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Fluorine in PDB 5uj0: Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3

Enzymatic activity of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3

All present enzymatic activity of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3:
2.7.1.78; 3.1.3.34;

Protein crystallography data

The structure of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3, PDB code: 5uj0 was solved by S.Shuman, D.Chatterjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.75 / 2.30
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 99.790, 99.790, 194.150, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.9

Other elements in 5uj0:

The structure of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 (pdb code 5uj0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3, PDB code: 5uj0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 1 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F165

b:44.2
occ:1.00
 F1 A:BFD165 0.0 44.2 1.0
BE A:BFD165 1.4 44.6 1.0
MG A:MG401 2.0 40.4 1.0
F3 A:BFD165 2.2 38.5 1.0
F2 A:BFD165 2.2 38.9 1.0
OD1 A:BFD165 2.4 41.5 1.0
OD2 A:BFD165 2.7 41.8 1.0
O A:HOH515 2.9 44.7 1.0
CG A:BFD165 2.9 37.8 1.0
O A:ASP167 3.1 39.9 1.0
O A:HOH520 3.2 41.7 1.0
CB A:ASP167 3.3 45.7 1.0
N A:ASP167 3.5 38.8 1.0
CA A:ASP167 3.7 39.7 1.0
O A:HOH547 3.7 53.5 1.0
C A:ASP167 3.8 42.4 1.0
O A:HOH560 3.9 56.3 1.0
O A:HOH532 4.1 48.2 1.0
OD1 A:ASP278 4.2 42.1 1.0
NZ A:LYS258 4.2 48.1 1.0
N A:VAL166 4.4 37.0 1.0
CG A:ASP167 4.4 49.3 1.0
C A:VAL166 4.4 39.9 1.0
CB A:BFD165 4.4 35.3 1.0
OD2 A:ASP167 4.5 55.6 1.0
OG A:SER211 4.6 43.4 1.0
N A:GLY212 4.8 47.1 1.0
CA A:VAL166 4.9 35.8 1.0
CE A:LYS258 5.0 49.2 1.0

Fluorine binding site 2 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 2 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F165

b:38.9
occ:1.00
 F2 A:BFD165 0.0 38.9 1.0
BE A:BFD165 1.4 44.6 1.0
F1 A:BFD165 2.2 44.2 1.0
F3 A:BFD165 2.3 38.5 1.0
OD1 A:BFD165 2.3 41.5 1.0
OG A:SER211 2.7 43.4 1.0
N A:ASP167 2.9 38.8 1.0
N A:VAL166 3.1 37.0 1.0
CG A:BFD165 3.3 37.8 1.0
CB A:SER211 3.3 42.4 1.0
CB A:VAL166 3.5 37.3 1.0
CA A:VAL166 3.6 35.8 1.0
CA A:SER211 3.6 40.9 1.0
C A:VAL166 3.7 39.9 1.0
OD2 A:BFD165 3.7 41.8 1.0
CB A:ASP167 3.7 45.7 1.0
CA A:ASP167 3.9 39.7 1.0
N A:GLY212 3.9 47.1 1.0
MG A:MG401 4.0 40.4 1.0
OD2 A:ASP167 4.2 55.6 1.0
C A:BFD165 4.2 40.4 1.0
CG A:ASP167 4.2 49.3 1.0
O A:VAL210 4.3 43.9 1.0
C A:SER211 4.3 45.2 1.0
CG2 A:VAL166 4.3 34.1 1.0
O A:ASP167 4.4 39.9 1.0
CB A:BFD165 4.5 35.3 1.0
CA A:BFD165 4.5 38.6 1.0
O A:HOH532 4.6 48.2 1.0
CG1 A:VAL166 4.6 32.9 1.0
C A:ASP167 4.6 42.4 1.0
CG A:ARG213 4.7 49.7 1.0
NZ A:LYS258 4.7 48.1 1.0
O A:HOH547 4.7 53.5 1.0
N A:SER211 4.7 41.1 1.0
O A:VAL166 4.8 39.4 1.0
O A:HOH515 4.9 44.7 1.0
N A:ARG213 4.9 45.1 1.0
C A:VAL210 4.9 38.3 1.0
NE A:ARG213 5.0 51.5 1.0

Fluorine binding site 3 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 3 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F165

b:38.5
occ:1.00
 F3 A:BFD165 0.0 38.5 1.0
BE A:BFD165 1.4 44.6 1.0
F1 A:BFD165 2.2 44.2 1.0
OD1 A:BFD165 2.2 41.5 1.0
F2 A:BFD165 2.3 38.9 1.0
N A:GLY212 2.8 47.1 1.0
NZ A:LYS258 3.0 48.1 1.0
CE A:LYS258 3.3 49.2 1.0
O A:HOH547 3.4 53.5 1.0
CG A:BFD165 3.5 37.8 1.0
CA A:SER211 3.5 40.9 1.0
C A:SER211 3.6 45.2 1.0
OG A:SER211 3.7 43.4 1.0
CA A:GLY212 3.7 44.9 1.0
O A:HOH515 3.7 44.7 1.0
MG A:MG401 3.9 40.4 1.0
OD2 A:BFD165 4.0 41.8 1.0
CB A:SER211 4.1 42.4 1.0
O A:VAL210 4.4 43.9 1.0
O A:HOH532 4.4 48.2 1.0
N A:ARG213 4.6 45.1 1.0
C A:GLY212 4.6 46.9 1.0
CB A:BFD165 4.7 35.3 1.0
N A:SER211 4.7 41.1 1.0
CD A:LYS258 4.7 47.1 1.0
N A:VAL166 4.8 37.0 1.0
O A:SER211 4.8 46.1 1.0
N A:ASP167 4.9 38.8 1.0
C A:VAL210 5.0 38.3 1.0
O A:HOH520 5.0 41.7 1.0

Fluorine binding site 4 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 4 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F165

b:47.8
occ:1.00
 F1 B:BFD165 0.0 47.8 1.0
BE B:BFD165 1.4 47.8 0.2
MG B:MG401 2.1 48.4 1.0
F2 B:BFD165 2.2 43.5 1.0
F3 B:BFD165 2.2 46.0 1.0
OD1 B:BFD165 2.4 48.2 1.0
OD2 B:BFD165 2.7 47.8 1.0
CG B:BFD165 2.9 47.1 1.0
O B:ASP167 2.9 48.5 1.0
N B:ASP167 3.0 51.7 1.0
O B:HOH514 3.0 44.6 1.0
O B:HOH523 3.0 44.4 1.0
CB B:ASP167 3.1 55.4 1.0
CA B:ASP167 3.3 52.7 1.0
C B:ASP167 3.6 50.9 1.0
O B:HOH540 3.9 54.1 1.0
C B:VAL166 4.0 48.2 1.0
N B:VAL166 4.0 45.1 1.0
OD1 B:ASP278 4.1 50.7 1.0
CG B:ASP167 4.2 61.8 1.0
OD2 B:ASP167 4.3 66.2 1.0
NZ B:LYS258 4.4 48.1 1.0
CB B:BFD165 4.4 46.2 1.0
CA B:VAL166 4.5 44.7 1.0
OG B:SER211 4.7 50.6 1.0
C B:BFD165 4.9 45.1 1.0
N B:GLY168 4.9 51.1 1.0
N B:GLY212 4.9 49.8 1.0
O B:VAL166 5.0 47.0 1.0
CB B:VAL166 5.0 50.0 1.0

Fluorine binding site 5 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 5 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F165

b:43.5
occ:1.00
 F2 B:BFD165 0.0 43.5 1.0
BE B:BFD165 1.4 47.8 0.2
F1 B:BFD165 2.2 47.8 1.0
F3 B:BFD165 2.2 46.0 1.0
OD1 B:BFD165 2.3 48.2 1.0
N B:ASP167 2.8 51.7 1.0
OG B:SER211 2.8 50.6 1.0
N B:VAL166 2.9 45.1 1.0
CB B:VAL166 3.3 50.0 1.0
CB B:SER211 3.3 45.7 1.0
CG B:BFD165 3.3 47.1 1.0
CA B:VAL166 3.3 44.7 1.0
C B:VAL166 3.5 48.2 1.0
OD2 B:BFD165 3.5 47.8 1.0
CA B:SER211 3.6 48.1 1.0
CB B:ASP167 3.8 55.4 1.0
CA B:ASP167 3.8 52.7 1.0
N B:GLY212 4.0 49.8 1.0
C B:BFD165 4.0 45.1 1.0
MG B:MG401 4.0 48.4 1.0
CG2 B:VAL166 4.1 42.6 1.0
OD2 B:ASP167 4.1 66.2 1.0
O B:VAL210 4.2 51.2 1.0
CG B:ASP167 4.2 61.8 1.0
C B:SER211 4.3 50.1 1.0
CG1 B:VAL166 4.4 45.4 1.0
CA B:BFD165 4.4 42.0 1.0
CB B:BFD165 4.4 46.2 1.0
O B:ASP167 4.5 48.5 1.0
O B:HOH540 4.5 54.1 1.0
NZ B:LYS258 4.5 48.1 1.0
C B:ASP167 4.6 50.9 1.0
O B:VAL166 4.7 47.0 1.0
N B:SER211 4.8 49.0 1.0
O B:HOH523 4.8 44.4 1.0
C B:VAL210 4.9 47.6 1.0
CG B:ARG213 5.0 56.5 1.0

Fluorine binding site 6 out of 6 in 5uj0

Go back to Fluorine Binding Sites List in 5uj0
Fluorine binding site 6 out of 6 in the Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of T4PNKP 3' Phosphatase Covalently Bound to BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F165

b:46.0
occ:1.00
 F3 B:BFD165 0.0 46.0 1.0
BE B:BFD165 1.4 47.8 0.2
F1 B:BFD165 2.2 47.8 1.0
F2 B:BFD165 2.2 43.5 1.0
OD1 B:BFD165 2.2 48.2 1.0
N B:GLY212 2.9 49.8 1.0
NZ B:LYS258 3.1 48.1 1.0
CE B:LYS258 3.4 49.5 1.0
CG B:BFD165 3.5 47.1 1.0
O B:HOH523 3.6 44.4 1.0
CA B:SER211 3.6 48.1 1.0
OG B:SER211 3.6 50.6 1.0
C B:SER211 3.7 50.1 1.0
CA B:GLY212 3.8 49.7 1.0
MG B:MG401 3.8 48.4 1.0
O B:HOH540 3.8 54.1 1.0
OD2 B:BFD165 4.1 47.8 1.0
CB B:SER211 4.1 45.7 1.0
OD2 B:ASP254 4.2 60.9 1.0
O B:VAL210 4.5 51.2 1.0
N B:VAL166 4.6 45.1 1.0
N B:ASP167 4.6 51.7 1.0
N B:ARG213 4.7 50.1 1.0
CB B:BFD165 4.7 46.2 1.0
C B:GLY212 4.7 52.5 1.0
O B:HOH514 4.7 44.6 1.0
N B:SER211 4.8 49.0 1.0
CB B:ASP167 4.9 55.4 1.0
CD B:LYS258 4.9 44.8 1.0
O B:SER211 4.9 49.0 1.0

Reference:

S.Shuman, D.Chatterjee. Truncated T4PNK Covalently Bound to BEF3 To Be Published.
Page generated: Tue Jul 15 08:14:19 2025

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