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Fluorine in PDB 5qtm: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639:
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-2639, PDB code: 5qtm 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) 47.50 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.270, 59.808, 80.068, 79.33, 81.48, 75.66
R / Rfree (%) 21.4 / 24.7

Other elements in 5qtm:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639 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-2639 (pdb code 5qtm). 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-2639, PDB code: 5qtm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5qtm

Go back to Fluorine Binding Sites List in 5qtm
Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:38.0
occ:0.86
 F A:PWA304 0.0 38.0 0.9
C A:PWA304 1.4 38.5 0.9
C3 A:PWA304 2.3 37.1 0.9
C1 A:PWA304 2.5 35.9 0.9
CZ3 B:TRP28 3.5 42.5 0.9
C4 A:PWA304 3.6 31.6 0.9
C2 A:PWA304 3.7 32.8 0.9
CD1 B:LEU98 3.8 37.3 1.0
CH2 B:TRP28 3.8 41.2 0.9
CE3 B:TRP28 4.0 38.7 0.9
C6 A:PWA304 4.2 30.2 0.9
O B:HOH472 4.5 31.2 0.9
CZ2 B:TRP28 4.6 41.2 0.9
CG B:LEU98 4.6 33.5 1.0
N A:PWA304 4.7 28.3 0.9
CD2 B:TRP28 4.7 38.5 0.9
CH2 A:TRP46 4.8 29.7 1.0
CE2 B:TRP28 4.9 41.1 0.9

Fluorine binding site 2 out of 4 in 5qtm

Go back to Fluorine Binding Sites List in 5qtm
Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:33.8
occ:0.75
 F B:PWA304 0.0 33.8 0.8
C B:PWA304 1.3 30.7 0.8
C3 B:PWA304 2.3 28.9 0.8
C1 B:PWA304 2.4 28.2 0.8
C4 B:PWA304 3.6 26.8 0.8
C2 B:PWA304 3.6 27.1 0.8
CZ3 A:TRP28 3.6 34.1 0.8
CD1 A:LEU98 3.9 29.3 1.0
CH2 A:TRP28 3.9 31.8 0.8
O A:HOH469 4.0 36.0 1.0
C6 B:PWA304 4.1 26.5 0.8
CE3 A:TRP28 4.1 33.4 0.8
CH2 B:TRP46 4.4 25.4 0.8
CG A:LEU98 4.6 24.7 1.0
N B:PWA304 4.7 23.8 0.8
CZ2 A:TRP28 4.7 33.9 0.8
O A:HOH459 4.7 20.9 0.8
CD2 A:TRP28 4.8 31.0 0.8
CZ2 B:TRP46 5.0 24.3 0.8

Fluorine binding site 3 out of 4 in 5qtm

Go back to Fluorine Binding Sites List in 5qtm
Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:42.0
occ:0.81
 F D:PWA501 0.0 42.0 0.8
C D:PWA501 1.4 41.2 0.8
C3 D:PWA501 2.4 41.1 0.8
C1 D:PWA501 2.4 42.0 0.8
C4 D:PWA501 3.6 37.4 0.8
CD1 D:LEU98 3.7 41.7 1.0
C2 D:PWA501 3.7 38.6 0.8
CZ3 D:TRP28 3.8 44.9 0.8
CH2 D:TRP28 4.0 47.4 0.8
O D:HOH645 4.0 33.0 0.8
C6 D:PWA501 4.2 38.8 0.8
CE3 D:TRP28 4.3 44.3 0.8
CG D:LEU98 4.5 40.4 1.0
CZ2 D:TRP28 4.7 47.0 0.8
N D:PWA501 4.7 38.3 0.8
O D:HOH636 4.7 33.7 0.8
CH2 C:TRP46 4.8 33.5 0.8
CD2 D:TRP28 4.9 45.6 0.8

Fluorine binding site 4 out of 4 in 5qtm

Go back to Fluorine Binding Sites List in 5qtm
Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Fs-2639


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-2639 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F505

b:51.5
occ:0.88
 F D:PWA505 0.0 51.5 0.9
C D:PWA505 1.4 45.9 0.9
C3 D:PWA505 2.4 46.4 0.9
C1 D:PWA505 2.4 44.8 0.9
CZ3 C:TRP28 3.6 55.7 1.0
C4 D:PWA505 3.6 39.7 0.9
C2 D:PWA505 3.7 40.6 0.9
CD1 C:LEU98 3.8 38.4 1.0
CH2 C:TRP28 3.9 56.8 1.0
O C:HOH457 4.0 42.6 0.9
C2 C:EDO306 4.0 43.4 0.9
CE3 C:TRP28 4.1 57.5 1.0
C6 D:PWA505 4.1 40.6 0.9
O2 C:EDO306 4.6 44.3 0.9
CZ2 C:TRP28 4.7 55.6 1.0
CG C:LEU98 4.7 34.1 1.0
CH2 D:TRP46 4.7 43.6 1.0
N D:PWA505 4.8 40.0 0.9
CD2 C:TRP28 4.8 53.4 1.0

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 06:31:44 2025

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