Fluorine in PDB 5qtp: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227:
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 Ae-0227, PDB code: 5qtp 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) 42.67 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.246, 59.826, 80.052, 79.42, 81.55, 75.70
R / Rfree (%) 22.9 / 26.1

Other elements in 5qtp:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 5 atoms

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 Ae-0227 (pdb code 5qtp). 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 Ae-0227, PDB code: 5qtp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5qtp

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Fluorine binding site 1 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:46.0
occ:0.83
 F A:PWJ303 0.0 46.0 0.8
C6 A:PWJ303 1.4 43.5 0.8
F1 A:PWJ303 2.1 42.3 0.8
F2 A:PWJ303 2.1 47.8 0.8
C5 A:PWJ303 2.5 42.7 0.8
C4 A:PWJ303 2.8 40.8 0.8
CZ3 B:TRP28 3.5 46.5 0.8
CD1 B:LEU98 3.8 35.1 1.0
C7 A:PWJ303 3.8 42.0 0.8
CH2 B:TRP28 3.9 45.6 0.8
CE3 B:TRP28 4.1 40.6 0.8
N1 A:PWJ303 4.2 37.0 0.8
O B:HOH456 4.3 29.7 0.8
CG B:LEU98 4.3 32.7 1.0
C8 A:PWJ303 4.5 43.5 0.8
CZ2 B:TRP28 4.8 44.0 0.8
CH2 A:TRP46 4.9 31.7 0.8
C A:PWJ303 4.9 41.1 0.8
CD2 B:TRP28 5.0 40.8 0.8

Fluorine binding site 2 out of 12 in 5qtp

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Fluorine binding site 2 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:42.3
occ:0.83
 F1 A:PWJ303 0.0 42.3 0.8
C6 A:PWJ303 1.3 43.5 0.8
F2 A:PWJ303 2.1 47.8 0.8
F A:PWJ303 2.1 46.0 0.8
C5 A:PWJ303 2.5 42.7 0.8
CH2 B:TRP28 3.1 45.6 0.8
C8 A:PWJ303 3.1 43.5 0.8
C7 A:PWJ303 3.2 42.0 0.8
N2 A:PWJ303 3.5 42.1 0.8
CZ3 B:TRP28 3.6 46.5 0.8
C4 A:PWJ303 3.6 40.8 0.8
CZ2 B:TRP28 3.7 44.0 0.8
CE3 B:TRP28 4.5 40.6 0.8
C A:PWJ303 4.5 41.1 0.8
CE2 B:TRP28 4.6 43.5 0.8
N1 A:PWJ303 4.8 37.0 0.8
CD2 B:TRP28 4.9 40.8 0.8
CH2 A:TRP46 5.0 31.7 0.8

Fluorine binding site 3 out of 12 in 5qtp

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Fluorine binding site 3 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:47.8
occ:0.83
 F2 A:PWJ303 0.0 47.8 0.8
C6 A:PWJ303 1.4 43.5 0.8
F1 A:PWJ303 2.1 42.3 0.8
F A:PWJ303 2.1 46.0 0.8
C5 A:PWJ303 2.5 42.7 0.8
C7 A:PWJ303 3.3 42.0 0.8
C4 A:PWJ303 3.3 40.8 0.8
CH2 A:TRP46 3.4 31.7 0.8
C8 A:PWJ303 3.6 43.5 0.8
O B:HOH456 3.9 29.7 0.8
N2 A:PWJ303 4.1 42.1 0.8
CZ3 A:TRP46 4.1 29.9 0.8
CZ2 A:TRP46 4.2 29.5 0.8
N1 A:PWJ303 4.5 37.0 0.8
C A:PWJ303 4.5 41.1 0.8
CH2 B:TRP28 4.9 45.6 0.8

Fluorine binding site 4 out of 12 in 5qtp

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Fluorine binding site 4 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:47.1
occ:0.70
 F B:PWJ305 0.0 47.1 0.7
C6 B:PWJ305 1.3 41.0 0.7
F1 B:PWJ305 2.1 42.8 0.7
F2 B:PWJ305 2.2 43.9 0.7
C5 B:PWJ305 2.4 38.9 0.7
C8 B:PWJ305 2.9 40.0 0.7
CH2 A:TRP28 2.9 37.2 0.7
C7 B:PWJ305 3.0 38.6 0.7
N2 B:PWJ305 3.2 45.8 0.7
CZ2 A:TRP28 3.3 34.8 0.7
CZ3 A:TRP28 3.5 35.8 0.7
C4 B:PWJ305 3.5 34.2 0.7
CE2 A:TRP28 4.2 34.2 0.7
C B:PWJ305 4.3 33.1 0.7
CE3 A:TRP28 4.4 36.2 0.7
CD2 A:TRP28 4.7 33.3 0.7
N1 B:PWJ305 4.7 33.1 0.7
CH2 B:TRP46 4.8 25.7 0.7

Fluorine binding site 5 out of 12 in 5qtp

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Fluorine binding site 5 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:42.8
occ:0.70
 F1 B:PWJ305 0.0 42.8 0.7
C6 B:PWJ305 1.3 41.0 0.7
F2 B:PWJ305 2.0 43.9 0.7
F B:PWJ305 2.1 47.1 0.7
C5 B:PWJ305 2.5 38.9 0.7
C7 B:PWJ305 3.3 38.6 0.7
CH2 B:TRP46 3.4 25.7 0.7
C4 B:PWJ305 3.4 34.2 0.7
C8 B:PWJ305 3.4 40.0 0.7
N2 B:PWJ305 3.9 45.8 0.7
CZ3 B:TRP46 4.0 24.1 0.7
O A:HOH447 4.2 19.6 0.7
CZ2 B:TRP46 4.2 24.7 0.7
O A:HOH465 4.4 36.8 1.0
C B:PWJ305 4.5 33.1 0.7
N1 B:PWJ305 4.6 33.1 0.7
CH2 A:TRP28 4.9 37.2 0.7
O A:HOH460 5.0 26.0 0.7

Fluorine binding site 6 out of 12 in 5qtp

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Fluorine binding site 6 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F305

b:43.9
occ:0.70
 F2 B:PWJ305 0.0 43.9 0.7
C6 B:PWJ305 1.3 41.0 0.7
F1 B:PWJ305 2.0 42.8 0.7
F B:PWJ305 2.2 47.1 0.7
C5 B:PWJ305 2.4 38.9 0.7
C4 B:PWJ305 2.7 34.2 0.7
CZ3 A:TRP28 3.7 35.8 0.7
C7 B:PWJ305 3.7 38.6 0.7
O A:HOH465 3.8 36.8 1.0
CH2 A:TRP28 3.9 37.2 0.7
N1 B:PWJ305 4.1 33.1 0.7
O A:HOH460 4.3 26.0 0.7
CD1 A:LEU98 4.3 29.6 1.0
C8 B:PWJ305 4.3 40.0 0.7
CE3 A:TRP28 4.4 36.2 0.7
O A:HOH447 4.5 19.6 0.7
CG A:LEU98 4.6 27.2 1.0
CH2 B:TRP46 4.6 25.7 0.7
CZ2 A:TRP28 4.7 34.8 0.7
C B:PWJ305 4.9 33.1 0.7
CZ2 B:TRP46 5.0 24.7 0.7
N2 B:PWJ305 5.0 45.8 0.7

Fluorine binding site 7 out of 12 in 5qtp

Go back to Fluorine Binding Sites List in 5qtp
Fluorine binding site 7 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F306

b:50.0
occ:0.87
 F C:PWJ306 0.0 50.0 0.9
C6 C:PWJ306 1.4 56.2 0.9
F2 C:PWJ306 2.1 58.2 0.9
F1 C:PWJ306 2.2 51.4 0.9
C5 C:PWJ306 2.5 48.5 0.9
C8 C:PWJ306 2.7 54.3 0.9
C7 C:PWJ306 3.0 54.3 0.9
N2 C:PWJ306 3.1 56.9 0.9
C4 C:PWJ306 3.8 49.0 0.9
CH2 C:TRP28 3.8 55.2 0.9
CZ3 C:TRP28 4.1 51.6 0.9
CZ2 C:TRP28 4.3 51.0 0.9
C C:PWJ306 4.4 48.7 0.9
CH2 D:TRP46 4.5 40.2 1.0
CZ3 D:TRP46 4.9 38.8 1.0
N1 C:PWJ306 4.9 45.9 0.9
CE3 C:TRP28 4.9 51.6 0.9
O C:HOH476 5.0 46.9 1.0

Fluorine binding site 8 out of 12 in 5qtp

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Fluorine binding site 8 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F306

b:51.4
occ:0.87
 F1 C:PWJ306 0.0 51.4 0.9
C6 C:PWJ306 1.3 56.2 0.9
F2 C:PWJ306 2.1 58.2 0.9
F C:PWJ306 2.2 50.0 0.9
C5 C:PWJ306 2.4 48.5 0.9
C4 C:PWJ306 2.9 49.0 0.9
CZ3 C:TRP28 3.2 51.6 0.9
CH2 C:TRP28 3.6 55.2 0.9
C7 C:PWJ306 3.7 54.3 0.9
CE3 C:TRP28 3.9 51.6 0.9
CD1 C:LEU98 4.1 40.3 1.0
C8 C:PWJ306 4.2 54.3 0.9
N1 C:PWJ306 4.3 45.9 0.9
C1 C:EDO304 4.6 35.8 0.9
CZ2 C:TRP28 4.6 51.0 0.9
O1 C:EDO304 4.7 34.3 0.9
CG C:LEU98 4.7 36.3 1.0
CD2 C:TRP28 4.8 54.1 0.9
C C:PWJ306 4.8 48.7 0.9
N2 C:PWJ306 4.9 56.9 0.9

Fluorine binding site 9 out of 12 in 5qtp

Go back to Fluorine Binding Sites List in 5qtp
Fluorine binding site 9 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F306

b:58.2
occ:0.87
 F2 C:PWJ306 0.0 58.2 0.9
C6 C:PWJ306 1.4 56.2 0.9
F1 C:PWJ306 2.1 51.4 0.9
F C:PWJ306 2.1 50.0 0.9
C5 C:PWJ306 2.5 48.5 0.9
C4 C:PWJ306 3.1 49.0 0.9
O1 C:EDO304 3.3 34.3 0.9
C7 C:PWJ306 3.6 54.3 0.9
C1 C:EDO304 3.6 35.8 0.9
CH2 D:TRP46 3.6 40.2 1.0
C8 C:PWJ306 4.0 54.3 0.9
CZ2 D:TRP46 4.2 38.5 1.0
N1 C:PWJ306 4.4 45.9 0.9
CZ3 D:TRP46 4.5 38.8 1.0
N2 C:PWJ306 4.6 56.9 0.9
C C:PWJ306 4.7 48.7 0.9
C2 C:EDO304 4.7 39.4 0.9
O C:HOH461 4.9 42.9 1.0

Fluorine binding site 10 out of 12 in 5qtp

Go back to Fluorine Binding Sites List in 5qtp
Fluorine binding site 10 out of 12 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:58.4
occ:0.80
 F D:PWJ501 0.0 58.4 0.8
C6 D:PWJ501 1.4 57.9 0.8
F2 D:PWJ501 2.2 68.6 0.8
F1 D:PWJ501 2.2 57.4 0.8
C5 D:PWJ501 2.5 52.2 0.8
C4 D:PWJ501 2.8 47.8 0.8
CD1 D:LEU98 3.5 43.6 1.0
C7 D:PWJ501 3.8 47.0 0.8
CG D:LEU98 4.2 39.0 1.0
N1 D:PWJ501 4.2 44.5 0.8
C8 D:PWJ501 4.3 46.4 0.8
O D:HOH632 4.4 48.0 1.0
CZ3 D:TRP28 4.5 53.7 0.8
O D:HOH634 4.6 47.1 1.0
CE3 D:TRP28 4.9 49.5 0.8
C D:PWJ501 4.9 45.9 0.8
CH2 C:TRP46 4.9 40.1 0.8
CH2 D:TRP28 5.0 50.3 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: Sun Dec 13 12:32:43 2020

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