Fluorine in PDB 7rue: Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone

Enzymatic activity of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone

All present enzymatic activity of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone:
2.5.1.54;

Protein crystallography data

The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue 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) 50.21 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.281, 53.2, 150.79, 90, 116.01, 90
R / Rfree (%) 20.1 / 26.3

Other elements in 7rue:

The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone (pdb code 7rue). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7rue

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Fluorine binding site 1 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:67.6
occ:0.86
 F01 A:7QH401 0.0 67.6 0.9
C01 A:7QH401 1.3 56.8 0.9
F02 A:7QH401 2.1 58.7 0.9
F03 A:7QH401 2.2 50.4 0.9
C02 A:7QH401 2.4 54.4 0.9
C03 A:7QH401 2.8 58.3 0.9
CB A:ALA164 3.1 47.7 1.0
O01 A:7QH401 3.2 56.1 0.9
NE A:ARG234 3.2 62.3 1.0
O02 A:7QH401 3.3 59.7 0.9
O A:HOH511 3.3 46.7 1.0
NH1 A:ARG234 3.6 64.0 1.0
CZ A:ARG234 3.6 60.2 1.0
N01 A:7QH401 3.6 55.4 0.9
CD A:ARG234 4.0 59.6 1.0
N A:ALA164 4.1 49.7 1.0
CA A:ALA164 4.2 47.2 1.0
NZ A:LYS186 4.3 52.9 1.0
NH2 A:ARG234 4.6 64.5 1.0
N02 A:7QH401 4.6 58.3 0.9
CD A:LYS186 4.6 51.9 1.0
NH1 A:ARG165 4.8 59.7 1.0
CE A:LYS186 4.8 51.4 1.0

Fluorine binding site 2 out of 12 in 7rue

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Fluorine binding site 2 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:58.7
occ:0.86
 F02 A:7QH401 0.0 58.7 0.9
C01 A:7QH401 1.4 56.8 0.9
F01 A:7QH401 2.1 67.6 0.9
F03 A:7QH401 2.2 50.4 0.9
C02 A:7QH401 2.4 54.4 0.9
O A:HOH511 2.7 46.7 1.0
N01 A:7QH401 3.0 55.4 0.9
NH1 A:ARG234 3.1 64.0 1.0
CD2 A:HIS268 3.4 53.2 1.0
CG A:HIS268 3.4 56.0 1.0
CB A:HIS268 3.6 58.8 1.0
C03 A:7QH401 3.6 58.3 0.9
NE A:ARG234 3.7 62.3 1.0
CZ A:ARG234 3.8 60.2 1.0
O02 A:7QH401 4.0 59.7 0.9
NE2 A:HIS268 4.1 49.4 1.0
ND1 A:HIS268 4.2 54.5 1.0
N02 A:7QH401 4.3 58.3 0.9
O01 A:7QH401 4.4 56.1 0.9
CE1 A:HIS268 4.5 52.4 1.0
NZ A:LYS186 4.5 52.9 1.0
CA A:HIS268 4.8 63.2 1.0
CD A:ARG234 4.9 59.6 1.0
NH2 A:ARG234 5.0 64.5 1.0

Fluorine binding site 3 out of 12 in 7rue

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Fluorine binding site 3 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:50.4
occ:0.86
 F03 A:7QH401 0.0 50.4 0.9
C01 A:7QH401 1.4 56.8 0.9
F01 A:7QH401 2.2 67.6 0.9
F02 A:7QH401 2.2 58.7 0.9
NZ A:LYS186 2.4 52.9 1.0
C02 A:7QH401 2.4 54.4 0.9
NE A:ARG234 2.8 62.3 1.0
N01 A:7QH401 3.1 55.4 0.9
CE A:LYS186 3.4 51.4 1.0
C03 A:7QH401 3.5 58.3 0.9
ND1 A:HIS268 3.6 54.5 1.0
CG A:HIS268 3.6 56.0 1.0
O01 A:7QH401 3.6 56.1 0.9
CD A:ARG234 3.6 59.6 1.0
CZ A:ARG234 3.7 60.2 1.0
NH1 A:ARG234 3.7 64.0 1.0
CD A:LYS186 3.8 51.9 1.0
N02 A:7QH401 3.9 58.3 0.9
CE1 A:HIS268 3.9 52.4 1.0
CD2 A:HIS268 4.0 53.2 1.0
CB A:HIS268 4.0 58.8 1.0
NE2 A:HIS268 4.1 49.4 1.0
CB A:ARG234 4.4 53.4 1.0
O02 A:7QH401 4.5 59.7 0.9
CB A:ALA164 4.5 47.7 1.0
C04 A:7QH401 4.6 48.9 0.9
OD2 A:ASP265 4.6 47.6 1.0
CG A:ARG234 4.6 50.8 1.0
N03 A:7QH401 4.7 44.3 0.9
O A:HOH511 4.7 46.7 1.0
CG A:LYS186 4.8 45.5 1.0
NH2 A:ARG234 4.9 64.5 1.0

Fluorine binding site 4 out of 12 in 7rue

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Fluorine binding site 4 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:31.3
occ:0.79
 F01 B:7QH401 0.0 31.3 0.8
C01 B:7QH401 1.3 33.4 0.8
F03 B:7QH401 2.1 40.2 0.8
F02 B:7QH401 2.2 36.1 0.8
C02 B:7QH401 2.4 36.3 0.8
N01 B:7QH401 3.1 34.9 0.8
NE B:ARG234 3.2 29.6 1.0
NZ B:LYS186 3.3 26.8 1.0
CG B:HIS268 3.3 24.5 1.0
ND1 B:HIS268 3.4 28.2 1.0
C03 B:7QH401 3.6 34.0 0.8
CB B:HIS268 3.6 25.6 1.0
CD B:ARG234 3.7 34.0 1.0
O02 B:7QH401 3.8 32.7 0.8
CE B:LYS186 3.8 37.4 1.0
CD2 B:HIS268 3.9 25.7 1.0
CD B:LYS186 3.9 29.5 1.0
CE1 B:HIS268 4.0 27.6 1.0
OD2 B:ASP265 4.0 27.9 1.0
N02 B:7QH401 4.0 31.5 0.8
CB B:ARG234 4.1 27.1 1.0
CZ B:ARG234 4.3 35.6 1.0
NE2 B:HIS268 4.3 25.2 1.0
NH2 B:ARG234 4.4 38.6 1.0
CG B:ARG234 4.5 29.1 1.0
O01 B:7QH401 4.6 33.1 0.8
CB B:ALA164 4.7 32.1 1.0
C04 B:7QH401 4.8 28.4 0.8
N03 B:7QH401 4.9 23.3 0.8

Fluorine binding site 5 out of 12 in 7rue

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Fluorine binding site 5 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:36.1
occ:0.79
 F02 B:7QH401 0.0 36.1 0.8
C01 B:7QH401 1.4 33.4 0.8
F03 B:7QH401 2.1 40.2 0.8
F01 B:7QH401 2.2 31.3 0.8
C02 B:7QH401 2.4 36.3 0.8
N01 B:7QH401 3.1 34.9 0.8
CG B:HIS268 3.6 24.5 1.0
C03 B:7QH401 3.6 34.0 0.8
CB B:HIS268 3.6 25.6 1.0
CD2 B:HIS268 3.7 25.7 1.0
NE B:ARG234 3.7 29.6 1.0
NH2 B:ARG234 3.7 38.6 1.0
O01 B:7QH401 4.0 33.1 0.8
CZ B:ARG234 4.2 35.6 1.0
O02 B:7QH401 4.4 32.7 0.8
ND1 B:HIS268 4.4 28.2 1.0
N02 B:7QH401 4.4 31.5 0.8
NE2 B:HIS268 4.5 25.2 1.0
CD B:ARG234 4.8 34.0 1.0
CE1 B:HIS268 4.8 27.6 1.0
CA B:HIS268 4.9 30.1 1.0
CB B:ALA164 4.9 32.1 1.0

Fluorine binding site 6 out of 12 in 7rue

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Fluorine binding site 6 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:40.2
occ:0.79
 F03 B:7QH401 0.0 40.2 0.8
C01 B:7QH401 1.3 33.4 0.8
F01 B:7QH401 2.1 31.3 0.8
F02 B:7QH401 2.1 36.1 0.8
C02 B:7QH401 2.4 36.3 0.8
C03 B:7QH401 2.8 34.0 0.8
NE B:ARG234 2.9 29.6 1.0
CB B:ALA164 3.0 32.1 1.0
O02 B:7QH401 3.1 32.7 0.8
CD B:ARG234 3.5 34.0 1.0
O01 B:7QH401 3.6 33.1 0.8
N01 B:7QH401 3.6 34.9 0.8
CZ B:ARG234 3.7 35.6 1.0
NH2 B:ARG234 3.9 38.6 1.0
CD B:LYS186 4.0 29.5 1.0
N B:ALA164 4.0 34.0 1.0
CA B:ALA164 4.1 35.0 1.0
CE B:LYS186 4.5 37.4 1.0
N02 B:7QH401 4.6 31.5 0.8
NZ B:LYS186 4.6 26.8 1.0
NH1 B:ARG234 4.7 45.1 1.0
CG B:ARG234 4.8 29.1 1.0
CB B:ARG234 5.0 27.1 1.0

Fluorine binding site 7 out of 12 in 7rue

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Fluorine binding site 7 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:57.9
occ:0.80
 F01 C:7QH401 0.0 57.9 0.8
C01 C:7QH401 1.3 65.3 0.8
F02 C:7QH401 2.2 64.4 0.8
F03 C:7QH401 2.2 71.5 0.8
NZ C:LYS186 2.3 52.7 1.0
C02 C:7QH401 2.4 61.1 0.8
C03 C:7QH401 3.2 58.6 0.8
N01 C:7QH401 3.3 58.3 0.8
NE C:ARG234 3.3 58.7 1.0
CG C:ARG234 3.4 55.0 1.0
CE C:LYS186 3.5 56.6 1.0
CG C:HIS268 3.6 56.8 1.0
ND1 C:HIS268 3.7 57.7 1.0
CD C:LYS186 3.7 57.7 1.0
O01 C:7QH401 3.7 62.1 0.8
O02 C:7QH401 3.8 54.4 0.8
CD C:ARG234 3.9 53.7 1.0
CB C:HIS268 3.9 57.8 1.0
CD2 C:HIS268 4.0 52.3 1.0
CE1 C:HIS268 4.1 56.7 1.0
CB C:ALA164 4.2 53.1 1.0
NE2 C:HIS268 4.3 57.8 1.0
CZ C:ARG234 4.4 67.2 1.0
N02 C:7QH401 4.4 54.0 0.8
NH1 C:ARG234 4.5 65.3 1.0
N03 C:7QH401 4.5 55.1 0.8
OD2 C:ASP265 4.7 53.6 1.0
CB C:ARG234 4.7 53.0 1.0
C04 C:7QH401 4.8 54.3 0.8

Fluorine binding site 8 out of 12 in 7rue

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Fluorine binding site 8 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:64.4
occ:0.80
 F02 C:7QH401 0.0 64.4 0.8
C01 C:7QH401 1.4 65.3 0.8
F03 C:7QH401 2.2 71.5 0.8
F01 C:7QH401 2.2 57.9 0.8
C02 C:7QH401 2.4 61.1 0.8
O02 C:7QH401 2.6 54.4 0.8
C03 C:7QH401 2.8 58.6 0.8
NH2 C:ARG165 3.3 62.0 1.0
CB C:ALA164 3.4 53.1 1.0
N01 C:7QH401 3.5 58.3 0.8
NH1 C:ARG165 3.6 64.9 1.0
NE C:ARG234 3.7 58.7 1.0
CZ C:ARG165 3.7 64.7 1.0
O01 C:7QH401 3.9 62.1 0.8
NH1 C:ARG234 4.0 65.3 1.0
NZ C:LYS186 4.2 52.7 1.0
CZ C:ARG234 4.3 67.2 1.0
N C:ALA164 4.4 56.8 1.0
CA C:ALA164 4.5 49.7 1.0
CD C:ARG234 4.6 53.7 1.0
N02 C:7QH401 4.7 54.0 0.8
CD C:LYS186 4.7 57.7 1.0
NE C:ARG165 4.8 57.7 1.0
CG C:ARG234 4.9 55.0 1.0

Fluorine binding site 9 out of 12 in 7rue

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Fluorine binding site 9 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

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

b:71.5
occ:0.80
 F03 C:7QH401 0.0 71.5 0.8
C01 C:7QH401 1.4 65.3 0.8
F02 C:7QH401 2.2 64.4 0.8
F01 C:7QH401 2.2 57.9 0.8
C02 C:7QH401 2.3 61.1 0.8
N01 C:7QH401 2.7 58.3 0.8
CD2 C:HIS268 3.2 52.3 1.0
CG C:HIS268 3.3 56.8 1.0
CB C:HIS268 3.6 57.8 1.0
C03 C:7QH401 3.7 58.6 0.8
NE2 C:HIS268 3.9 57.8 1.0
NH1 C:ARG165 3.9 64.9 1.0
N02 C:7QH401 4.0 54.0 0.8
O02 C:7QH401 4.1 54.4 0.8
ND1 C:HIS268 4.1 57.7 1.0
NZ C:LYS186 4.2 52.7 1.0
NE C:ARG234 4.3 58.7 1.0
NH1 C:ARG234 4.3 65.3 1.0
CE1 C:HIS268 4.4 56.7 1.0
NH2 C:ARG165 4.6 62.0 1.0
O01 C:7QH401 4.6 62.1 0.8
CZ C:ARG165 4.7 64.7 1.0
CZ C:ARG234 4.8 67.2 1.0
C04 C:7QH401 4.8 54.3 0.8
CA C:HIS268 4.9 55.9 1.0

Fluorine binding site 10 out of 12 in 7rue

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Fluorine binding site 10 out of 12 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:58.6
occ:0.70
 F01 D:7QH401 0.0 58.6 0.7
C01 D:7QH401 1.3 49.8 0.7
F03 D:7QH401 2.1 53.2 0.7
F02 D:7QH401 2.2 46.3 0.7
C02 D:7QH401 2.4 52.2 0.7
CG D:HIS268 2.8 41.0 1.0
CB D:HIS268 3.1 42.7 1.0
CD2 D:HIS268 3.1 41.5 1.0
N01 D:7QH401 3.2 50.4 0.7
NH1 D:ARG234 3.3 54.4 1.0
C03 D:7QH401 3.3 55.1 0.7
ND1 D:HIS268 3.4 38.1 1.0
O02 D:7QH401 3.6 52.9 0.7
NE2 D:HIS268 3.7 43.0 1.0
CE1 D:HIS268 3.8 42.3 1.0
NE D:ARG234 4.0 52.6 1.0
CZ D:ARG234 4.1 56.4 1.0
O01 D:7QH401 4.2 50.6 0.7
N02 D:7QH401 4.3 42.3 0.7
CA D:HIS268 4.5 38.5 1.0
OD2 D:ASP265 4.7 35.0 1.0
NZ D:LYS186 4.8 52.6 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 12:33:55 2024

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