Fluorine in PDB 5s59: Tubulin-Z1324080698-Complex

The structure of Tubulin-Z1324080698-Complex, PDB code: 5s59 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)	59.84 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.56, 158.9, 179.33, 90, 90, 90
R / Rfree (%)	22 / 26.8

The structure of Tubulin-Z1324080698-Complex also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Tubulin-Z1324080698-Complex (pdb code 5s59). 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-Z1324080698-Complex, PDB code: 5s59:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:83.6 occ:0.75 F A:UR1504 0.0 83.6 0.8 C3 A:UR1504 1.4 79.8 0.8 C4 A:UR1504 2.4 78.2 0.8 C2 A:UR1504 2.4 80.0 0.8 H4 A:UR1504 2.5 94.1 0.8 H3 A:UR1504 2.6 96.2 0.8 OD1 A:ASN18 2.9 92.4 1.0 CG A:ASN18 3.6 78.9 1.0 C5 A:UR1504 3.6 75.6 0.8 C1 A:UR1504 3.6 80.0 0.8 CB A:ASN18 3.8 80.1 1.0 O A:ASN18 4.1 77.8 1.0 C6 A:UR1504 4.1 76.6 0.8 C A:ASN18 4.4 78.0 1.0 H7 A:UR1504 4.5 87.9 0.8 CA A:ASN18 4.6 75.7 1.0 ND2 A:ASN18 4.6 78.9 1.0 C A:UR1504 4.9 80.2 0.8 H1 A:UR1504 4.9 96.6 0.8

Fluorine binding site 2 out of 3 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:76.6 occ:0.81 F C:UR1504 0.0 76.6 0.8 C3 C:UR1504 1.4 72.3 0.8 C4 C:UR1504 2.3 70.1 0.8 C2 C:UR1504 2.4 73.4 0.8 NE C:ARG229 2.5 76.5 1.0 H4 C:UR1504 2.5 84.4 0.8 H3 C:UR1504 2.6 88.3 0.8 OE1 C:GLU22 2.6 76.0 1.0 CZ C:ARG229 3.2 73.8 1.0 NH2 C:ARG229 3.2 78.0 1.0 CD C:ARG229 3.4 72.6 1.0 CA C:ALA19 3.5 63.9 1.0 C5 C:UR1504 3.6 72.8 0.8 C1 C:UR1504 3.6 73.8 0.8 CD C:GLU22 3.7 82.3 1.0 CB C:ALA19 3.8 68.0 1.0 CG C:ARG229 3.9 70.4 1.0 N C:ALA19 4.1 64.5 1.0 C6 C:UR1504 4.1 71.9 0.8 OE2 C:GLU22 4.4 80.8 1.0 NH1 C:ARG229 4.4 68.6 1.0 CB C:GLU22 4.5 72.8 1.0 O C:ASN18 4.5 67.9 1.0 C C:ASN18 4.5 63.4 1.0 C C:ALA19 4.6 67.0 1.0 O C:ALA19 4.6 67.9 1.0 CG C:GLU22 4.7 78.5 1.0 CG2 C:THR225 4.8 69.3 1.0 C C:UR1504 4.9 67.3 0.8 H2 C:UR1504 4.9 81.1 0.8

Fluorine binding site 3 out of 3 in the Tubulin-Z1324080698-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-Z1324080698-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:78.0 occ:0.76 F D:UR1503 0.0 78.0 0.8 C3 D:UR1503 1.4 79.4 0.8 C4 D:UR1503 2.3 76.7 0.8 C2 D:UR1503 2.4 80.4 0.8 H4 D:UR1503 2.5 92.4 0.8 H3 D:UR1503 2.6 96.8 0.8 CZ2 C:TRP407 3.2 72.0 1.0 CH2 C:TRP407 3.2 71.5 1.0 O D:ASP199 3.3 82.5 1.0 CA D:ASP199 3.4 80.0 1.0 CB D:ASP199 3.5 78.4 1.0 OD1 D:ASP199 3.6 83.8 1.0 C5 D:UR1503 3.6 79.0 0.8 C1 D:UR1503 3.6 80.0 0.8 C D:ASP199 3.8 81.2 1.0 CG1 D:VAL260 4.0 76.5 1.0 CG D:ASP199 4.0 84.5 1.0 C6 D:UR1503 4.1 79.6 0.8 CG2 D:VAL260 4.2 73.8 1.0 CB D:VAL260 4.3 76.6 1.0 CZ3 C:TRP407 4.3 67.5 1.0 CE2 C:TRP407 4.3 69.6 1.0 CE1 C:HIS406 4.5 75.4 1.0 O D:THR198 4.6 86.7 1.0 O D:PRO263 4.6 78.1 1.0 N D:ASP199 4.6 81.5 1.0 CB D:ALA256 4.8 72.9 1.0 CB D:HIS266 4.8 77.4 1.0 C D:UR1503 4.9 80.1 0.8 H2 D:UR1503 4.9 96.4 0.8 CA D:PRO263 5.0 77.9 1.0

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