Fluorine in PDB 5s5e: Tubulin-Z1515654336-Complex

The structure of Tubulin-Z1515654336-Complex, PDB code: 5s5e was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.76 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.407, 159.503, 179.362, 90, 90, 90
R / Rfree (%)	18.7 / 22.7

The structure of Tubulin-Z1515654336-Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Fluorine atom in the Tubulin-Z1515654336-Complex (pdb code 5s5e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Tubulin-Z1515654336-Complex, PDB code: 5s5e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F505 b:56.7 occ:1.00 F B:UQJ505 0.0 56.7 1.0 C5 B:UQJ505 1.3 54.0 1.0 H6 B:UQJ505 1.9 64.9 1.0 F1 B:UQJ505 2.1 68.7 1.0 C4 B:UQJ505 2.3 49.1 1.0 N2 B:UQJ505 2.7 48.6 1.0 CD2 B:TYR224 3.0 42.6 1.0 O B:HOH663 3.4 53.4 1.0 CE2 B:TYR224 3.4 43.5 1.0 CG B:TYR224 3.6 46.6 1.0 C2 B:UQJ505 3.7 54.5 1.0 O B:HOH662 3.8 46.4 1.0 N B:UQJ505 4.0 48.6 1.0 CB B:TYR224 4.1 48.0 1.0 N B:TYR224 4.2 54.4 1.0 CZ B:TYR224 4.3 48.0 1.0 O B:UQJ505 4.4 59.2 1.0 CD1 B:TYR224 4.4 47.4 1.0 C1 B:UQJ505 4.5 55.1 1.0 C3 B:UQJ505 4.5 55.3 1.0 CD2 C:LEU248 4.6 58.1 1.0 CE1 B:TYR224 4.7 46.9 1.0 CA B:TYR224 4.8 50.8 1.0 H B:UQJ505 5.0 59.7 1.0

Fluorine binding site 2 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F505 b:68.7 occ:1.00 F1 B:UQJ505 0.0 68.7 1.0 C5 B:UQJ505 1.3 54.0 1.0 H6 B:UQJ505 1.9 64.9 1.0 F B:UQJ505 2.1 56.7 1.0 C4 B:UQJ505 2.3 49.1 1.0 O B:HOH662 2.6 46.4 1.0 N2 B:UQJ505 3.2 48.6 1.0 C2 B:UQJ505 3.2 54.5 1.0 O B:UQJ505 3.5 59.2 1.0 O C:HOH762 3.5 47.0 1.0 C3 B:UQJ505 3.6 55.3 1.0 CA B:THR223 4.0 53.8 1.0 N B:TYR224 4.1 54.4 1.0 CD2 C:LEU248 4.2 58.1 1.0 N B:UQJ505 4.3 48.6 1.0 C1 B:UQJ505 4.3 55.1 1.0 CB B:THR223 4.3 56.6 1.0 O B:HOH664 4.4 47.3 1.0 O B:PRO222 4.5 58.7 1.0 C B:THR223 4.6 54.6 1.0 CG2 B:THR223 4.6 49.6 1.0 N1 B:UQJ505 4.7 59.4 1.0 CD2 B:TYR224 4.8 42.6 1.0 CG B:TYR224 4.9 46.6 1.0

Fluorine binding site 3 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F506 b:46.3 occ:0.76 F B:UQJ506 0.0 46.3 0.8 C5 B:UQJ506 1.3 48.2 0.8 H6 B:UQJ506 1.9 57.9 0.8 F1 B:UQJ506 2.1 48.0 0.8 C4 B:UQJ506 2.3 45.5 0.8 O B:HOH608 2.9 52.6 1.0 CD B:LYS105 2.9 45.4 1.0 CE B:LYS105 3.0 50.0 1.0 N2 B:UQJ506 3.1 39.3 0.8 C2 B:UQJ506 3.3 47.3 0.8 O B:UQJ506 3.5 44.8 0.8 NZ B:LYS105 3.6 53.5 1.0 C3 B:UQJ506 3.8 42.5 0.8 CA B:GLY100 4.1 40.0 1.0 N B:UQJ506 4.2 40.9 0.8 O B:ALA99 4.2 38.1 1.0 C1 B:UQJ506 4.3 40.7 0.8 CG B:LYS105 4.4 44.0 1.0 O B:GLY100 4.5 39.7 1.0 N B:GLY100 4.5 40.6 1.0 O C:HOH741 4.6 55.8 1.0 C B:ALA99 4.6 41.4 1.0 CB B:ASN102 4.7 35.8 1.0 C B:GLY100 4.7 40.0 1.0 ND2 B:ASN102 4.8 39.3 1.0

Fluorine binding site 4 out of 4 in the Tubulin-Z1515654336-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Tubulin-Z1515654336-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F506 b:48.0 occ:0.76 F1 B:UQJ506 0.0 48.0 0.8 C5 B:UQJ506 1.3 48.2 0.8 H6 B:UQJ506 1.9 57.9 0.8 F B:UQJ506 2.1 46.3 0.8 C4 B:UQJ506 2.3 45.5 0.8 N2 B:UQJ506 2.7 39.3 0.8 CD B:LYS105 3.2 45.4 1.0 O B:HOH638 3.3 46.8 1.0 ND2 B:ASN102 3.6 39.3 1.0 C2 B:UQJ506 3.7 47.3 0.8 NZ B:LYS105 3.7 53.5 1.0 CE B:LYS105 3.7 50.0 1.0 OE2 B:GLU411 3.8 51.0 1.0 N B:UQJ506 4.0 40.9 0.8 CG B:LYS105 4.2 44.0 1.0 O B:UQJ506 4.3 44.8 0.8 CD B:GLU411 4.4 48.6 1.0 O B:TRP407 4.4 39.5 1.0 C3 B:UQJ506 4.5 42.5 0.8 C1 B:UQJ506 4.5 40.7 0.8 CG B:ASN102 4.5 38.6 1.0 CE3 B:TRP407 4.5 41.9 1.0 CG B:GLU411 4.5 44.2 1.0 CB B:ASN102 4.5 35.8 1.0 O B:HOH608 4.7 52.6 1.0 H B:UQJ506 4.9 50.0 0.8

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273