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Fluorine in PDB 5qto: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641, PDB code: 5qto was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.52 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.260, 59.871, 79.887, 79.47, 81.46, 75.59
R / Rfree (%) 22.9 / 26.2

Other elements in 5qto:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641 (pdb code 5qto). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 20 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641, PDB code: 5qto:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 20 in 5qto

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Fluorine binding site 1 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:49.6
occ:0.82
 F A:PWG304 0.0 49.6 0.8
C A:PWG304 1.3 47.5 0.8
F1 A:PWG304 2.1 50.6 0.8
F4 A:PWG304 2.1 51.6 0.8
C1 A:PWG304 2.4 45.1 0.8
C2 A:PWG304 2.8 46.5 0.8
C5 A:PWG304 3.7 44.7 0.8
CZ2 B:TRP28 3.8 74.5 0.8
O A:HOH464 4.1 54.3 0.8
C3 A:PWG304 4.2 45.6 0.8
CE2 B:TRP28 4.3 69.8 0.8
CH2 B:TRP28 4.3 76.1 0.8
N1 A:PWG304 4.4 43.6 0.8
CZ3 A:TRP46 4.6 33.6 0.8
NE1 B:TRP28 4.6 67.2 0.8
N A:PWG304 4.8 42.9 0.8

Fluorine binding site 2 out of 20 in 5qto

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Fluorine binding site 2 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:50.6
occ:0.82
 F1 A:PWG304 0.0 50.6 0.8
C A:PWG304 1.3 47.5 0.8
F4 A:PWG304 2.1 51.6 0.8
F A:PWG304 2.1 49.6 0.8
C1 A:PWG304 2.4 45.1 0.8
O A:HOH464 3.1 54.3 0.8
CZ3 A:TRP46 3.1 33.6 0.8
C5 A:PWG304 3.1 44.7 0.8
N1 A:PWG304 3.4 43.6 0.8
CE3 A:TRP46 3.4 34.0 0.8
C2 A:PWG304 3.5 46.5 0.8
CH2 A:TRP46 4.0 33.2 0.8
O A:THR45 4.2 31.9 1.0
N A:PWG304 4.5 42.9 0.8
CD2 A:TRP46 4.5 34.1 0.8
N2 A:PWG304 4.7 41.7 0.8
C3 A:PWG304 4.7 45.6 0.8
CZ2 B:TRP28 5.0 74.5 0.8
CZ2 A:TRP46 5.0 34.5 0.8

Fluorine binding site 3 out of 20 in 5qto

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Fluorine binding site 3 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:43.1
occ:0.82
 F2 A:PWG304 0.0 43.1 0.8
C7 A:PWG304 1.3 41.0 0.8
F3 A:PWG304 2.0 41.2 0.8
C6 A:PWG304 2.3 42.2 0.8
NE1 A:TRP46 2.9 34.2 0.8
N A:PWG304 2.9 42.9 0.8
O A:HOH425 3.0 36.0 0.8
O A:GLY135 3.0 30.2 1.0
C4 A:PWG304 3.2 45.4 0.8
CE2 A:TRP46 3.4 34.1 0.8
N2 A:PWG304 3.4 41.7 0.8
O A:GLU47 3.6 31.6 0.8
CZ2 A:TRP46 3.6 34.5 0.8
CD1 A:TRP46 3.8 33.8 0.8
CD1 A:LEU136 4.0 34.5 1.0
NH1 B:ARG51 4.1 32.5 1.0
C A:GLY135 4.2 28.5 1.0
C5 A:PWG304 4.2 44.7 0.8
CA A:LEU136 4.3 32.4 1.0
CG2 B:VAL29 4.3 43.8 1.0
N1 A:PWG304 4.4 43.6 0.8
CD2 A:TRP46 4.5 34.1 0.8
C3 A:PWG304 4.5 45.6 0.8
CG A:TRP46 4.7 32.8 0.8
N A:LEU136 4.7 29.1 1.0
C A:GLU47 4.7 29.6 0.8
CB B:TRP28 4.7 50.4 0.8
CH2 A:TRP46 4.7 33.2 0.8
CB A:LEU136 4.8 30.1 1.0
NH2 B:ARG51 4.8 37.5 1.0
CZ B:ARG51 4.9 32.4 1.0

Fluorine binding site 4 out of 20 in 5qto

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Fluorine binding site 4 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:41.2
occ:0.82
 F3 A:PWG304 0.0 41.2 0.8
C7 A:PWG304 1.3 41.0 0.8
F2 A:PWG304 2.0 43.1 0.8
C6 A:PWG304 2.3 42.2 0.8
CB B:TRP28 2.8 50.4 0.8
N A:PWG304 3.0 42.9 0.8
CG2 B:VAL29 3.1 43.8 1.0
C4 A:PWG304 3.3 45.4 0.8
N2 A:PWG304 3.4 41.7 0.8
CG B:TRP28 3.7 59.8 0.8
O B:HOH441 3.8 26.9 0.8
C B:TRP28 3.9 41.9 0.8
CA B:TRP28 3.9 44.6 0.8
NH1 B:ARG51 4.0 32.5 1.0
O B:TRP28 4.0 35.9 0.8
O A:GLU47 4.1 31.6 0.8
CD1 B:TRP28 4.1 62.1 0.8
CD1 A:LEU136 4.2 34.5 1.0
C5 A:PWG304 4.2 44.7 0.8
N B:VAL29 4.3 40.6 1.0
O A:HOH425 4.3 36.0 0.8
N1 A:PWG304 4.4 43.6 0.8
CB A:GLU47 4.4 34.6 0.8
CB B:VAL29 4.5 39.6 1.0
OE2 A:GLU47 4.6 37.9 0.8
C3 A:PWG304 4.6 45.6 0.8
NE1 A:TRP46 4.7 34.2 0.8
CD2 B:TRP28 4.7 64.5 0.8
CA B:VAL29 4.9 38.3 1.0
N B:TRP28 5.0 44.7 0.8
CZ B:ARG51 5.0 32.4 1.0
O A:GLY135 5.0 30.2 1.0

Fluorine binding site 5 out of 20 in 5qto

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Fluorine binding site 5 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:51.6
occ:0.82
 F4 A:PWG304 0.0 51.6 0.8
C A:PWG304 1.3 47.5 0.8
F1 A:PWG304 2.1 50.6 0.8
F A:PWG304 2.1 49.6 0.8
C1 A:PWG304 2.4 45.1 0.8
C5 A:PWG304 3.0 44.7 0.8
CH2 B:TRP28 3.1 76.1 0.8
N1 A:PWG304 3.1 43.6 0.8
CZ2 B:TRP28 3.2 74.5 0.8
CZ3 B:TRP28 3.5 74.1 0.8
C2 A:PWG304 3.6 46.5 0.8
CE2 B:TRP28 3.7 69.8 0.8
O A:HOH464 3.8 54.3 0.8
CE3 B:TRP28 4.0 67.0 0.8
CD2 B:TRP28 4.1 64.5 0.8
N A:PWG304 4.3 42.9 0.8
N2 A:PWG304 4.3 41.7 0.8
NE1 B:TRP28 4.5 67.2 0.8
O A:THR45 4.7 31.9 1.0
C3 A:PWG304 4.8 45.6 0.8
CZ3 A:TRP46 4.8 33.6 0.8
CE3 A:TRP46 4.9 34.0 0.8
C6 A:PWG304 5.0 42.2 0.8

Fluorine binding site 6 out of 20 in 5qto

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Fluorine binding site 6 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:46.0
occ:0.76
 F B:PWG304 0.0 46.0 0.8
C B:PWG304 1.3 43.6 0.8
F1 B:PWG304 2.1 44.9 0.8
F4 B:PWG304 2.1 47.7 0.8
C1 B:PWG304 2.4 40.8 0.8
O B:HOH432 2.9 36.4 0.8
C5 B:PWG304 3.0 37.4 0.8
N1 B:PWG304 3.2 33.3 0.8
CZ3 B:TRP46 3.2 31.6 0.8
O B:HOH459 3.4 49.9 1.0
CE3 B:TRP46 3.4 30.6 0.8
C2 B:PWG304 3.5 40.2 0.8
O B:THR45 4.0 33.7 1.0
CH2 B:TRP46 4.2 32.7 0.8
O B:HOH460 4.2 38.3 1.0
N B:PWG304 4.3 37.4 0.8
N2 B:PWG304 4.4 34.6 0.8
CD2 B:TRP46 4.5 30.1 0.8
C3 B:PWG304 4.7 41.0 0.8
NE1 A:TRP28 4.7 40.8 0.8
CE2 A:TRP28 4.9 40.2 0.8
CZ2 A:TRP28 4.9 42.3 0.8

Fluorine binding site 7 out of 20 in 5qto

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Fluorine binding site 7 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:44.9
occ:0.76
 F1 B:PWG304 0.0 44.9 0.8
C B:PWG304 1.4 43.6 0.8
F B:PWG304 2.1 46.0 0.8
F4 B:PWG304 2.1 47.7 0.8
C1 B:PWG304 2.4 40.8 0.8
NE1 A:TRP28 2.8 40.8 0.8
C5 B:PWG304 3.0 37.4 0.8
N1 B:PWG304 3.1 33.3 0.8
CE2 A:TRP28 3.1 40.2 0.8
CZ2 A:TRP28 3.2 42.3 0.8
C2 B:PWG304 3.5 40.2 0.8
O B:HOH460 3.6 38.3 1.0
CD1 A:TRP28 3.8 39.9 0.8
CD2 A:TRP28 4.2 40.6 0.8
N B:PWG304 4.3 37.4 0.8
CH2 A:TRP28 4.3 42.1 0.8
N2 B:PWG304 4.4 34.6 0.8
CG A:TRP28 4.6 39.8 0.8
O B:HOH459 4.6 49.9 1.0
O B:HOH432 4.6 36.4 0.8
C3 B:PWG304 4.7 41.0 0.8
O B:THR45 4.8 33.7 1.0
CZ3 B:TRP46 4.9 31.6 0.8
C6 B:PWG304 5.0 36.3 0.8

Fluorine binding site 8 out of 20 in 5qto

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Fluorine binding site 8 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:35.4
occ:0.76
 F2 B:PWG304 0.0 35.4 0.8
C7 B:PWG304 1.3 34.7 0.8
F3 B:PWG304 2.1 36.9 0.8
C6 B:PWG304 2.2 36.3 0.8
N B:PWG304 2.8 37.4 0.8
NE1 B:TRP46 2.9 30.7 0.8
O B:GLY135 2.9 30.3 1.0
O A:HOH459 2.9 33.6 0.8
C4 B:PWG304 3.0 39.7 0.8
CE2 B:TRP46 3.2 31.2 0.8
CZ2 B:TRP46 3.2 31.8 0.8
N2 B:PWG304 3.4 34.6 0.8
O B:GLU47 3.7 34.1 1.0
CD1 B:TRP46 3.9 30.4 0.8
C5 B:PWG304 4.0 37.4 0.8
C B:GLY135 4.1 29.1 1.0
CD1 B:LEU136 4.2 38.9 1.0
CD2 B:TRP46 4.2 30.1 0.8
NH1 A:ARG51 4.2 30.7 1.0
N1 B:PWG304 4.3 33.3 0.8
CH2 B:TRP46 4.3 32.7 0.8
C3 B:PWG304 4.3 41.0 0.8
CA B:LEU136 4.4 28.6 1.0
CG B:TRP46 4.6 31.2 0.8
NH2 A:ARG51 4.7 34.0 1.0
N B:LEU136 4.7 26.2 1.0
CZ A:ARG51 4.9 32.4 1.0
C B:GLU47 4.9 32.8 1.0
CG2 A:VAL29 4.9 44.5 1.0
CB A:TRP28 4.9 37.9 0.8
CB B:LEU136 4.9 30.2 1.0

Fluorine binding site 9 out of 20 in 5qto

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Fluorine binding site 9 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:36.9
occ:0.76
 F3 B:PWG304 0.0 36.9 0.8
C7 B:PWG304 1.3 34.7 0.8
F2 B:PWG304 2.1 35.4 0.8
C6 B:PWG304 2.3 36.3 0.8
N B:PWG304 3.0 37.4 0.8
CB A:TRP28 3.1 37.9 0.8
C4 B:PWG304 3.3 39.7 0.8
CG2 A:VAL29 3.4 44.5 1.0
N2 B:PWG304 3.4 34.6 0.8
O A:HOH436 3.8 34.5 1.0
CD1 B:LEU136 3.8 38.9 1.0
NH1 A:ARG51 3.9 30.7 1.0
O B:GLU47 3.9 34.1 1.0
CG A:TRP28 4.0 39.8 0.8
C A:TRP28 4.1 33.1 0.8
O A:TRP28 4.1 31.5 0.8
CA A:TRP28 4.2 35.9 0.8
O A:HOH459 4.2 33.6 0.8
C5 B:PWG304 4.3 37.4 0.8
N1 B:PWG304 4.4 33.3 0.8
N A:VAL29 4.6 32.6 1.0
CD2 A:TRP28 4.6 40.6 0.8
CB B:GLU47 4.6 33.0 1.0
C3 B:PWG304 4.7 41.0 0.8
NE1 B:TRP46 4.7 30.7 0.8
O B:GLY135 4.7 30.3 1.0
CZ A:ARG51 4.8 32.4 1.0
CB A:VAL29 4.8 39.6 1.0
CE3 A:TRP28 4.8 42.2 0.8
CD1 A:TRP28 4.8 39.9 0.8
C B:GLU47 4.9 32.8 1.0
CE2 B:TRP46 4.9 31.2 0.8

Fluorine binding site 10 out of 20 in 5qto

Go back to Fluorine Binding Sites List in 5qto
Fluorine binding site 10 out of 20 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 1R-0641


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 NUDT5 in Complex with 1R-0641 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:47.7
occ:0.76
 F4 B:PWG304 0.0 47.7 0.8
C B:PWG304 1.3 43.6 0.8
F B:PWG304 2.1 46.0 0.8
F1 B:PWG304 2.1 44.9 0.8
C1 B:PWG304 2.4 40.8 0.8
C2 B:PWG304 2.8 40.2 0.8
CZ2 A:TRP28 3.6 42.3 0.8
C5 B:PWG304 3.7 37.4 0.8
CH2 A:TRP28 4.2 42.1 0.8
CE2 A:TRP28 4.2 40.2 0.8
O B:HOH459 4.2 49.9 1.0
C3 B:PWG304 4.3 41.0 0.8
N1 B:PWG304 4.4 33.3 0.8
NE1 A:TRP28 4.5 40.8 0.8
CZ3 B:TRP46 4.6 31.6 0.8
O B:HOH432 4.7 36.4 0.8
N B:PWG304 4.8 37.4 0.8

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Thu Aug 1 13:24:47 2024

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