Fluorine in PDB 5xja: The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx, PDB code: 5xja was solved by T.Ogawa, X.Jiang, N.Hirokawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.43
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.098, 166.989, 74.991, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms

The binding sites of Fluorine atom in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx (pdb code 5xja). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx, PDB code: 5xja:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:32.3 occ:1.00 F1 A:AF3603 0.0 32.3 1.0 AL A:AF3603 1.9 34.8 1.0 O1B A:ADP602 2.8 54.2 1.0 F3 A:AF3603 3.1 36.9 1.0 OG A:SER464 3.2 69.7 1.0 F2 A:AF3603 3.4 32.1 1.0 PB A:ADP602 3.6 47.0 1.0 O3B A:ADP602 3.7 49.8 1.0 CE A:LYS350 3.7 68.1 1.0 NZ A:LYS350 3.9 74.5 1.0 OG A:SER463 4.0 54.2 1.0 OG1 A:THR351 4.0 39.2 1.0 CA A:SER464 4.0 58.8 1.0 O A:LEU489 4.0 53.6 1.0 OD1 A:ASP488 4.0 42.6 1.0 N A:SER464 4.1 57.2 1.0 CB A:SER464 4.2 59.3 1.0 O2B A:ADP602 4.2 46.5 1.0 MG A:MG601 4.2 1.0 1.0 C A:SER463 4.6 56.0 1.0 O A:SER463 4.9 43.0 1.0 N A:GLY491 5.0 54.8 1.0 CB A:LYS350 5.0 58.4 1.0 CG A:ASP488 5.0 45.5 1.0

Fluorine binding site 2 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:32.1 occ:1.00 F2 A:AF3603 0.0 32.1 1.0 AL A:AF3603 1.9 34.8 1.0 OG A:SER463 2.5 54.2 1.0 MG A:MG601 2.6 1.0 1.0 O1B A:ADP602 2.7 54.2 1.0 F3 A:AF3603 3.2 36.9 1.0 F1 A:AF3603 3.4 32.3 1.0 OG1 A:THR351 3.4 39.2 1.0 O2A A:ADP602 3.7 51.4 1.0 CB A:SER463 3.7 52.3 1.0 PB A:ADP602 4.1 47.0 1.0 C A:SER463 4.3 56.0 1.0 CA A:SER463 4.3 52.2 1.0 CB A:THR351 4.4 51.6 1.0 O3A A:ADP602 4.5 50.6 1.0 N A:SER464 4.5 57.2 1.0 PA A:ADP602 4.6 50.7 1.0 O A:SER463 4.7 43.0 1.0 O3B A:ADP602 4.8 49.8 1.0

Fluorine binding site 3 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:36.9 occ:1.00 F3 A:AF3603 0.0 36.9 1.0 AL A:AF3603 1.9 34.8 1.0 OG1 A:THR351 2.5 39.2 1.0 OD2 A:ASP488 2.9 47.6 1.0 F1 A:AF3603 3.1 32.3 1.0 F2 A:AF3603 3.2 32.1 1.0 OD1 A:ASP488 3.3 42.6 1.0 NH1 A:ARG452 3.3 71.4 1.0 CG A:ASP488 3.4 45.5 1.0 CB A:THR351 3.8 51.6 1.0 NH2 A:ARG452 3.8 69.5 1.0 CZ A:ARG452 4.0 75.6 1.0 O1B A:ADP602 4.0 54.2 1.0 CG2 A:THR351 4.1 58.9 1.0 MG A:MG601 4.2 1.0 1.0 O A:SER463 4.4 43.0 1.0 OG A:SER463 4.7 54.2 1.0 CA A:THR351 4.8 54.2 1.0 C A:SER463 4.8 56.0 1.0 CB A:ASP488 4.9 42.0 1.0 O A:LEU489 4.9 53.6 1.0 N A:THR351 5.0 53.5 1.0

Fluorine binding site 4 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:34.3 occ:1.00 F1 B:AF3603 0.0 34.3 1.0 AL B:AF3603 1.9 35.0 1.0 O3B B:ADP602 2.7 46.3 1.0 O2B B:ADP602 2.7 61.6 1.0 MG B:MG601 2.9 58.4 1.0 OG B:SER463 3.0 89.1 1.0 PB B:ADP602 3.1 57.4 1.0 F3 B:AF3603 3.2 34.7 1.0 F2 B:AF3603 3.2 33.9 1.0 OG B:SER464 3.4 54.1 1.0 O2A B:ADP602 3.7 57.0 1.0 N B:SER464 3.8 63.8 1.0 O1B B:ADP602 4.1 64.2 1.0 CB B:SER463 4.1 0.7 1.0 OG1 B:THR351 4.2 39.5 1.0 C B:SER463 4.2 0.8 1.0 CA B:SER464 4.2 51.9 1.0 O3A B:ADP602 4.4 56.4 1.0 CB B:SER464 4.5 50.8 1.0 CG2 B:THR346 4.6 40.4 1.0 PA B:ADP602 4.6 51.8 1.0 O B:SER463 4.6 80.5 1.0 CA B:SER463 4.9 0.3 1.0 N B:GLY347 4.9 51.1 1.0

Fluorine binding site 5 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:33.9 occ:1.00 F2 B:AF3603 0.0 33.9 1.0 AL B:AF3603 1.9 35.0 1.0 MG B:MG601 2.8 58.4 1.0 OG1 B:THR351 3.0 39.5 1.0 F1 B:AF3603 3.2 34.3 1.0 F3 B:AF3603 3.3 34.7 1.0 OG B:SER463 3.3 89.1 1.0 O3B B:ADP602 3.9 46.3 1.0 O B:SER463 4.0 80.5 1.0 CB B:THR351 4.0 56.4 1.0 NH2 B:ARG452 4.0 0.6 1.0 CG2 B:THR351 4.2 60.6 1.0 NH1 B:ARG452 4.3 1.0 1.0 C B:SER463 4.3 0.8 1.0 CZ B:ARG452 4.5 95.3 1.0 CB B:SER463 4.6 0.7 1.0 OD2 B:ASP488 4.6 43.7 1.0 CA B:SER463 4.8 0.3 1.0 N B:SER464 4.9 63.8 1.0

Fluorine binding site 6 out of 6 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:34.7 occ:1.00 F3 B:AF3603 0.0 34.7 1.0 AL B:AF3603 1.9 35.0 1.0 OD1 B:ASP488 2.7 35.5 1.0 O3B B:ADP602 3.1 46.3 1.0 OG1 B:THR351 3.2 39.5 1.0 F1 B:AF3603 3.2 34.3 1.0 F2 B:AF3603 3.3 33.9 1.0 O B:LEU489 3.4 38.0 1.0 CG B:ASP488 3.5 40.9 1.0 OD2 B:ASP488 3.7 43.7 1.0 MG B:MG601 3.9 58.4 1.0 CE B:LYS350 4.0 70.8 1.0 PB B:ADP602 4.1 57.4 1.0 NH2 B:ARG452 4.3 0.6 1.0 O1B B:ADP602 4.4 64.2 1.0 O B:ASP488 4.4 53.5 1.0 CB B:LYS350 4.6 54.7 1.0 CB B:THR351 4.6 56.4 1.0 C B:LEU489 4.6 39.8 1.0 O B:SER466 4.8 58.8 1.0 NZ B:LYS350 4.8 76.0 1.0 O2B B:ADP602 4.8 61.6 1.0 N B:THR351 4.8 59.0 1.0 C B:ASP488 4.9 41.1 1.0 CA B:SER464 4.9 51.9 1.0 O B:SER463 4.9 80.5 1.0 OG B:SER464 4.9 54.1 1.0 CB B:ASP488 5.0 40.6 1.0

T.Ogawa, S.Saijo, N.Shimizu, X.Jiang, N.Hirokawa. Mechanism of Catalytic Microtubule Depolymerization Via KIF2-Tubulin Transitional Conformation Cell Rep V. 20 2626 2017.
ISSN: ESSN 2211-1247
PubMed: 28903043
DOI: 10.1016/J.CELREP.2017.08.067