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Fluorine in PDB 5m8g: Tubulin-MTD265 Complex

Protein crystallography data

The structure of Tubulin-MTD265 Complex, PDB code: 5m8g 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) 49.29 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.768, 157.508, 179.235, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.8

Other elements in 5m8g:

The structure of Tubulin-MTD265 Complex also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tubulin-MTD265 Complex (pdb code 5m8g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Tubulin-MTD265 Complex, PDB code: 5m8g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 1 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:60.6
occ:1.00
FAZ B:918501 0.0 60.6 1.0
CAO B:918501 1.3 57.7 1.0
FBB B:918501 2.1 56.0 1.0
FBA B:918501 2.1 44.7 1.0
CAN B:918501 2.2 47.3 1.0
N3 B:918501 2.8 39.0 1.0
CAH B:918501 3.0 45.5 1.0
CAM B:918501 3.2 41.0 1.0
C4 B:918501 3.3 37.9 1.0
CAU B:918501 3.4 42.5 1.0
CD1 B:LEU248 3.7 70.2 1.0
CD2 B:LEU255 3.7 46.8 1.0
C2 B:918501 3.8 39.7 1.0
SG B:CYS241 3.9 63.1 1.0
CB B:CYS241 4.0 50.5 1.0
NAG B:918501 4.1 46.0 1.0
CB B:ALA250 4.1 53.2 1.0
CAJ B:918501 4.3 48.2 1.0
CAL B:918501 4.4 48.5 1.0
CD2 B:LEU248 4.4 66.8 1.0
CG B:LEU248 4.6 69.9 1.0
C5 B:918501 4.6 37.2 1.0
CAT B:918501 4.6 47.4 1.0
NZ B:LYS352 4.7 75.0 1.0
NAK B:918501 4.8 44.5 1.0
CB B:LEU248 4.9 69.4 1.0
N1 B:918501 4.9 34.2 1.0
CB B:ALA354 4.9 41.6 1.0

Fluorine binding site 2 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 2 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:44.7
occ:1.00
FBA B:918501 0.0 44.7 1.0
CAO B:918501 1.3 57.7 1.0
FAZ B:918501 2.1 60.6 1.0
FBB B:918501 2.1 56.0 1.0
CAN B:918501 2.2 47.3 1.0
CAH B:918501 2.8 45.5 1.0
C4 B:918501 2.8 37.9 1.0
N3 B:918501 2.9 39.0 1.0
CAM B:918501 3.4 41.0 1.0
C5 B:918501 3.7 37.2 1.0
CG B:LYS352 3.7 45.1 1.0
C2 B:918501 3.7 39.7 1.0
CB B:ALA354 3.8 41.6 1.0
NZ B:LYS352 4.1 75.0 1.0
CAJ B:918501 4.1 48.2 1.0
CD1 B:LEU248 4.3 70.2 1.0
CAU B:918501 4.4 42.5 1.0
C6 B:918501 4.4 38.7 1.0
CB B:LYS352 4.4 39.8 1.0
NAG B:918501 4.4 46.0 1.0
N1 B:918501 4.4 34.2 1.0
CB B:ALA316 4.5 41.4 1.0
CAL B:918501 4.6 48.5 1.0
CD2 B:LEU248 4.8 66.8 1.0
NAK B:918501 4.8 44.5 1.0
CG1 B:ILE318 4.9 49.0 1.0
CD B:LYS352 4.9 51.6 1.0

Fluorine binding site 3 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 3 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:56.0
occ:1.00
FBB B:918501 0.0 56.0 1.0
CAO B:918501 1.3 57.7 1.0
FAZ B:918501 2.1 60.6 1.0
FBA B:918501 2.1 44.7 1.0
CAN B:918501 2.3 47.3 1.0
CAM B:918501 2.6 41.0 1.0
CB B:CYS241 3.5 50.5 1.0
CAH B:918501 3.6 45.5 1.0
CB B:ALA354 3.6 41.6 1.0
CD1 B:LEU248 3.7 70.2 1.0
SG B:CYS241 3.8 63.1 1.0
CG1 B:ILE318 3.8 49.0 1.0
O B:HOH679 3.9 50.2 1.0
CAL B:918501 4.0 48.5 1.0
C4 B:918501 4.3 37.9 1.0
N3 B:918501 4.3 39.0 1.0
CD1 B:ILE318 4.5 54.7 0.8
CAJ B:918501 4.7 48.2 1.0
NAP B:918501 4.8 54.8 1.0
NAK B:918501 4.8 44.5 1.0
CA B:CYS241 4.9 51.1 1.0

Fluorine binding site 4 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 4 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:59.5
occ:1.00
FAZ D:918501 0.0 59.5 1.0
CAO D:918501 1.3 60.2 1.0
FBA D:918501 2.1 56.3 1.0
FBB D:918501 2.1 52.9 1.0
CAN D:918501 2.2 52.5 1.0
N3 D:918501 2.8 48.3 1.0
CAH D:918501 3.0 44.2 1.0
CD1 D:LEU248 3.0 92.7 1.0
CAM D:918501 3.2 48.7 1.0
C4 D:918501 3.3 47.1 1.0
CAU D:918501 3.5 55.5 1.0
CD2 D:LEU255 3.7 50.4 1.0
C2 D:918501 3.8 54.9 1.0
CB D:CYS241 3.9 56.5 1.0
SG D:CYS241 3.9 68.7 1.0
NAG D:918501 4.1 57.4 1.0
CAJ D:918501 4.3 47.4 1.0
CG D:LEU248 4.4 84.2 1.0
CAL D:918501 4.4 51.9 1.0
CB D:ALA250 4.5 61.5 1.0
C5 D:918501 4.6 49.0 1.0
CB D:ALA354 4.6 44.3 1.0
CD2 D:LEU248 4.7 77.8 1.0
CAT D:918501 4.7 57.6 1.0
NAK D:918501 4.8 56.6 1.0
N1 D:918501 4.9 44.3 1.0
CG D:LYS352 5.0 46.1 1.0

Fluorine binding site 5 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 5 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:56.3
occ:1.00
FBA D:918501 0.0 56.3 1.0
CAO D:918501 1.3 60.2 1.0
FBB D:918501 2.0 52.9 1.0
FAZ D:918501 2.1 59.5 1.0
CAN D:918501 2.2 52.5 1.0
CAM D:918501 2.6 48.7 1.0
CB D:ALA354 3.5 44.3 1.0
CAH D:918501 3.5 44.2 1.0
CB D:CYS241 3.6 56.5 1.0
CG1 D:ILE318 3.7 60.4 1.0
CD1 D:LEU248 3.7 92.7 1.0
SG D:CYS241 3.8 68.7 1.0
O D:HOH624 3.8 50.8 1.0
CAL D:918501 4.0 51.9 1.0
C4 D:918501 4.2 47.1 1.0
CD1 D:ILE318 4.3 63.0 0.6
N3 D:918501 4.4 48.3 1.0
CAJ D:918501 4.6 47.4 1.0
NAK D:918501 4.8 56.6 1.0
NAP D:918501 4.8 49.9 1.0
CA D:CYS241 4.9 51.0 1.0
CA D:ALA354 4.9 48.3 1.0
CB D:ALA316 4.9 34.9 1.0

Fluorine binding site 6 out of 6 in 5m8g

Go back to Fluorine Binding Sites List in 5m8g
Fluorine binding site 6 out of 6 in the Tubulin-MTD265 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Tubulin-MTD265 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:52.9
occ:1.00
FBB D:918501 0.0 52.9 1.0
CAO D:918501 1.3 60.2 1.0
FBA D:918501 2.0 56.3 1.0
FAZ D:918501 2.1 59.5 1.0
CAN D:918501 2.3 52.5 1.0
CAH D:918501 2.8 44.2 1.0
C4 D:918501 2.9 47.1 1.0
N3 D:918501 3.0 48.3 1.0
CG D:LYS352 3.4 46.1 1.0
CAM D:918501 3.4 48.7 1.0
C5 D:918501 3.7 49.0 1.0
CB D:ALA354 3.8 44.3 1.0
C2 D:918501 3.8 54.9 1.0
CD1 D:LEU248 3.9 92.7 1.0
CB D:ALA316 4.1 34.9 1.0
CAJ D:918501 4.1 47.4 1.0
CB D:LYS352 4.3 44.2 1.0
C6 D:918501 4.5 50.8 1.0
N1 D:918501 4.5 44.3 1.0
CAU D:918501 4.5 55.5 1.0
NAG D:918501 4.6 57.4 1.0
CE D:LYS352 4.6 65.5 1.0
CAL D:918501 4.6 51.9 1.0
CD D:LYS352 4.6 59.5 1.0
N D:ALA354 4.9 47.3 1.0
NAK D:918501 4.9 56.6 1.0
CA D:ALA354 4.9 48.3 1.0
CG1 D:ILE318 4.9 60.4 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 12:27:54 2020

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