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Fluorine in PDB 5qtl: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804, PDB code: 5qtl 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) 78.34 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.330, 59.820, 80.180, 79.34, 81.47, 75.65
R / Rfree (%) 22.1 / 25.3

Other elements in 5qtl:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 (pdb code 5qtl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804, PDB code: 5qtl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5qtl

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Fluorine binding site 1 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:51.6
occ:0.84
 F B:PW7501 0.0 51.6 0.8
C B:PW7501 1.3 46.4 0.8
F1 B:PW7501 2.1 51.8 0.8
F2 B:PW7501 2.1 46.1 0.8
C1 B:PW7501 2.4 42.4 0.8
CH2 A:TRP46 3.1 35.1 1.0
N B:PW7501 3.2 39.6 0.8
C4 B:PW7501 3.2 39.2 0.8
CZ2 A:TRP46 3.3 34.1 1.0
CZ3 A:TRP46 4.0 33.3 1.0
CE2 A:TRP46 4.4 32.2 1.0
C2 B:PW7501 4.4 37.9 0.8
C3 B:PW7501 4.4 37.1 0.8
CE3 A:TRP46 4.9 33.5 1.0
N2 B:PW7501 4.9 36.3 0.8
CZ3 B:TRP28 5.0 50.2 0.8
CE3 B:TRP28 5.0 48.8 0.8

Fluorine binding site 2 out of 12 in 5qtl

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Fluorine binding site 2 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:51.8
occ:0.84
 F1 B:PW7501 0.0 51.8 0.8
C B:PW7501 1.3 46.4 0.8
F B:PW7501 2.1 51.6 0.8
F2 B:PW7501 2.1 46.1 0.8
C1 B:PW7501 2.4 42.4 0.8
C4 B:PW7501 2.8 39.2 0.8
CZ3 B:TRP28 3.1 50.2 0.8
CH2 B:TRP28 3.1 50.3 0.8
CE3 B:TRP28 3.4 48.8 0.8
CZ2 B:TRP28 3.4 50.0 0.8
N B:PW7501 3.5 39.6 0.8
CE2 B:TRP28 3.7 47.6 0.8
CD2 B:TRP28 3.7 46.9 0.8
C3 B:PW7501 4.2 37.1 0.8
NE1 B:TRP28 4.6 48.0 0.8
C2 B:PW7501 4.6 37.9 0.8
CH2 A:TRP46 4.6 35.1 1.0
CG B:TRP28 4.7 45.4 0.8
N2 B:PW7501 4.9 36.3 0.8
CZ2 A:TRP46 5.0 34.1 1.0

Fluorine binding site 3 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 3 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:46.1
occ:0.84
 F2 B:PW7501 0.0 46.1 0.8
C B:PW7501 1.4 46.4 0.8
F B:PW7501 2.1 51.6 0.8
F1 B:PW7501 2.1 51.8 0.8
C1 B:PW7501 2.4 42.4 0.8
N B:PW7501 2.7 39.6 0.8
CE3 B:TRP28 3.4 48.8 0.8
CZ3 B:TRP28 3.6 50.2 0.8
C4 B:PW7501 3.6 39.2 0.8
CD1 B:LEU98 3.7 41.7 1.0
NH1 B:ARG51 4.0 39.1 1.0
C2 B:PW7501 4.1 37.9 0.8
CD2 B:TRP28 4.1 46.9 0.8
O B:HOH640 4.3 34.1 0.8
CH2 B:TRP28 4.3 50.3 0.8
CG B:LEU98 4.7 36.9 1.0
C3 B:PW7501 4.7 37.1 0.8
CE2 B:TRP28 4.8 47.6 0.8
CG B:TRP28 4.8 45.4 0.8
CZ2 B:TRP28 4.9 50.0 0.8
CZ2 A:TRP46 4.9 34.1 1.0
N1 B:PW7501 4.9 35.9 0.8
N2 B:PW7501 5.0 36.3 0.8

Fluorine binding site 4 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 4 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


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 Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:38.7
occ:0.68
 F B:PW7505 0.0 38.7 0.7
C B:PW7505 1.3 35.9 0.7
F2 B:PW7505 2.1 36.4 0.7
F1 B:PW7505 2.1 41.2 0.7
C1 B:PW7505 2.4 33.6 0.7
O A:HOH487 2.7 31.6 0.7
N B:PW7505 2.9 31.1 0.7
CH2 B:TRP46 3.1 31.1 0.7
CZ2 B:TRP46 3.3 29.9 0.7
C4 B:PW7505 3.4 31.2 0.7
O A:HOH439 3.9 26.4 0.7
CZ3 B:TRP46 4.2 30.1 0.7
C2 B:PW7505 4.2 29.6 0.7
CE2 B:TRP46 4.4 29.7 0.7
C3 B:PW7505 4.5 30.9 0.7
CZ3 A:TRP28 4.7 39.0 0.7
CE3 A:TRP28 4.7 38.2 0.7
NH1 A:ARG51 4.9 35.4 1.0
N2 B:PW7505 4.9 30.4 0.7
CD1 A:LEU98 4.9 31.6 1.0

Fluorine binding site 5 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 5 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:41.2
occ:0.68
 F1 B:PW7505 0.0 41.2 0.7
C B:PW7505 1.3 35.9 0.7
F B:PW7505 2.1 38.7 0.7
F2 B:PW7505 2.1 36.4 0.7
C1 B:PW7505 2.4 33.6 0.7
C4 B:PW7505 2.8 31.2 0.7
CZ3 A:TRP28 3.1 39.0 0.7
CH2 A:TRP28 3.1 38.5 0.7
CE3 A:TRP28 3.4 38.2 0.7
CZ2 A:TRP28 3.5 37.7 0.7
N B:PW7505 3.6 31.1 0.7
CD2 A:TRP28 3.7 36.6 0.7
CE2 A:TRP28 3.7 36.1 0.7
CH2 B:TRP46 4.2 31.1 0.7
C3 B:PW7505 4.2 30.9 0.7
O A:HOH487 4.5 31.6 0.7
CZ2 B:TRP46 4.6 29.9 0.7
CZ3 B:TRP46 4.7 30.1 0.7
NE1 A:TRP28 4.7 37.1 0.7
C2 B:PW7505 4.7 29.6 0.7
CG A:TRP28 4.7 36.2 0.7

Fluorine binding site 6 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 6 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:36.4
occ:0.68
 F2 B:PW7505 0.0 36.4 0.7
C B:PW7505 1.3 35.9 0.7
F B:PW7505 2.1 38.7 0.7
F1 B:PW7505 2.1 41.2 0.7
C1 B:PW7505 2.3 33.6 0.7
N B:PW7505 2.7 31.1 0.7
CE3 A:TRP28 3.0 38.2 0.7
CZ3 A:TRP28 3.2 39.0 0.7
C4 B:PW7505 3.5 31.2 0.7
O A:HOH487 3.6 31.6 0.7
CD2 A:TRP28 3.7 36.6 0.7
O A:HOH413 3.7 50.9 0.7
CD1 A:LEU98 3.7 31.6 1.0
NH1 A:ARG51 3.9 35.4 1.0
C2 B:PW7505 4.0 29.6 0.7
CH2 A:TRP28 4.1 38.5 0.7
CE2 A:TRP28 4.4 36.1 0.7
CG A:TRP28 4.4 36.2 0.7
C3 B:PW7505 4.6 30.9 0.7
CZ2 A:TRP28 4.6 37.7 0.7
CG A:LEU98 4.7 26.8 1.0
CB A:TRP28 4.7 35.7 0.7
CZ2 B:TRP46 4.8 29.9 0.7
N1 B:PW7505 4.8 28.5 0.7
N2 B:PW7505 4.9 30.4 0.7
CH2 B:TRP46 4.9 31.1 0.7

Fluorine binding site 7 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 7 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F305

b:49.2
occ:0.81
 F C:PW7305 0.0 49.2 0.8
C C:PW7305 1.3 49.9 0.8
F1 C:PW7305 2.1 55.5 0.8
F2 C:PW7305 2.1 58.0 0.8
C1 C:PW7305 2.4 44.8 0.8
N C:PW7305 2.9 42.6 0.8
CE3 C:TRP28 3.1 61.9 0.8
CZ3 C:TRP28 3.1 62.5 0.8
C4 C:PW7305 3.5 42.7 0.8
CD2 C:TRP28 3.8 60.4 0.8
CH2 C:TRP28 3.9 62.3 0.8
CD1 C:LEU98 4.0 43.1 1.0
C2 C:PW7305 4.2 39.5 0.8
NH1 C:ARG51 4.4 43.3 0.8
CE2 C:TRP28 4.5 60.9 0.8
CZ2 C:TRP28 4.5 62.8 0.8
CG C:TRP28 4.7 58.6 0.8
C3 C:PW7305 4.7 40.9 0.8
CG C:LEU98 4.8 39.5 1.0
N2 C:PW7305 5.0 40.0 0.8

Fluorine binding site 8 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 8 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F305

b:55.5
occ:0.81
 F1 C:PW7305 0.0 55.5 0.8
C C:PW7305 1.3 49.9 0.8
F C:PW7305 2.1 49.2 0.8
F2 C:PW7305 2.1 58.0 0.8
C1 C:PW7305 2.4 44.8 0.8
N C:PW7305 3.0 42.6 0.8
CH2 D:TRP46 3.3 39.2 1.0
C4 C:PW7305 3.4 42.7 0.8
CZ2 D:TRP46 3.4 42.0 1.0
CZ3 D:TRP46 4.2 42.9 1.0
C2 C:PW7305 4.3 39.5 0.8
CE2 D:TRP46 4.4 40.7 1.0
C3 C:PW7305 4.6 40.9 0.8
CZ3 C:TRP28 4.9 62.5 0.8
CE3 C:TRP28 4.9 61.9 0.8

Fluorine binding site 9 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 9 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F305

b:58.0
occ:0.81
 F2 C:PW7305 0.0 58.0 0.8
C C:PW7305 1.4 49.9 0.8
F C:PW7305 2.1 49.2 0.8
F1 C:PW7305 2.1 55.5 0.8
C1 C:PW7305 2.4 44.8 0.8
C4 C:PW7305 2.7 42.7 0.8
CH2 C:TRP28 3.2 62.3 0.8
CZ3 C:TRP28 3.3 62.5 0.8
CZ2 C:TRP28 3.5 62.8 0.8
N C:PW7305 3.6 42.6 0.8
CE3 C:TRP28 3.7 61.9 0.8
CE2 C:TRP28 3.8 60.9 0.8
CD2 C:TRP28 3.9 60.4 0.8
C3 C:PW7305 4.1 40.9 0.8
CH2 D:TRP46 4.5 39.2 1.0
NE1 C:TRP28 4.7 58.9 0.8
C2 C:PW7305 4.7 39.5 0.8
CZ3 D:TRP46 4.8 42.9 1.0
CG C:TRP28 4.9 58.6 0.8
CZ2 D:TRP46 4.9 42.0 1.0
N2 C:PW7305 5.0 40.0 0.8

Fluorine binding site 10 out of 12 in 5qtl

Go back to Fluorine Binding Sites List in 5qtl
Fluorine binding site 10 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Gb-0804 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:65.1
occ:0.81
 F D:PW7501 0.0 65.1 0.8
C D:PW7501 1.3 59.9 0.8
F1 D:PW7501 2.1 66.6 0.8
F2 D:PW7501 2.1 61.1 0.8
C1 D:PW7501 2.4 52.8 0.8
N D:PW7501 2.8 48.1 0.8
CD1 D:LEU98 3.1 45.1 1.0
O D:HOH646 3.4 44.4 0.8
CE3 D:TRP28 3.4 53.1 0.8
O D:HOH611 3.5 47.5 0.8
C4 D:PW7501 3.5 49.3 0.8
CZ3 D:TRP28 3.5 56.4 0.8
NH1 D:ARG51 4.1 40.8 0.8
C2 D:PW7501 4.2 45.7 0.8
CD2 D:TRP28 4.2 51.9 0.8
CG D:LEU98 4.3 45.0 1.0
CH2 D:TRP28 4.4 54.2 0.8
C3 D:PW7501 4.7 46.8 0.8
CE2 D:TRP28 4.9 50.5 0.8
CD2 D:LEU98 5.0 45.0 1.0
CG D:TRP28 5.0 50.1 0.8
N2 D:PW7501 5.0 45.5 0.8

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: Thu Aug 1 13:24:19 2024

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