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Fluorine in PDB 5qjx: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778

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 Z2856434778:
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 Z2856434778, PDB code: 5qjx 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) 78.96 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.520, 59.520, 80.620, 79.68, 82.36, 76.36
R / Rfree (%) 22 / 25.6

Other elements in 5qjx:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778 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 Z2856434778 (pdb code 5qjx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778, PDB code: 5qjx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5qjx

Go back to Fluorine Binding Sites List in 5qjx
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:66.5
occ:0.98
 F B:K2P304 0.0 66.5 1.0
C7 B:K2P304 1.4 69.2 1.0
F1 B:K2P304 2.1 70.0 1.0
O2 B:K2P304 2.2 69.0 1.0
F2 B:K2P304 2.2 69.5 1.0
O B:LYS81 3.4 31.3 1.0
C6 B:K2P304 3.5 67.2 1.0
CE2 B:TYR90 3.6 35.5 1.0
CD2 B:TYR90 3.8 31.1 1.0
CG B:LYS81 3.8 45.3 1.0
CE B:LYS81 3.9 55.5 1.0
C B:LYS81 3.9 32.3 1.0
O1 B:K2P304 4.0 58.0 1.0
CB B:GLU169 4.0 53.3 1.0
CA B:GLN82 4.1 33.8 1.0
CD B:LYS81 4.2 51.8 1.0
N B:GLN82 4.3 32.1 1.0
C5 B:K2P304 4.3 65.5 1.0
O B:PHE167 4.3 48.4 1.0
C1 B:K2P304 4.4 68.8 1.0
C B:K2P304 4.4 66.5 1.0
N B:GLU169 4.6 48.7 1.0
CB B:LYS81 4.6 37.2 1.0
C B:GLN82 4.6 27.9 1.0
OE1 B:GLU169 4.7 56.2 1.0
O B:HOH419 4.7 45.5 1.0
CD B:GLU169 4.7 61.0 1.0
CZ B:TYR90 4.8 35.0 1.0
N B:PHE83 4.8 28.9 1.0
CA B:LYS81 4.9 31.9 1.0
CA B:GLU169 5.0 48.7 1.0
CG B:TYR90 5.0 29.8 1.0

Fluorine binding site 2 out of 3 in 5qjx

Go back to Fluorine Binding Sites List in 5qjx
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778


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 of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:70.0
occ:0.98
 F1 B:K2P304 0.0 70.0 1.0
C7 B:K2P304 1.3 69.2 1.0
F B:K2P304 2.1 66.5 1.0
F2 B:K2P304 2.2 69.5 1.0
O2 B:K2P304 2.2 69.0 1.0
O B:PHE167 2.7 48.4 1.0
C6 B:K2P304 3.0 67.2 1.0
C5 B:K2P304 3.1 65.5 1.0
O B:LYS81 3.1 31.3 1.0
C B:PHE167 3.2 42.3 1.0
N B:GLU169 3.2 48.7 1.0
C B:VAL168 3.4 47.9 1.0
CA B:VAL168 3.4 43.1 1.0
N B:VAL168 3.5 43.4 1.0
CB B:GLU169 3.7 53.3 1.0
CA B:GLU169 4.1 48.7 1.0
C B:LYS81 4.1 32.3 1.0
O B:VAL168 4.2 49.4 1.0
O B:HOH419 4.2 45.5 1.0
C1 B:K2P304 4.2 68.8 1.0
CA B:GLN82 4.3 33.8 1.0
CA B:PHE167 4.4 48.0 1.0
CB B:PHE167 4.4 49.5 1.0
C4 B:K2P304 4.4 66.8 1.0
N B:GLN82 4.6 32.1 1.0
O1 B:K2P304 4.7 58.0 1.0
C B:K2P304 4.9 66.5 1.0
CB B:VAL168 4.9 49.4 1.0
CG B:GLU169 5.0 57.4 1.0

Fluorine binding site 3 out of 3 in 5qjx

Go back to Fluorine Binding Sites List in 5qjx
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778


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 of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:69.5
occ:0.98
 F2 B:K2P304 0.0 69.5 1.0
C7 B:K2P304 1.3 69.2 1.0
F1 B:K2P304 2.2 70.0 1.0
F B:K2P304 2.2 66.5 1.0
O2 B:K2P304 2.3 69.0 1.0
O B:HOH419 2.9 45.5 1.0
O1 B:K2P304 2.9 58.0 1.0
C6 B:K2P304 2.9 67.2 1.0
O B:PHE167 3.0 48.4 1.0
NE2 A:GLN15 3.3 41.3 1.0
CE2 B:TYR90 3.5 35.5 1.0
C1 B:K2P304 3.6 68.8 1.0
C B:K2P304 3.6 66.5 1.0
C5 B:K2P304 3.8 65.5 1.0
N B:PHE83 3.9 28.9 1.0
C B:PHE167 4.0 42.3 1.0
CA B:GLN82 4.0 33.8 1.0
CB B:PHE167 4.1 49.5 1.0
CD2 B:TYR90 4.2 31.1 1.0
C B:GLN82 4.3 27.9 1.0
O B:LYS81 4.3 31.3 1.0
CZ B:TYR90 4.6 35.0 1.0
OH B:TYR90 4.6 36.1 1.0
CD A:GLN15 4.6 37.4 1.0
CA B:PHE167 4.7 48.0 1.0
O B:K2P304 4.8 69.9 1.0
C2 B:K2P304 4.8 70.6 1.0
N B:VAL168 4.8 43.4 1.0
CB B:PHE83 4.9 32.3 1.0
N B:GLN82 4.9 32.1 1.0
C B:LYS81 4.9 32.3 1.0
C4 B:K2P304 4.9 66.8 1.0
CA B:PHE83 5.0 29.5 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 06:27:01 2025

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