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Fluorine in PDB 5qj8: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

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 Z2856434829:
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 Z2856434829, PDB code: 5qj8 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) 77.81 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.530, 59.990, 79.650, 79.56, 81.09, 75.49
R / Rfree (%) 23.5 / 27.8

Other elements in 5qj8:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 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 Z2856434829 (pdb code 5qj8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 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 Z2856434829, PDB code: 5qj8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5qj8

Go back to Fluorine Binding Sites List in 5qj8
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:59.3
occ:0.70
 F16 B:ELQ305 0.0 59.3 0.7
C14 B:ELQ305 1.3 59.7 0.7
C13 B:ELQ305 2.3 61.0 0.7
C15 B:ELQ305 2.4 60.2 0.7
O B:GLU47 2.5 34.5 1.0
F17 B:ELQ305 2.6 56.2 0.7
O B:GLY135 3.1 29.4 1.0
NE1 B:TRP46 3.3 30.4 1.0
C12 B:ELQ305 3.6 62.5 0.7
C10 B:ELQ305 3.6 61.9 0.7
C B:GLU47 3.7 33.6 1.0
CG2 A:VAL29 3.8 35.7 1.0
CD1 B:TRP46 3.8 31.9 1.0
CE2 B:TRP46 4.1 34.0 1.0
CA B:LEU136 4.1 29.2 1.0
C11 B:ELQ305 4.1 62.4 0.7
CD1 B:LEU136 4.2 36.5 1.0
C B:GLY135 4.2 30.4 1.0
N B:GLU47 4.5 30.2 1.0
CA B:GLU47 4.5 35.0 1.0
CB B:GLU47 4.5 34.5 1.0
N B:LEU136 4.6 27.2 1.0
CZ2 B:TRP46 4.7 36.0 1.0
O B:LEU136 4.7 35.5 1.0
CG B:TRP46 4.7 34.8 1.0
CB B:LEU136 4.8 33.1 1.0
N B:SER48 4.8 28.8 1.0
C08 B:ELQ305 4.8 61.9 0.7
CD2 B:TRP46 4.9 30.9 1.0
C B:LEU136 4.9 31.8 1.0
O09 B:ELQ305 5.0 64.1 0.7
NH1 A:ARG51 5.0 30.1 1.0

Fluorine binding site 2 out of 2 in 5qj8

Go back to Fluorine Binding Sites List in 5qj8
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829


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 Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:56.2
occ:0.70
 F17 B:ELQ305 0.0 56.2 0.7
C13 B:ELQ305 1.3 61.0 0.7
C14 B:ELQ305 2.3 59.7 0.7
C12 B:ELQ305 2.4 62.5 0.7
NH1 A:ARG51 2.6 30.1 1.0
F16 B:ELQ305 2.6 59.3 0.7
O A:HOH425 3.1 45.0 1.0
CZ A:ARG51 3.3 32.1 1.0
C15 B:ELQ305 3.6 60.2 0.7
C11 B:ELQ305 3.7 62.4 0.7
NH2 A:ARG51 3.7 33.4 1.0
CG2 A:VAL29 3.8 35.7 1.0
CD1 B:LEU136 3.9 36.5 1.0
C10 B:ELQ305 4.1 61.9 0.7
O A:TRP28 4.2 34.1 0.7
NE A:ARG51 4.2 31.7 1.0
CG A:ARG51 4.3 27.3 1.0
CB A:TRP28 4.4 46.1 0.7
O B:GLY135 4.5 29.4 1.0
CD A:ARG51 4.6 30.3 1.0
C A:TRP28 4.7 38.1 0.7
CB B:LEU136 5.0 33.1 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: Sun Dec 13 12:31:59 2020

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