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Fluorine in PDB 5qtq: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169:
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 Fs-1169, PDB code: 5qtq 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) 47.30 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.998, 59.703, 80.195, 79.38, 81.67, 75.86
R / Rfree (%) 21.1 / 25

Other elements in 5qtq:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169 (pdb code 5qtq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169, PDB code: 5qtq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5qtq

Go back to Fluorine Binding Sites List in 5qtq
Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169


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 Fs-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:36.4
occ:0.86
 F A:PWM303 0.0 36.4 0.9
C A:PWM303 1.3 32.4 0.9
C1 A:PWM303 2.3 33.8 0.9
C7 A:PWM303 2.4 29.5 0.9
O A:PWM303 2.8 26.6 0.9
C6 A:PWM303 3.0 29.6 0.9
NE1 B:TRP28 3.2 32.0 0.9
CD1 B:TRP28 3.5 33.7 0.9
CE2 B:TRP28 3.6 34.0 0.9
O B:HOH467 3.6 40.0 0.9
CZ3 A:TRP46 3.6 26.8 1.0
CE3 A:TRP46 3.6 27.4 1.0
C2 A:PWM303 3.6 34.4 0.9
C4 A:PWM303 3.7 30.9 0.9
CG B:TRP28 4.0 33.0 0.9
CH2 A:TRP46 4.1 28.7 1.0
CD2 B:TRP28 4.1 32.6 0.9
CD2 A:TRP46 4.1 26.9 1.0
CZ2 B:TRP28 4.2 33.2 0.9
C3 A:PWM303 4.2 34.0 0.9
N1 A:PWM303 4.3 26.5 0.9
CZ2 A:TRP46 4.5 28.4 1.0
CE2 A:TRP46 4.5 28.5 1.0
O A:HOH423 4.6 27.9 0.9
O A:THR45 4.7 31.2 1.0
N A:PWM303 4.9 27.0 0.9
CG A:TRP46 4.9 27.0 1.0
CA A:TRP46 4.9 28.0 1.0

Fluorine binding site 2 out of 4 in 5qtq

Go back to Fluorine Binding Sites List in 5qtq
Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169


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 Fs-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:32.4
occ:0.84
 F B:PWM305 0.0 32.4 0.8
C B:PWM305 1.3 29.0 0.8
C1 B:PWM305 2.3 30.9 0.8
C7 B:PWM305 2.3 28.5 0.8
O B:PWM305 2.7 26.3 0.8
C6 B:PWM305 2.9 27.4 0.8
NE1 A:TRP28 3.2 32.7 0.8
O B:HOH454 3.3 37.0 0.8
CE2 A:TRP28 3.4 33.6 0.8
O A:HOH461 3.6 39.4 0.8
CZ3 B:TRP46 3.6 27.1 1.0
C2 B:PWM305 3.6 31.6 0.8
C4 B:PWM305 3.6 28.6 0.8
CD1 A:TRP28 3.7 33.3 0.8
CE3 B:TRP46 3.7 25.2 1.0
CZ2 A:TRP28 3.8 34.2 0.8
CD2 A:TRP28 3.9 32.1 0.8
CH2 B:TRP46 4.0 28.0 1.0
CG A:TRP28 4.0 31.9 0.8
C3 B:PWM305 4.1 30.0 0.8
CD2 B:TRP46 4.2 23.3 1.0
N1 B:PWM305 4.2 27.8 0.8
O B:HOH426 4.2 32.1 0.8
CZ2 B:TRP46 4.5 26.0 1.0
CE2 B:TRP46 4.6 25.5 1.0
O B:THR45 4.6 26.2 1.0
CH2 A:TRP28 4.6 34.5 0.8
CE3 A:TRP28 4.7 34.9 0.8
N B:PWM305 4.8 27.2 0.8
C5 B:PWM305 4.9 28.7 0.8
CZ3 A:TRP28 5.0 35.0 0.8

Fluorine binding site 3 out of 4 in 5qtq

Go back to Fluorine Binding Sites List in 5qtq
Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169


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 Fs-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F305

b:43.7
occ:0.86
 F C:PWM305 0.0 43.7 0.9
C C:PWM305 1.4 40.5 0.9
C1 C:PWM305 2.4 40.0 0.9
C7 C:PWM305 2.4 39.1 0.9
O C:PWM305 2.6 31.9 0.9
C6 C:PWM305 2.9 35.2 0.9
NE1 C:TRP28 3.0 48.8 0.9
CD1 C:TRP28 3.3 49.2 0.9
CE2 C:TRP28 3.4 48.9 0.9
C2 C:PWM305 3.7 41.1 0.9
CE3 D:TRP46 3.7 36.0 0.9
C4 C:PWM305 3.7 39.5 0.9
CZ3 D:TRP46 3.7 38.0 0.9
CG C:TRP28 3.8 48.1 0.9
CD2 C:TRP28 3.8 49.6 0.9
CZ2 C:TRP28 4.0 49.4 0.9
CD2 D:TRP46 4.1 37.7 0.9
C3 C:PWM305 4.2 41.8 0.9
CH2 D:TRP46 4.2 37.2 0.9
N1 C:PWM305 4.2 37.8 0.9
CE2 D:TRP46 4.6 37.8 0.9
CZ2 D:TRP46 4.6 36.6 0.9
O D:THR45 4.7 38.4 1.0
CE3 C:TRP28 4.8 50.9 0.9
CB C:TRP28 4.8 48.8 0.9
CG D:TRP46 4.8 36.4 0.9
N C:PWM305 4.9 40.9 0.9
CH2 C:TRP28 4.9 50.2 0.9
CA D:TRP46 4.9 38.1 0.9

Fluorine binding site 4 out of 4 in 5qtq

Go back to Fluorine Binding Sites List in 5qtq
Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-1169


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 Fs-1169 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:36.0
occ:0.86
 F D:PWM501 0.0 36.0 0.9
C D:PWM501 1.3 35.0 0.9
C1 D:PWM501 2.3 36.4 0.9
C7 D:PWM501 2.4 35.3 0.9
O D:PWM501 2.7 34.4 0.9
C6 D:PWM501 2.9 33.2 0.9
NE1 D:TRP28 3.1 38.5 0.9
CD1 D:TRP28 3.4 39.9 0.9
CE2 D:TRP28 3.6 39.2 0.9
C2 D:PWM501 3.7 37.9 0.9
CE3 C:TRP46 3.7 36.9 1.0
C4 D:PWM501 3.7 34.4 0.9
CZ3 C:TRP46 3.8 37.8 1.0
CD2 C:TRP46 4.0 33.3 1.0
CG D:TRP28 4.1 40.1 0.9
C3 D:PWM501 4.2 36.8 0.9
CD2 D:TRP28 4.2 40.7 0.9
CZ2 D:TRP28 4.2 42.1 0.9
N1 D:PWM501 4.3 36.5 0.9
CH2 C:TRP46 4.3 37.9 1.0
O C:THR45 4.3 30.4 1.0
CE2 C:TRP46 4.5 31.1 1.0
CZ2 C:TRP46 4.6 32.8 1.0
CA C:TRP46 4.7 35.5 1.0
CG C:TRP46 4.7 30.7 1.0
N D:PWM501 4.8 37.0 0.9
C5 D:PWM501 5.0 36.7 0.9

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 06:32:32 2025

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