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Fluorine in PDB 5qk6: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025

All present enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025, PDB code: 5qk6 was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.45 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.260, 59.800, 80.310, 79.26, 81.50, 75.67
R / Rfree (%) 22.7 / 25.5

Other elements in 5qk6:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025 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 of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025 (pdb code 5qk6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025, PDB code: 5qk6:

Fluorine binding site 1 out of 1 in 5qk6

Go back to Fluorine Binding Sites List in 5qk6
Fluorine binding site 1 out of 1 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025


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 of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1343633025 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:47.5
occ:0.92
 F A:K3M303 0.0 47.5 0.9
C6 A:K3M303 1.3 44.9 0.9
C7 A:K3M303 2.4 46.7 0.9
C4 A:K3M303 2.4 41.3 0.9
N A:K3M303 2.6 29.2 0.9
NH1 B:ARG51 2.8 26.0 1.0
C5 A:K3M303 2.9 36.5 0.9
O B:HOH451 3.5 27.1 0.9
C3 A:K3M303 3.7 42.0 0.9
C1 A:K3M303 3.7 47.3 0.9
CB B:TRP28 3.7 33.6 0.9
CZ B:ARG51 4.0 26.6 1.0
CG B:TRP28 4.0 37.0 0.9
CE3 B:TRP28 4.0 41.8 0.9
CD2 B:TRP28 4.1 38.4 0.9
O A:K3M303 4.1 36.8 0.9
C2 A:K3M303 4.1 45.9 0.9
O A:GLY135 4.3 23.7 1.0
NH2 B:ARG51 4.4 28.1 1.0
CG2 B:VAL29 4.8 34.3 1.0
CZ2 A:TRP46 4.8 28.7 1.0
NE1 A:TRP46 4.8 23.8 1.0
CD1 B:TRP28 4.9 38.5 0.9
O B:TRP28 4.9 26.6 0.9
C A:K3M303 4.9 47.8 0.9
CA B:TRP28 4.9 29.6 0.9
CZ3 B:TRP28 4.9 43.1 0.9
CE2 A:TRP46 5.0 27.9 1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) To Be Published.
Page generated: Tue Jul 15 06:27:10 2025

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