Fluorine in PDB 5s4m: Tubulin-Z2142244288-Complex

The structure of Tubulin-Z2142244288-Complex, PDB code: 5s4m 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)	63.02 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.67, 157.87, 179.17, 90, 90, 90
R / Rfree (%)	20.6 / 24.4

The structure of Tubulin-Z2142244288-Complex also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Tubulin-Z2142244288-Complex (pdb code 5s4m). 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-Z2142244288-Complex, PDB code: 5s4m:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:68.7 occ:0.72 F1 A:WV4505 0.0 68.7 0.7 C1 A:WV4505 1.4 65.7 0.7 C2 A:WV4505 2.4 63.9 0.7 C6 A:WV4505 2.4 65.8 0.7 H7 A:WV4505 2.4 81.5 0.7 H1 A:WV4505 2.6 76.7 0.7 N1 A:WV4505 2.8 67.9 0.7 OE1 A:GLU22 3.0 71.2 1.0 NE A:ARG229 3.3 69.4 1.0 CA A:ALA19 3.3 60.4 1.0 CB A:ALA19 3.4 58.4 1.0 C3 A:WV4505 3.6 66.3 0.7 C5 A:WV4505 3.6 64.6 0.7 O A:HOH617 3.8 64.3 1.0 N A:ALA19 3.8 57.2 1.0 CG A:ARG229 3.8 65.4 1.0 CZ A:ARG229 3.9 69.4 1.0 NH2 A:ARG229 4.0 73.2 1.0 CD A:ARG229 4.1 69.3 1.0 C4 A:WV4505 4.1 62.8 0.7 CD A:GLU22 4.1 71.7 1.0 C8 A:WV4505 4.2 74.9 0.7 C A:ASN18 4.3 56.1 1.0 O A:ASN18 4.4 58.5 1.0 H3 A:WV4505 4.4 77.6 0.7 C A:ALA19 4.6 59.0 1.0 H8 A:WV4505 4.6 89.9 0.7 H9 A:WV4505 4.7 89.9 0.7 OE2 A:GLU22 4.7 74.8 1.0 CG2 A:THR225 4.7 61.4 1.0 O A:ALA19 4.8 61.9 1.0 H11 A:WV4505 4.9 90.5 0.7 H12 A:WV4505 4.9 90.5 0.7 CB A:GLU22 4.9 62.0 1.0 C9 A:WV4505 4.9 75.4 0.7 CB A:ASN18 5.0 60.0 1.0

Fluorine binding site 2 out of 3 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F505 b:80.7 occ:1.00 F1 B:WV4505 0.0 80.7 1.0 C1 B:WV4505 1.4 67.7 1.0 C2 B:WV4505 2.4 65.1 1.0 C6 B:WV4505 2.4 65.8 1.0 H7 B:WV4505 2.4 95.5 1.0 H1 B:WV4505 2.6 78.2 1.0 N1 B:WV4505 2.8 79.6 1.0 O B:HOH634 3.6 62.3 1.0 C3 B:WV4505 3.6 62.6 1.0 C5 B:WV4505 3.6 65.9 1.0 CG1 B:VAL23 3.8 62.5 1.0 CB B:ALA233 4.1 55.3 1.0 CB B:PRO360 4.1 67.1 1.0 C4 B:WV4505 4.1 65.7 1.0 CA B:ALA233 4.2 55.5 1.0 C8 B:WV4505 4.2 77.7 1.0 H3 B:WV4505 4.4 79.0 1.0 OE2 B:GLU27 4.6 63.0 1.0 H8 B:WV4505 4.6 93.2 1.0 H9 B:WV4505 4.7 93.2 1.0 H11 B:WV4505 4.8 93.8 1.0 H12 B:WV4505 4.8 93.8 1.0 CG2 B:VAL23 4.9 60.9 1.0 C9 B:WV4505 4.9 78.2 1.0 CB B:VAL23 5.0 61.1 1.0

Fluorine binding site 3 out of 3 in the Tubulin-Z2142244288-Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-Z2142244288-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:73.1 occ:0.82 F1 D:WV4503 0.0 73.1 0.8 C1 D:WV4503 1.4 69.0 0.8 H9 D:WV4503 2.3 86.8 0.8 C2 D:WV4503 2.3 66.6 0.8 C6 D:WV4503 2.4 69.8 0.8 H1 D:WV4503 2.5 79.9 0.8 C8 D:WV4503 2.7 72.3 0.8 H8 D:WV4503 2.7 86.8 0.8 N1 D:WV4503 2.8 71.2 0.8 C3 D:WV4503 3.6 65.7 0.8 C5 D:WV4503 3.6 67.9 0.8 H7 D:WV4503 3.7 85.5 0.8 CD1 D:LEU371 3.8 62.8 1.0 C4 D:WV4503 4.1 65.9 0.8 C9 D:WV4503 4.2 74.0 0.8 CB D:PRO360 4.2 63.7 1.0 CB D:ALA233 4.4 57.6 1.0 H3 D:WV4503 4.4 81.5 0.8 CG D:LEU371 4.5 71.1 1.0 H10 D:WV4503 4.5 88.8 0.8 H12 D:WV4503 4.5 88.8 0.8 O D:ARG369 4.6 72.5 1.0 H11 D:WV4503 4.8 88.8 0.8 CG D:PRO360 4.8 63.7 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