Fluorine in PDB 6s9e: Tubulin-Gdp.Alf Complex

The structure of Tubulin-Gdp.Alf Complex, PDB code: 6s9e was solved by M.A.Oliva, J.Estevez-Gallego, J.F.Diaz, A.E.Prota, M.O.Steinmetz, F.A.Balaguer, D.Lucena-Agell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.999, 157.357, 180.261, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.8

The structure of Tubulin-Gdp.Alf Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Aluminium	(Al)	1 atom
Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Tubulin-Gdp.Alf Complex (pdb code 6s9e). 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-Gdp.Alf Complex, PDB code: 6s9e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:78.8 occ:0.87 F1 B:AF3507 0.0 78.8 0.9 AL B:AF3507 1.7 96.0 0.9 OE2 B:GLU71 2.4 67.0 1.0 HB2 B:GLN11 2.6 50.4 1.0 F2 B:AF3507 3.0 63.9 0.9 F3 B:AF3507 3.0 71.9 0.9 OE1 B:GLN11 3.4 53.5 1.0 CB B:GLN11 3.5 45.9 1.0 CD B:GLU71 3.5 67.4 1.0 HB3 B:GLN11 3.6 50.4 1.0 CD B:GLN11 3.7 51.6 1.0 MG B:MG502 3.7 34.5 1.0 O1B B:GDP501 3.8 28.3 1.0 HG1 B:THR74 3.9 81.0 1.0 O B:HOH612 3.9 28.4 1.0 O C:HOH651 4.0 45.7 1.0 H B:GLN11 4.1 52.4 1.0 CG B:GLN11 4.1 47.3 1.0 HG2 B:GLU71 4.2 65.4 1.0 NE2 B:GLN11 4.3 54.3 1.0 OG1 B:THR74 4.3 61.0 1.0 CG B:GLU71 4.3 67.7 1.0 OE1 B:GLU71 4.4 67.7 1.0 HG3 B:GLU71 4.4 65.4 1.0 O B:HOH633 4.4 40.8 1.0 HE22 B:GLN11 4.5 59.8 1.0 HG3 B:GLN11 4.5 60.5 1.0 CA B:GLN11 4.5 44.2 1.0 HA B:GLN11 4.6 56.2 1.0 N B:GLN11 4.6 42.6 1.0 O1A B:GDP501 4.7 32.7 1.0 HE21 B:GLN11 4.8 59.8 1.0 PB B:GDP501 4.9 42.1 1.0 O3A B:GDP501 4.9 34.9 1.0 HG2 B:GLN11 4.9 60.5 1.0

Fluorine binding site 2 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:63.9 occ:0.87 F2 B:AF3507 0.0 63.9 0.9 AL B:AF3507 1.7 96.0 0.9 MG B:MG502 1.7 34.5 1.0 O1A B:GDP501 2.5 32.7 1.0 O B:HOH626 2.7 39.9 1.0 O3A B:GDP501 2.8 34.9 1.0 F1 B:AF3507 3.0 78.8 0.9 F3 B:AF3507 3.0 71.9 0.9 O C:HOH651 3.0 45.7 1.0 OE1 B:GLN11 3.1 53.5 1.0 PA B:GDP501 3.2 35.3 1.0 HB3 B:GLN11 3.4 50.4 1.0 O1B B:GDP501 3.5 28.3 1.0 PB B:GDP501 3.6 42.1 1.0 HB2 B:GLN11 3.7 50.4 1.0 OD1 B:ASN101 3.8 41.5 1.0 O B:HOH608 3.8 51.6 1.0 CB B:GLN11 4.0 45.9 1.0 O B:HOH625 4.0 35.8 1.0 HD21 B:ASN101 4.1 47.9 1.0 CD B:GLN11 4.1 51.6 1.0 O2B B:GDP501 4.2 37.0 1.0 O5' B:GDP501 4.2 34.6 1.0 O2A B:GDP501 4.3 34.9 1.0 H B:GLN11 4.5 52.4 1.0 CG B:ASN101 4.5 42.5 1.0 C5' B:GDP501 4.6 34.6 1.0 ND2 B:ASN101 4.6 45.1 1.0 H8 B:GDP501 4.6 54.5 1.0 CG B:GLN11 4.6 47.3 1.0 O B:HOH612 4.9 28.4 1.0 HA3 B:GLY143 4.9 40.9 1.0 HG2 B:GLN11 5.0 60.5 1.0 O3B B:GDP501 5.0 32.0 1.0 O B:HOH633 5.0 40.8 1.0

Fluorine binding site 3 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:71.9 occ:0.87 F3 B:AF3507 0.0 71.9 0.9 AL B:AF3507 1.7 96.0 0.9 F2 B:AF3507 3.0 63.9 0.9 F1 B:AF3507 3.0 78.8 0.9 O C:HOH651 3.1 45.7 1.0 OE2 B:GLU71 3.5 67.0 1.0 O B:HOH625 3.5 35.8 1.0 O B:HOH633 3.7 40.8 1.0 MG B:MG502 3.9 34.5 1.0 HD21 B:ASN101 3.9 47.9 1.0 O B:HOH637 4.1 54.6 1.0 OE1 B:GLU71 4.1 67.7 1.0 CD B:GLU71 4.2 67.4 1.0 OE1 C:GLU254 4.2 48.1 1.0 ND2 B:ASN101 4.3 45.1 1.0 H B:ASN101 4.5 47.0 1.0 O B:HOH626 4.6 39.9 1.0 HD22 B:ASN101 4.7 47.9 1.0 HA2 B:GLY100 4.8 40.2 1.0 H B:GLY100 4.8 45.3 1.0 OD1 B:ASN101 4.8 41.5 1.0 CG B:ASN101 4.8 42.5 1.0 O C:HOH653 4.8 42.0 1.0 OE1 B:GLN11 4.9 53.5 1.0 O B:HOH612 4.9 28.4 1.0

J.Estevez-Gallego, F.Josa-Prado, R.M.Buey, F.A.Balaguer, A.E.Prota, D.Lucenal-Agell, C.Kamma-Lorger, M.O.Steinmetz, I.Barasoain, S.Kamimura, J.F.Diaz, M.A.Oliva. Structural Model For Differential Cap Maturation at Growing Microtubule Ends Elife 2020.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.50155