7 1.0
CE C:LYS186 4.2 47.8 1.0
O3 C:7QE401 4.4 50.0 1.0
N C:ALA164 4.5 41.0 1.0
CG C:HIS268 4.5 51.9 1.0
CD2 C:HIS268 4.6 49.3 1.0
NH1 C:ARG165 4.6 73.1 1.0
CZ C:ARG165 4.6 65.6 1.0
H31 C:7QE401 4.7 59.8 1.0
CB C:HIS268 4.7 49.2 1.0
CA C:ALA164 4.8 41.9 1.0
NH2 C:ARG234 4.8 50.7 1.0
ND1 C:HIS268 4.9 48.6 1.0
CG C:ARG234 4.9 45.5 1.0

Fluorine binding site 5 out of 9 in 7rud

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Fluorine binding site 5 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:64.2
occ:1.00
 F2 C:7QE401 0.0 64.2 1.0
C3 C:7QE401 1.3 63.9 1.0
F1 C:7QE401 2.1 62.3 1.0
F3 C:7QE401 2.2 61.2 1.0
C2 C:7QE401 2.4 60.1 1.0
CD2 C:HIS268 2.8 49.3 1.0
N1 C:7QE401 3.1 57.9 1.0
O3 C:7QE401 3.2 50.0 1.0
CG C:HIS268 3.3 51.9 1.0
NE2 C:HIS268 3.3 47.4 1.0
C1 C:7QE401 3.4 55.5 1.0
H31 C:7QE401 3.7 59.8 1.0
O1 C:7QE401 3.7 52.1 1.0
CE1 C:HIS268 3.9 49.1 1.0
ND1 C:HIS268 3.9 48.6 1.0
CB C:HIS268 3.9 49.2 1.0
NH2 C:ARG165 4.2 61.8 1.0
O2 C:7QE401 4.4 52.4 1.0
NH1 C:ARG234 4.4 54.1 1.0
NH1 C:ARG165 4.5 73.1 1.0
NE C:ARG234 4.5 55.3 1.0
NZ C:LYS186 4.6 48.5 1.0
CZ C:ARG165 4.9 65.6 1.0
CZ C:ARG234 4.9 51.8 1.0
CE C:LYS186 5.0 47.8 1.0

Fluorine binding site 6 out of 9 in 7rud

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Fluorine binding site 6 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:61.2
occ:1.00
 F3 C:7QE401 0.0 61.2 1.0
C3 C:7QE401 1.3 63.9 1.0
F1 C:7QE401 2.1 62.3 1.0
F2 C:7QE401 2.2 64.2 1.0
C2 C:7QE401 2.4 60.1 1.0
NZ C:LYS186 2.4 48.5 1.0
CE C:LYS186 3.0 47.8 1.0
N1 C:7QE401 3.1 57.9 1.0
H31 C:7QE401 3.2 59.8 1.0
O3 C:7QE401 3.2 50.0 1.0
ND1 C:HIS268 3.3 48.6 1.0
C1 C:7QE401 3.3 55.5 1.0
CG C:HIS268 3.4 51.9 1.0
CE1 C:HIS268 3.4 49.1 1.0
CD2 C:HIS268 3.6 49.3 1.0
NE2 C:HIS268 3.6 47.4 1.0
CD C:LYS186 3.6 44.7 1.0
O2 C:7QE401 3.7 52.4 1.0
NE C:ARG234 3.7 55.3 1.0
OD2 C:ASP265 3.9 40.4 1.0
CB C:HIS268 4.1 49.2 1.0
O1 C:7QE401 4.2 52.1 1.0
CD C:ARG234 4.3 49.1 1.0
CE C:MET300 4.4 45.5 1.0
CZ C:ARG234 4.7 51.8 1.0
NH1 C:ARG234 4.7 54.1 1.0
CB C:ARG234 4.8 46.1 1.0
CG C:LYS186 4.9 42.4 1.0

Fluorine binding site 7 out of 9 in 7rud

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Fluorine binding site 7 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:51.3
occ:0.86
 F1 D:7QE401 0.0 51.3 0.9
C3 D:7QE401 1.3 60.0 0.9
F2 D:7QE401 2.2 67.0 0.9
F3 D:7QE401 2.2 57.0 0.9
C2 D:7QE401 2.4 58.9 0.9
C1 D:7QE401 2.7 55.4 0.9
O2 D:7QE401 3.1 50.2 0.9
CE1 D:HIS268 3.2 49.5 1.0
ND1 D:HIS268 3.2 49.2 1.0
CD D:LYS186 3.3 47.1 1.0
O1 D:7QE401 3.5 47.0 0.9
CG D:LYS186 3.6 44.7 1.0
N1 D:7QE401 3.6 58.9 0.9
NE2 D:HIS268 3.7 48.3 1.0
CG D:HIS268 3.7 51.5 1.0
NH2 D:ARG234 3.9 48.3 1.0
CD2 D:HIS268 4.0 47.0 1.0
O3 D:7QE401 4.1 49.9 0.9
H31 D:7QE401 4.2 59.7 0.9
OD2 D:ASP265 4.3 39.4 1.0
CD D:ARG234 4.3 54.4 1.0
CB D:HIS268 4.6 51.5 1.0
CB D:ARG234 4.6 45.5 1.0
CG D:ASP265 4.8 39.0 1.0
CB D:LYS186 4.9 42.5 1.0
CZ D:ARG234 4.9 49.7 1.0
CG D:ARG234 4.9 51.1 1.0

Fluorine binding site 8 out of 9 in 7rud

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Fluorine binding site 8 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:67.0
occ:0.86
 F2 D:7QE401 0.0 67.0 0.9
C3 D:7QE401 1.3 60.0 0.9
F3 D:7QE401 2.1 57.0 0.9
F1 D:7QE401 2.2 51.3 0.9
C2 D:7QE401 2.3 58.9 0.9
H31 D:7QE401 2.5 59.7 0.9
CD D:LYS186 2.7 47.1 1.0
O3 D:7QE401 2.8 49.9 0.9
N1 D:7QE401 2.9 58.9 0.9
CG D:LYS186 3.0 44.7 1.0
N D:ALA164 3.3 58.6 1.0
C1 D:7QE401 3.3 55.4 0.9
NH2 D:ARG234 3.5 48.3 1.0
CB D:ALA164 3.5 52.0 1.0
O2 D:7QE401 3.6 50.2 0.9
CB D:LYS186 3.7 42.5 1.0
CA D:ALA164 3.8 58.0 1.0
CD D:ARG234 4.0 54.4 1.0
C D:GLY163 4.1 51.1 1.0
CA D:GLY163 4.4 47.9 1.0
O1 D:7QE401 4.4 47.0 0.9
CZ D:ARG234 4.6 49.7 1.0
NE D:ARG234 4.8 50.3 1.0
O D:ILE162 5.0 51.0 1.0

Fluorine binding site 9 out of 9 in 7rud

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Fluorine binding site 9 out of 9 in the Dahp Synthase Complex with Trifluoropyruvate Oxime


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Dahp Synthase Complex with Trifluoropyruvate Oxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:57.0
occ:0.86
 F3 D:7QE401 0.0 57.0 0.9
C3 D:7QE401 1.3 60.0 0.9
F2 D:7QE401 2.1 67.0 0.9
F1 D:7QE401 2.2 51.3 0.9
C2 D:7QE401 2.4 58.9 0.9
O3 D:7QE401 2.8 49.9 0.9
NH2 D:ARG234 2.9 48.3 1.0
N1 D:7QE401 3.0 58.9 0.9
H31 D:7QE401 3.0 59.7 0.9
C1 D:7QE401 3.5 55.4 0.9
CD2 D:HIS268 3.7 47.0 1.0
CG D:HIS268 3.9 51.5 1.0
NE2 D:HIS268 3.9 48.3 1.0
O1 D:7QE401 4.0 47.0 0.9
ND1 D:HIS268 4.1 49.2 1.0
CE1 D:HIS268 4.2 49.5 1.0
CZ D:ARG234 4.2 49.7 1.0
O2 D:7QE401 4.3 50.2 0.9
CB D:ALA164 4.3 52.0 1.0
CB D:HIS268 4.4 51.5 1.0
NH1 D:ARG165 4.5 73.3 1.0
CD D:LYS186 4.6 47.1 1.0
CD D:ARG234 4.7 54.4 1.0
N D:ALA164 4.7 58.6 1.0
CG D:LYS186 4.8 44.7 1.0
NE D:ARG234 4.9 50.3 1.0

Reference:

M.Heimhalt, P.Mukherjee, R.A.Grainger, R.Szabla, C.Brown, R.Turner, M.S.Junop, P.J.Berti. An Inhibitor-in-Pieces Approach to Dahp Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
DOI: 10.1021/ACSINFECDIS.1C00462
Page generated: Fri Aug 2 12:33:46 2024

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