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Fluorine in PDB 5qts: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S:
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 8J-537S, PDB code: 5qts 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) 50.11 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.315, 59.910, 80.078, 79.34, 81.27, 75.59
R / Rfree (%) 21.7 / 25.1

Other elements in 5qts:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S 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 - 12;

Binding sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S (pdb code 5qts). 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 NUDT5 in Complex with 8J-537S, PDB code: 5qts:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5qts

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Fluorine binding site 1 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:37.3
occ:0.74
 F A:PWS304 0.0 37.3 0.7
C4 A:PWS304 1.3 36.9 0.7
F1 A:PWS304 2.1 37.2 0.7
F2 A:PWS304 2.1 36.0 0.7
C3 A:PWS304 2.4 36.1 0.7
O A:HOH432 2.8 32.3 0.7
N1 A:PWS304 2.8 36.6 0.7
NH1 B:ARG51 3.0 27.9 0.7
O A:GLY135 3.0 25.1 0.7
NH2 B:ARG51 3.2 29.6 0.7
CZ B:ARG51 3.3 28.1 0.7
CD1 A:LEU136 3.4 34.2 1.0
C5 A:PWS304 3.4 34.0 0.7
CA A:LEU136 3.6 24.8 1.0
C A:GLY135 3.7 24.6 0.7
CB A:LEU136 3.8 26.0 1.0
N A:LEU136 4.0 24.9 1.0
C1 A:PWS304 4.1 35.2 0.7
CG A:LEU136 4.2 27.2 1.0
NE B:ARG51 4.3 27.3 0.7
O B:HOH444 4.4 25.5 0.7
C6 A:PWS304 4.6 32.2 0.7
NE1 A:TRP46 4.6 27.4 1.0
O A:GLU47 4.8 29.1 1.0
CG B:ARG51 4.8 27.8 0.7
C A:LEU136 4.9 25.1 1.0
N A:PWS304 4.9 33.1 0.7
CA A:GLY135 4.9 24.2 0.7
C A:PWS304 4.9 38.4 0.7

Fluorine binding site 2 out of 12 in 5qts

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Fluorine binding site 2 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:37.2
occ:0.74
 F1 A:PWS304 0.0 37.2 0.7
C4 A:PWS304 1.4 36.9 0.7
F A:PWS304 2.1 37.3 0.7
F2 A:PWS304 2.2 36.0 0.7
C3 A:PWS304 2.4 36.1 0.7
C5 A:PWS304 2.8 34.0 0.7
CD1 A:LEU136 3.1 34.2 1.0
O A:GLU47 3.2 29.1 1.0
CG1 B:VAL29 3.6 30.9 0.7
N1 A:PWS304 3.7 36.6 0.7
CB B:VAL29 3.8 32.6 0.7
CA A:LEU136 3.9 24.8 1.0
O A:GLY135 4.0 25.1 0.7
C6 A:PWS304 4.2 32.2 0.7
CG A:LEU136 4.2 27.2 1.0
O A:LEU136 4.2 25.3 1.0
C A:GLU47 4.2 28.4 1.0
CB A:LEU136 4.3 26.0 1.0
CB B:TRP28 4.5 36.7 0.7
NE1 A:TRP46 4.6 27.4 1.0
C A:LEU136 4.6 25.1 1.0
CG2 B:VAL29 4.6 33.7 0.7
CB A:GLU47 4.7 30.3 1.0
C1 A:PWS304 4.8 35.2 0.7
NH1 B:ARG51 4.8 27.9 0.7
O A:HOH432 4.8 32.3 0.7
C A:GLY135 4.8 24.6 0.7
C B:TRP28 4.8 33.6 0.7
N A:LEU136 4.9 24.9 1.0
N B:VAL29 4.9 33.6 0.7
CA B:VAL29 4.9 32.8 0.7
O B:TRP28 4.9 31.4 0.7
O A:PWS304 4.9 30.2 0.7

Fluorine binding site 3 out of 12 in 5qts

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Fluorine binding site 3 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:36.0
occ:0.74
 F2 A:PWS304 0.0 36.0 0.7
C4 A:PWS304 1.4 36.9 0.7
F A:PWS304 2.1 37.3 0.7
F1 A:PWS304 2.2 37.2 0.7
C3 A:PWS304 2.4 36.1 0.7
O B:HOH444 3.0 25.5 0.7
N1 A:PWS304 3.0 36.6 0.7
NH1 B:ARG51 3.2 27.9 0.7
O B:TRP28 3.2 31.4 0.7
C5 A:PWS304 3.4 34.0 0.7
CB B:TRP28 3.5 36.7 0.7
C B:TRP28 3.6 33.6 0.7
CD1 A:LEU136 3.7 34.2 1.0
CZ B:ARG51 3.8 28.1 0.7
CG B:ARG51 3.8 27.8 0.7
CB B:VAL29 3.9 32.6 0.7
N B:VAL29 4.1 33.6 0.7
CA B:TRP28 4.1 35.0 0.7
CG1 B:VAL29 4.2 30.9 0.7
C1 A:PWS304 4.3 35.2 0.7
CA B:VAL29 4.3 32.8 0.7
NH2 B:ARG51 4.4 29.6 0.7
NE B:ARG51 4.4 27.3 0.7
CD B:ARG51 4.6 28.8 0.7
O A:HOH432 4.6 32.3 0.7
C6 A:PWS304 4.7 32.2 0.7
CG B:TRP28 4.7 40.3 0.7
CB B:ARG51 4.7 28.5 0.7
CA B:ARG51 4.9 29.4 0.7
CG2 B:VAL29 5.0 33.7 0.7

Fluorine binding site 4 out of 12 in 5qts

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Fluorine binding site 4 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:53.8
occ:0.74
 F A:PWS308 0.0 53.8 0.7
C4 A:PWS308 1.3 50.2 0.7
F2 A:PWS308 2.1 49.9 0.7
F1 A:PWS308 2.1 50.8 0.7
C3 A:PWS308 2.4 48.4 0.7
N1 A:PWS308 2.7 51.0 0.7
O B:GLY135 2.8 24.9 1.0
NH1 A:ARG51 2.9 28.0 0.7
O A:HOH467 2.9 41.5 0.7
NH2 A:ARG51 3.0 30.3 0.7
CZ A:ARG51 3.2 29.4 0.7
C5 A:PWS308 3.5 46.2 0.7
C B:GLY135 3.5 23.4 1.0
CA B:LEU136 3.7 23.0 1.0
CD1 B:LEU136 3.9 27.4 1.0
CB B:LEU136 4.0 25.9 1.0
C1 A:PWS308 4.0 51.8 0.7
N B:LEU136 4.0 22.0 1.0
NE A:ARG51 4.3 28.2 0.7
NE1 B:TRP46 4.3 30.9 1.0
CG B:LEU136 4.6 28.5 1.0
CA B:GLY135 4.6 23.5 1.0
O A:HOH420 4.6 27.0 1.0
C A:PWS308 4.6 57.4 0.7
O A:HOH470 4.7 19.9 1.0
CG2 A:VAL29 4.7 33.9 0.7
CZ2 B:TRP46 4.7 32.5 1.0
C6 A:PWS308 4.7 46.5 0.7
O B:GLU47 4.7 26.6 1.0
CE2 B:TRP46 4.8 30.1 1.0
N A:PWS308 4.9 48.9 0.7

Fluorine binding site 5 out of 12 in 5qts

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Fluorine binding site 5 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:50.8
occ:0.74
 F1 A:PWS308 0.0 50.8 0.7
C4 A:PWS308 1.3 50.2 0.7
F A:PWS308 2.1 53.8 0.7
F2 A:PWS308 2.2 49.9 0.7
C3 A:PWS308 2.4 48.4 0.7
C5 A:PWS308 2.8 46.2 0.7
O B:GLU47 2.9 26.6 1.0
CG2 A:VAL29 2.9 33.9 0.7
CD1 B:LEU136 3.5 27.4 1.0
O B:GLY135 3.5 24.9 1.0
N1 A:PWS308 3.6 51.0 0.7
CA B:LEU136 3.8 23.0 1.0
C B:GLU47 4.0 25.2 1.0
NE1 B:TRP46 4.1 30.9 1.0
C6 A:PWS308 4.2 46.5 0.7
O B:LEU136 4.3 27.3 1.0
CB B:LEU136 4.3 25.9 1.0
CB A:VAL29 4.4 33.8 0.7
CG B:LEU136 4.4 28.5 1.0
C B:GLY135 4.5 23.4 1.0
NH1 A:ARG51 4.5 28.0 0.7
CB A:TRP28 4.6 34.1 0.7
C B:LEU136 4.6 22.9 1.0
CD1 B:TRP46 4.6 26.3 1.0
C1 A:PWS308 4.7 51.8 0.7
N B:LEU136 4.7 22.0 1.0
CB B:GLU47 4.7 27.4 1.0
CA B:GLU47 4.8 25.5 1.0
CG1 A:VAL29 4.8 34.4 0.7
CZ A:ARG51 4.9 29.4 0.7
NH2 A:ARG51 4.9 30.3 0.7
O A:HOH467 4.9 41.5 0.7
CE2 B:TRP46 5.0 30.1 1.0
N A:PWS308 5.0 48.9 0.7
N B:SER48 5.0 21.8 1.0

Fluorine binding site 6 out of 12 in 5qts

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Fluorine binding site 6 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F308

b:49.9
occ:0.74
 F2 A:PWS308 0.0 49.9 0.7
C4 A:PWS308 1.4 50.2 0.7
F A:PWS308 2.1 53.8 0.7
F1 A:PWS308 2.2 50.8 0.7
C3 A:PWS308 2.4 48.4 0.7
NH1 A:ARG51 2.8 28.0 0.7
N1 A:PWS308 3.0 51.0 0.7
O A:HOH420 3.1 27.0 1.0
CG2 A:VAL29 3.3 33.9 0.7
C5 A:PWS308 3.4 46.2 0.7
CZ A:ARG51 3.5 29.4 0.7
O A:TRP28 3.6 29.6 0.7
CB A:TRP28 3.8 34.1 0.7
CD1 B:LEU136 3.8 27.4 1.0
CG A:ARG51 3.9 25.6 0.7
C A:TRP28 4.0 31.1 0.7
NH2 A:ARG51 4.1 30.3 0.7
NE A:ARG51 4.2 28.2 0.7
C1 A:PWS308 4.2 51.8 0.7
CD A:ARG51 4.4 28.2 0.7
CA A:TRP28 4.4 33.5 0.7
CB A:VAL29 4.5 33.8 0.7
O A:HOH467 4.6 41.5 0.7
N A:VAL29 4.6 30.4 0.7
C6 A:PWS308 4.6 46.5 0.7
O B:GLY135 4.7 24.9 1.0
CG A:TRP28 4.8 35.6 0.7
CA A:VAL29 4.8 32.1 0.7
CB A:ARG51 4.9 25.5 0.7
O B:GLU47 4.9 26.6 1.0
CE3 A:TRP28 4.9 38.3 0.7
N A:PWS308 5.0 48.9 0.7

Fluorine binding site 7 out of 12 in 5qts

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Fluorine binding site 7 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F304

b:50.0
occ:0.74
 F C:PWS304 0.0 50.0 0.7
C4 C:PWS304 1.3 48.5 0.7
F1 C:PWS304 2.1 50.8 0.7
F2 C:PWS304 2.1 53.5 0.7
C3 C:PWS304 2.3 45.8 0.7
N1 C:PWS304 2.9 45.7 0.7
NH1 C:ARG51 3.1 44.7 0.7
C5 C:PWS304 3.3 44.0 0.7
CB C:TRP28 3.3 52.7 0.7
O C:TRP28 3.4 45.7 0.7
C C:TRP28 3.7 48.3 0.7
CD1 D:LEU136 3.8 40.4 1.0
CZ C:ARG51 3.9 45.4 0.7
C1 C:PWS304 4.0 46.0 0.7
CA C:TRP28 4.1 50.2 0.7
CB C:VAL29 4.2 45.0 0.7
CG C:ARG51 4.3 46.4 0.7
N C:VAL29 4.3 46.0 0.7
CG C:TRP28 4.4 51.1 0.7
C6 C:PWS304 4.5 42.7 0.7
NH2 C:ARG51 4.6 48.4 0.7
NE C:ARG51 4.6 43.6 0.7
CA C:VAL29 4.6 46.6 0.7
O D:GLY135 4.7 35.2 1.0
CD C:ARG51 4.8 46.6 0.7
N C:PWS304 4.8 43.6 0.7
C C:PWS304 4.8 52.0 0.7
CE3 C:TRP28 4.9 52.4 0.7
CB C:ARG51 4.9 47.8 0.7
CD2 C:TRP28 4.9 52.4 0.7
CG1 C:VAL29 4.9 45.0 0.7

Fluorine binding site 8 out of 12 in 5qts

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Fluorine binding site 8 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F304

b:50.8
occ:0.74
 F1 C:PWS304 0.0 50.8 0.7
C4 C:PWS304 1.3 48.5 0.7
F C:PWS304 2.1 50.0 0.7
F2 C:PWS304 2.1 53.5 0.7
C3 C:PWS304 2.4 45.8 0.7
N1 C:PWS304 2.8 45.7 0.7
O D:GLY135 2.8 35.2 1.0
NH1 C:ARG51 2.9 44.7 0.7
NH2 C:ARG51 3.3 48.4 0.7
CZ C:ARG51 3.3 45.4 0.7
CD1 D:LEU136 3.5 40.4 1.0
C5 C:PWS304 3.5 44.0 0.7
C D:GLY135 3.6 31.1 1.0
CA D:LEU136 3.7 36.4 1.0
CB D:LEU136 3.9 34.3 1.0
N D:LEU136 4.0 37.9 1.0
C1 C:PWS304 4.1 46.0 0.7
CG D:LEU136 4.3 36.0 1.0
NE C:ARG51 4.3 43.6 0.7
NE1 D:TRP46 4.5 42.7 1.0
C C:PWS304 4.6 52.0 0.7
C6 C:PWS304 4.7 42.7 0.7
CA D:GLY135 4.7 32.8 1.0
O D:GLU47 4.9 42.3 1.0
N C:PWS304 4.9 43.6 0.7
C D:LEU136 5.0 35.6 1.0

Fluorine binding site 9 out of 12 in 5qts

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Fluorine binding site 9 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F304

b:53.5
occ:0.74
 F2 C:PWS304 0.0 53.5 0.7
C4 C:PWS304 1.3 48.5 0.7
F1 C:PWS304 2.1 50.8 0.7
F C:PWS304 2.1 50.0 0.7
C3 C:PWS304 2.3 45.8 0.7
C5 C:PWS304 2.7 44.0 0.7
O D:GLU47 3.1 42.3 1.0
CD1 D:LEU136 3.4 40.4 1.0
N1 C:PWS304 3.5 45.7 0.7
O D:GLY135 3.7 35.2 1.0
CA D:LEU136 4.0 36.4 1.0
CB C:VAL29 4.0 45.0 0.7
C6 C:PWS304 4.1 42.7 0.7
CG1 C:VAL29 4.2 45.0 0.7
C D:GLU47 4.2 44.5 1.0
CG D:LEU136 4.3 36.0 1.0
CB C:TRP28 4.3 52.7 0.7
NE1 D:TRP46 4.4 42.7 1.0
O D:LEU136 4.4 45.6 1.0
CB D:LEU136 4.5 34.3 1.0
C1 C:PWS304 4.6 46.0 0.7
C D:GLY135 4.6 31.1 1.0
NH1 C:ARG51 4.6 44.7 0.7
CG2 C:VAL29 4.7 46.5 0.7
C D:LEU136 4.7 35.6 1.0
N D:LEU136 4.8 37.9 1.0
CB D:GLU47 4.8 49.9 1.0
CD1 D:TRP46 4.8 41.5 1.0
C C:TRP28 4.8 48.3 0.7
N C:VAL29 4.9 46.0 0.7
O C:PWS304 4.9 42.5 0.7
O C:TRP28 4.9 45.7 0.7
N C:PWS304 4.9 43.6 0.7
CA D:GLU47 5.0 46.6 1.0

Fluorine binding site 10 out of 12 in 5qts

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Fluorine binding site 10 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with 8J-537S


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 8J-537S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:59.9
occ:0.74
 F D:PWS501 0.0 59.9 0.7
C4 D:PWS501 1.4 57.1 0.7
F1 D:PWS501 2.2 55.1 0.7
F2 D:PWS501 2.2 50.5 0.7
C3 D:PWS501 2.3 54.6 0.7
NH1 D:ARG51 2.6 33.8 0.7
N1 D:PWS501 2.7 56.7 0.7
NH2 D:ARG51 2.8 33.0 0.7
O C:GLY135 2.9 38.4 0.7
CZ D:ARG51 3.0 34.9 0.7
C5 D:PWS501 3.5 53.2 0.7
C C:GLY135 3.6 39.2 0.7
C1 D:PWS501 3.9 59.8 0.7
CA C:LEU136 4.0 40.6 0.7
CD2 C:LEU136 4.1 45.5 0.7
NE D:ARG51 4.1 35.2 0.7
N C:LEU136 4.1 39.7 0.7
NE1 C:TRP46 4.4 39.2 0.7
CB C:LEU136 4.4 43.9 0.7
O D:HOH633 4.5 33.1 0.7
CA C:GLY135 4.6 40.2 0.7
C D:PWS501 4.6 69.5 0.7
C6 D:PWS501 4.6 55.9 0.7
CG2 D:VAL29 4.7 45.5 0.7
CZ2 C:TRP46 4.8 43.5 0.7
N D:PWS501 4.8 56.5 0.7
CG C:LEU136 4.9 46.3 0.7
CE2 C:TRP46 4.9 41.2 0.7
CD D:ARG51 5.0 37.6 0.7

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: Tue Jul 15 06:35:07 2025

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