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Fluorine in PDB 5m7e: Tubulin-BKM120 Complex

Protein crystallography data

The structure of Tubulin-BKM120 Complex, PDB code: 5m7e was solved by T.Bohnacker, A.E.Prota, M.O.Steinmetz, M.P.Wymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.93 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.593, 157.985, 179.728, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Other elements in 5m7e:

The structure of Tubulin-BKM120 Complex also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Calcium (Ca) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tubulin-BKM120 Complex (pdb code 5m7e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Tubulin-BKM120 Complex, PDB code: 5m7e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5m7e

Go back to Fluorine Binding Sites List in 5m7e
Fluorine binding site 1 out of 3 in the Tubulin-BKM120 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-BKM120 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:69.6
occ:1.00
F27 B:SD5505 0.0 69.6 1.0
C26 B:SD5505 1.3 73.8 1.0
F29 B:SD5505 2.0 77.1 1.0
F28 B:SD5505 2.1 72.7 1.0
C04 B:SD5505 2.2 61.9 1.0
C05 B:SD5505 2.8 54.2 1.0
C08 B:SD5505 2.9 46.0 1.0
N13 B:SD5505 3.0 45.6 1.0
C03 B:SD5505 3.4 59.6 1.0
C09 B:SD5505 3.7 45.7 1.0
CD2 B:LEU248 3.7 77.9 1.0
CB B:ALA354 3.8 47.5 1.0
C12 B:SD5505 3.8 46.0 1.0
CG B:LYS352 3.8 54.5 1.0
C06 B:SD5505 4.2 60.1 1.0
CB B:ALA316 4.4 41.1 1.0
C10 B:SD5505 4.4 44.9 1.0
CB B:LYS352 4.4 45.2 1.0
NZ B:LYS352 4.4 78.5 1.0
N11 B:SD5505 4.4 45.5 1.0
C19 B:SD5505 4.5 50.2 1.0
N14 B:SD5505 4.5 56.2 1.0
C02 B:SD5505 4.6 62.1 1.0
CG B:LEU248 4.7 73.7 1.0
CG1 B:ILE318 4.9 50.0 1.0
N07 B:SD5505 4.9 57.0 1.0
CA B:ALA354 4.9 50.6 1.0
N B:ALA354 5.0 48.7 1.0

Fluorine binding site 2 out of 3 in 5m7e

Go back to Fluorine Binding Sites List in 5m7e
Fluorine binding site 2 out of 3 in the Tubulin-BKM120 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-BKM120 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:72.7
occ:1.00
F28 B:SD5505 0.0 72.7 1.0
C26 B:SD5505 1.3 73.8 1.0
F29 B:SD5505 2.0 77.1 1.0
F27 B:SD5505 2.1 69.6 1.0
C04 B:SD5505 2.2 61.9 1.0
C03 B:SD5505 2.6 59.6 1.0
CD2 B:LEU248 3.5 77.9 1.0
CB B:ALA354 3.5 47.5 1.0
CB B:CYS241 3.5 58.8 1.0
C05 B:SD5505 3.6 54.2 1.0
CG1 B:ILE318 3.7 50.0 1.0
SG B:CYS241 3.8 61.8 1.0
C02 B:SD5505 4.0 62.1 1.0
O B:HOH693 4.0 55.0 1.0
C08 B:SD5505 4.2 46.0 1.0
N13 B:SD5505 4.3 45.6 1.0
CD1 B:ILE318 4.5 53.0 0.7
C06 B:SD5505 4.6 60.1 1.0
N01 B:SD5505 4.7 61.1 1.0
N07 B:SD5505 4.8 57.0 1.0
CG B:LEU248 4.8 73.7 1.0
CA B:CYS241 5.0 52.2 1.0
CA B:ALA354 5.0 50.6 1.0
CB B:ILE318 5.0 51.7 1.0

Fluorine binding site 3 out of 3 in 5m7e

Go back to Fluorine Binding Sites List in 5m7e
Fluorine binding site 3 out of 3 in the Tubulin-BKM120 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-BKM120 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:77.1
occ:1.00
F29 B:SD5505 0.0 77.1 1.0
C26 B:SD5505 1.2 73.8 1.0
F28 B:SD5505 2.0 72.7 1.0
F27 B:SD5505 2.0 69.6 1.0
C04 B:SD5505 2.1 61.9 1.0
N13 B:SD5505 2.7 45.6 1.0
C05 B:SD5505 2.9 54.2 1.0
C03 B:SD5505 3.1 59.6 1.0
CD2 B:LEU248 3.1 77.9 1.0
C08 B:SD5505 3.2 46.0 1.0
C19 B:SD5505 3.5 50.2 1.0
C12 B:SD5505 3.7 46.0 1.0
CD2 B:LEU255 3.7 64.1 1.0
SG B:CYS241 4.0 61.8 1.0
CG B:LEU248 4.0 73.7 1.0
N14 B:SD5505 4.1 56.2 1.0
CB B:CYS241 4.1 58.8 1.0
C06 B:SD5505 4.2 60.1 1.0
CB B:ALA250 4.2 52.3 1.0
C02 B:SD5505 4.3 62.1 1.0
C09 B:SD5505 4.4 45.7 1.0
CB B:ALA354 4.7 47.5 1.0
N07 B:SD5505 4.7 57.0 1.0
CB B:LEU248 4.8 70.5 1.0
C18 B:SD5505 4.8 55.0 1.0
N11 B:SD5505 4.8 45.5 1.0

Reference:

T.Bohnacker, A.E.Prota, F.Beaufils, J.E.Burke, A.Melone, A.J.Inglis, D.Rageot, A.M.Sele, V.Cmiljanovic, N.Cmiljanovic, K.Bargsten, A.Aher, A.Akhmanova, J.F.Diaz, D.Fabbro, M.Zvelebil, R.L.Williams, M.O.Steinmetz, M.P.Wymann. Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683
Page generated: Sun Dec 13 12:27:49 2020

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