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Fluorine in PDB 5qpp: Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A, PDB code: 5qpp was solved by J.K.Petrick, E.R.Nelson, L.Muenzker, T.Krojer, A.Douangamath, J.Brandao-Neto, F.Von Delft, C.Dekker, W.Jahnke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.96 / 1.48
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.992, 57.992, 395.770, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24

Other elements in 5qpp:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A (pdb code 5qpp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A, PDB code: 5qpp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5qpp

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Fluorine binding site 1 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:20.5
occ:0.67
 F A:LV4406 0.0 20.5 0.7
C7 A:LV4406 1.3 18.5 0.7
F1 A:LV4406 2.1 21.9 0.7
F2 A:LV4406 2.1 19.5 0.7
O A:LV4406 2.2 16.9 0.7
CD A:LYS48 3.2 23.6 0.7
NZ A:LYS48 3.4 26.6 0.7
C3 A:LV4406 3.5 15.1 0.7
O A:HOH815 3.5 37.1 0.7
O A:HOH647 3.7 29.6 0.7
CE A:LYS48 4.0 24.9 0.7
C2 A:LV4406 4.2 14.1 0.7
CB A:LYS48 4.3 19.0 0.7
CG A:LYS48 4.3 20.6 0.7
C4 A:LV4406 4.5 14.1 0.7
N A:LV4406 4.5 16.1 0.7
O A:HOH746 4.5 34.5 0.7
S A:LV4406 4.6 17.0 0.7
C6 A:LV4406 4.6 16.7 0.7

Fluorine binding site 2 out of 12 in 5qpp

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Fluorine binding site 2 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:21.9
occ:0.67
 F1 A:LV4406 0.0 21.9 0.7
C7 A:LV4406 1.3 18.5 0.7
F A:LV4406 2.1 20.5 0.7
F2 A:LV4406 2.1 19.5 0.7
O A:LV4406 2.2 16.9 0.7
C3 A:LV4406 2.8 15.1 0.7
C2 A:LV4406 2.9 14.1 0.7
O A:HOH815 3.4 37.1 0.7
O A:HOH647 3.7 29.6 0.7
CB A:LYS356 3.8 25.8 1.0
CD1 A:PHE50 3.8 15.3 1.0
O A:HOH746 4.0 34.5 0.7
C4 A:LV4406 4.0 14.1 0.7
O A:LYS356 4.1 21.8 1.0
C1 A:LV4406 4.1 13.5 0.7
CG A:LYS356 4.2 30.6 1.0
CE A:LYS356 4.2 40.6 1.0
CG A:PHE50 4.5 16.1 1.0
CE1 A:PHE50 4.5 16.3 1.0
CB A:PHE50 4.5 15.7 1.0
C A:LYS356 4.5 20.6 1.0
CA A:LYS356 4.6 24.5 1.0
N A:LV4406 4.6 16.1 0.7
CD A:LYS356 4.7 34.9 1.0
CD A:LYS48 4.9 23.6 0.7

Fluorine binding site 3 out of 12 in 5qpp

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Fluorine binding site 3 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:19.5
occ:0.67
 F2 A:LV4406 0.0 19.5 0.7
C7 A:LV4406 1.3 18.5 0.7
F1 A:LV4406 2.1 21.9 0.7
F A:LV4406 2.1 20.5 0.7
O A:LV4406 2.2 16.9 0.7
C3 A:LV4406 2.8 15.1 0.7
CB A:LYS48 3.4 19.0 0.7
O A:HOH746 3.4 34.5 0.7
C4 A:LV4406 3.4 14.1 0.7
N A:LV4406 3.4 16.1 0.7
CD A:LYS48 3.4 23.6 0.7
CB A:PHE50 3.5 15.7 1.0
C2 A:LV4406 3.7 14.1 0.7
CG A:LYS48 4.0 20.6 0.7
C6 A:LV4406 4.1 16.7 0.7
CD1 A:PHE50 4.1 15.3 1.0
CG A:PHE50 4.2 16.1 1.0
CA A:PHE50 4.2 15.5 1.0
N A:PHE50 4.4 14.6 1.0
O1 A:SO4401 4.6 16.3 0.7
C5 A:LV4406 4.6 13.7 0.7
CA A:LYS48 4.6 18.2 0.7
O A:LYS48 4.6 18.3 0.7
NZ A:LYS48 4.7 26.6 0.7
CE A:LYS48 4.7 24.9 0.7
O A:HOH815 4.7 37.1 0.7
N1 A:LV4406 4.7 16.9 0.7
C A:LYS48 4.7 17.4 0.7
S A:LV4406 4.8 17.0 0.7
C1 A:LV4406 4.8 13.5 0.7

Fluorine binding site 4 out of 12 in 5qpp

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Fluorine binding site 4 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:26.8
occ:0.54
 F A:LV4407 0.0 26.8 0.5
C7 A:LV4407 1.3 27.3 0.5
F2 A:LV4407 2.1 34.6 0.5
F1 A:LV4407 2.1 24.6 0.5
O A:LV4407 2.2 28.7 0.5
C3 A:LV4407 3.5 25.5 0.5
CB A:LYS158 3.6 16.0 1.0
CD1 A:LEU155 3.6 18.4 1.0
C5 A:LV4408 3.6 37.4 0.5
C A:LV4408 3.8 33.6 0.5
CD A:LYS158 4.0 26.2 1.0
O A:HOH714 4.2 31.4 0.5
CG2 A:VAL159 4.3 12.4 1.0
O A:LEU155 4.3 13.4 1.0
C4 A:LV4407 4.4 27.7 0.5
N A:LV4407 4.4 29.9 0.5
CG A:LYS158 4.4 19.8 1.0
C2 A:LV4407 4.5 24.9 0.5
C4 A:LV4408 4.5 38.0 0.5
N A:VAL159 4.6 12.3 1.0
CA A:LEU155 4.7 14.8 1.0
S A:LV4408 4.7 51.6 0.5
CD2 A:LEU214 4.7 24.5 1.0
C A:LYS158 4.8 13.1 1.0
CA A:LYS158 4.8 14.6 1.0
CG A:LEU155 4.9 18.7 1.0
O A:HOH503 4.9 38.3 0.5
C1 A:LV4408 4.9 34.0 0.5
N A:LV4408 4.9 42.2 0.5
C A:LEU155 5.0 14.4 1.0
C6 A:LV4408 5.0 46.0 0.5

Fluorine binding site 5 out of 12 in 5qpp

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Fluorine binding site 5 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:24.6
occ:0.54
 F1 A:LV4407 0.0 24.6 0.5
C7 A:LV4407 1.3 27.3 0.5
F2 A:LV4407 2.1 34.6 0.5
F A:LV4407 2.1 26.8 0.5
O A:LV4407 2.3 28.7 0.5
CD2 A:LEU214 3.0 24.5 1.0
C3 A:LV4407 3.1 25.5 0.5
C4 A:LV4407 3.4 27.7 0.5
CE1 A:PHE210 3.5 19.6 1.0
N A:LV4407 3.5 29.9 0.5
CD1 A:PHE210 3.5 18.6 1.0
OE1 A:GLU236 3.7 24.5 0.5
C A:LV4408 3.8 33.6 0.5
C2 A:LV4407 4.1 24.9 0.5
C5 A:LV4408 4.2 37.4 0.5
O A:HOH550 4.2 28.4 1.0
CG A:LEU214 4.2 18.7 1.0
CD A:GLU236 4.3 24.5 0.5
C5 A:LV4407 4.6 24.7 0.5
CG2 A:VAL159 4.6 12.4 1.0
CD1 A:LEU155 4.7 18.4 1.0
C6 A:LV4407 4.7 32.7 0.5
CZ A:PHE210 4.8 18.5 1.0
O A:HOH714 4.8 31.4 0.5
CG A:PHE210 4.9 16.1 1.0
C1 A:LV4408 4.9 34.0 0.5
OE2 A:GLU236 4.9 25.6 0.5
CG A:GLU236 5.0 22.8 0.5

Fluorine binding site 6 out of 12 in 5qpp

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Fluorine binding site 6 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:34.6
occ:0.54
 F2 A:LV4407 0.0 34.6 0.5
C7 A:LV4407 1.2 27.3 0.5
F1 A:LV4407 2.1 24.6 0.5
F A:LV4407 2.1 26.8 0.5
O A:LV4407 2.1 28.7 0.5
N A:LV4407 2.5 29.9 0.5
C3 A:LV4407 2.8 25.5 0.5
C5 A:LV4408 2.8 37.4 0.5
O A:HOH714 2.9 31.4 0.5
C4 A:LV4407 2.9 27.7 0.5
C A:LV4408 3.1 33.6 0.5
C6 A:LV4407 3.3 32.7 0.5
OE1 A:GLU236 3.6 24.5 0.5
N1 A:LV4407 3.7 34.4 0.5
O A:HOH503 3.8 38.3 0.5
C4 A:LV4408 4.1 38.0 0.5
C2 A:LV4407 4.1 24.9 0.5
CD A:GLU236 4.2 24.5 0.5
OE2 A:GLU236 4.2 25.6 0.5
C5 A:LV4407 4.3 24.7 0.5
S A:LV4407 4.4 34.6 0.5
N A:LV4408 4.5 42.2 0.5
C1 A:LV4408 4.5 34.0 0.5
CD A:LYS158 4.5 26.2 1.0
CD2 A:LEU214 4.6 24.5 1.0
O A:HOH550 4.9 28.4 1.0
C6 A:LV4408 5.0 46.0 0.5
CB A:LYS158 5.0 16.0 1.0

Fluorine binding site 7 out of 12 in 5qpp

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Fluorine binding site 7 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:39.3
occ:0.54
 F A:LV4408 0.0 39.3 0.5
C7 A:LV4408 1.3 36.4 0.5
F1 A:LV4408 2.1 34.8 0.5
F2 A:LV4408 2.1 36.1 0.5
O A:LV4408 2.2 37.8 0.5
C3 A:LV4408 3.1 38.1 0.5
C2 A:LV4408 3.3 34.9 0.5
O A:HOH786 3.4 42.4 1.0
CE A:MET232 3.6 31.4 1.0
O A:HOH720 3.8 41.6 1.0
CD2 A:LEU222 3.9 17.1 1.0
CG1 A:VAL218 4.1 14.7 1.0
CB A:ALA227 4.1 27.0 1.0
C4 A:LV4408 4.5 38.0 0.5
CG A:LEU222 4.6 15.8 1.0
C1 A:LV4408 4.6 34.0 0.5
SD A:MET232 4.7 27.4 1.0
CD1 A:LEU222 5.0 17.5 1.0

Fluorine binding site 8 out of 12 in 5qpp

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Fluorine binding site 8 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:34.8
occ:0.54
 F1 A:LV4408 0.0 34.8 0.5
C7 A:LV4408 1.3 36.4 0.5
F2 A:LV4408 2.1 36.1 0.5
F A:LV4408 2.1 39.3 0.5
O A:LV4408 2.3 37.8 0.5
CB A:ASP151 3.4 20.1 1.0
CG A:ASP151 3.5 25.7 1.0
C3 A:LV4408 3.6 38.1 0.5
OD2 A:ASP151 3.7 27.4 1.0
O A:HOH720 3.9 41.6 1.0
CD2 A:LEU222 3.9 17.1 1.0
OD1 A:ASP151 4.0 25.0 1.0
S A:LV4408 4.2 51.6 0.5
C2 A:LV4408 4.3 34.9 0.5
CA A:ASP151 4.3 17.0 1.0
O A:ASP151 4.4 13.8 1.0
C4 A:LV4408 4.5 38.0 0.5
C6 A:LV4408 4.5 46.0 0.5
N A:LV4408 4.6 42.2 0.5
CD1 A:LEU222 4.6 17.5 1.0
C A:ASP151 4.6 15.6 1.0
O A:HOH786 4.6 42.4 1.0
CG A:LEU222 4.7 15.8 1.0

Fluorine binding site 9 out of 12 in 5qpp

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Fluorine binding site 9 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:36.1
occ:0.54
 F2 A:LV4408 0.0 36.1 0.5
C7 A:LV4408 1.3 36.4 0.5
F1 A:LV4408 2.1 34.8 0.5
F A:LV4408 2.1 39.3 0.5
O A:LV4408 2.3 37.8 0.5
C3 A:LV4408 2.8 38.1 0.5
C2 A:LV4408 3.1 34.9 0.5
CG1 A:VAL218 3.4 14.7 1.0
CD1 A:LEU222 3.8 17.5 1.0
S A:LV4408 3.9 51.6 0.5
C4 A:LV4408 3.9 38.0 0.5
CD2 A:LEU222 3.9 17.1 1.0
CD2 A:LEU155 4.1 22.7 1.0
CG A:LEU222 4.1 15.8 1.0
C1 A:LV4408 4.2 34.0 0.5
CB A:LEU155 4.3 18.9 1.0
O A:ASP151 4.4 13.8 1.0
CD1 A:LEU155 4.4 18.4 1.0
CG A:LEU155 4.5 18.7 1.0
N A:LV4408 4.6 42.2 0.5
C6 A:LV4408 4.6 46.0 0.5
CB A:ASP151 4.6 20.1 1.0
CB A:VAL218 4.8 14.0 1.0
C5 A:LV4408 4.8 37.4 0.5
C A:ASP151 5.0 15.6 1.0
C A:LV4408 5.0 33.6 0.5

Fluorine binding site 10 out of 12 in 5qpp

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Fluorine binding site 10 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Pandda Analysis Group Deposition -- Crystal Structure of T. Cruzi Fpps in Complex with FMOPL000512A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:46.7
occ:0.72
 F A:LV4409 0.0 46.7 0.7
C7 A:LV4409 1.3 46.5 0.7
F1 A:LV4409 2.1 44.9 0.7
O A:LV4409 2.2 44.1 0.7
F2 A:LV4409 2.2 43.2 0.7
C3 A:LV4409 2.9 43.9 0.7
C2 A:LV4409 3.1 44.1 0.7
CG1 A:VAL252 4.0 27.6 1.0
C4 A:LV4409 4.1 43.9 0.7
C1 A:LV4409 4.4 43.3 0.7
N A:LV4409 4.5 45.9 0.7
OE1 A:GLN318 4.8 46.0 0.7
CB A:PHE256 4.9 33.1 1.0

Reference:

J.K.Petrick, L.Muenzker, F.Von Delft, W.Jahnke. Pandda Analysis Group Deposition - Fpps Screened Against the Dsi Fragment Library To Be Published.
Page generated: Thu Aug 1 13:21:46 2024

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