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

Protein crystallography data

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx, PDB code: 5xjb 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 / 3.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.452, 166.593, 75.500, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 26.1

Other elements in 5xjb:

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

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

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-Befx (pdb code 5xjb). 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-Befx, PDB code: 5xjb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.5
occ:1.00
 F1 A:BEF602 0.0 0.5 1.0
BE A:BEF602 1.8 0.3 1.0
OG A:SER463 2.0 0.7 1.0
N A:SER464 2.2 0.6 1.0
C A:SER463 2.7 0.4 1.0
CA A:SER463 2.7 0.5 1.0
CB A:SER463 2.8 1.0 1.0
MG A:MG603 2.9 66.9 1.0
F2 A:BEF602 3.0 0.8 1.0
F3 A:BEF602 3.1 0.5 1.0
CA A:SER464 3.3 0.7 1.0
NH1 A:ARG452 3.4 0.6 1.0
NH2 A:ARG452 3.5 0.5 1.0
O A:SER463 3.7 94.3 1.0
CB A:SER464 3.7 0.1 1.0
OG A:SER464 3.8 0.2 1.0
O A:SER466 3.9 59.3 1.0
CZ A:ARG452 3.9 0.8 1.0
N A:SER463 4.1 1.0 1.0
OG1 A:THR351 4.3 60.6 1.0
O2B A:ADP601 4.4 82.9 1.0
C A:SER464 4.6 0.4 1.0
OD1 A:ASP488 4.6 57.6 1.0
OD2 A:ASP488 4.7 67.2 1.0
O A:LEU489 4.7 61.7 1.0
N A:ARG465 4.7 96.2 1.0
OG A:SER466 4.8 71.3 1.0
CG A:ASP488 4.9 65.3 1.0

Fluorine binding site 2 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.8
occ:1.00
 F2 A:BEF602 0.0 0.8 1.0
BE A:BEF602 1.8 0.3 1.0
OD1 A:ASP488 2.4 57.6 1.0
O A:ASP488 2.4 72.6 1.0
O A:LEU489 2.6 61.7 1.0
CG A:ASP488 2.7 65.3 1.0
F1 A:BEF602 3.0 0.5 1.0
F3 A:BEF602 3.0 0.5 1.0
C A:ASP488 3.1 60.9 1.0
OD2 A:ASP488 3.2 67.2 1.0
NH2 A:ARG452 3.4 0.5 1.0
C A:LEU489 3.4 62.1 1.0
CB A:ASP488 3.5 61.8 1.0
O A:SER466 3.5 59.3 1.0
CA A:ASP488 3.9 58.9 1.0
N A:LEU489 3.9 59.5 1.0
CA A:LEU489 4.1 57.3 1.0
NH1 A:ARG452 4.2 0.6 1.0
CZ A:ARG452 4.3 0.8 1.0
N A:ALA468 4.3 58.9 1.0
N A:ALA490 4.3 63.1 1.0
OG1 A:THR351 4.4 60.6 1.0
N A:SER464 4.5 0.6 1.0
MG A:MG603 4.6 66.9 1.0
CA A:ALA490 4.6 62.1 1.0
C A:SER466 4.6 63.8 1.0
CE A:LYS350 4.7 71.0 1.0
CA A:HIS467 4.7 59.6 1.0
O2B A:ADP601 4.7 82.9 1.0
OG A:SER463 4.8 0.7 1.0
OG A:SER464 4.8 0.2 1.0
CB A:ALA468 4.9 57.2 1.0
CA A:SER464 4.9 0.7 1.0
C A:HIS467 4.9 57.1 1.0

Fluorine binding site 3 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:0.5
occ:1.00
 F3 A:BEF602 0.0 0.5 1.0
BE A:BEF602 1.8 0.3 1.0
OG A:SER464 1.9 0.2 1.0
O A:LEU489 2.6 61.7 1.0
CE A:LYS350 2.8 71.0 1.0
CB A:SER464 2.9 0.1 1.0
CA A:SER464 3.0 0.7 1.0
F2 A:BEF602 3.0 0.8 1.0
F1 A:BEF602 3.1 0.5 1.0
O2B A:ADP601 3.4 82.9 1.0
N A:SER464 3.4 0.6 1.0
NZ A:LYS350 3.5 68.5 1.0
CA A:ALA490 3.6 62.1 1.0
N A:GLY491 3.6 60.3 1.0
C A:LEU489 3.7 62.1 1.0
C A:ALA490 3.8 60.8 1.0
OD1 A:ASP488 3.9 57.6 1.0
MG A:MG603 4.0 66.9 1.0
N A:ALA490 4.1 63.1 1.0
CD A:LYS350 4.1 69.1 1.0
C A:SER464 4.4 0.4 1.0
C A:SER463 4.5 0.4 1.0
O A:SER466 4.5 59.3 1.0
CA A:GLY491 4.5 65.4 1.0
O A:ALA490 4.6 63.8 1.0
PB A:ADP601 4.6 75.8 1.0
OG A:SER463 4.7 0.7 1.0
CB A:ALA490 4.8 58.3 1.0
CB A:LYS350 4.9 61.2 1.0
O1B A:ADP601 4.9 76.2 1.0
O A:ASP488 4.9 72.6 1.0
CG A:ASP488 4.9 65.3 1.0
OG1 A:THR351 4.9 60.6 1.0

Fluorine binding site 4 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.5
occ:1.00
 F1 B:BEF602 0.0 0.5 1.0
BE B:BEF602 1.8 1.0 1.0
OG B:SER464 2.2 0.7 1.0
CB B:SER464 2.8 0.3 1.0
O B:LEU489 3.0 56.4 1.0
CA B:SER464 3.0 0.0 1.0
F2 B:BEF602 3.1 0.4 1.0
MG B:MG603 3.1 62.7 1.0
F3 B:BEF602 3.1 0.5 1.0
CE B:LYS350 3.2 70.5 1.0
NZ B:LYS350 3.7 75.5 1.0
OD1 B:ASP488 3.9 60.8 1.0
N B:SER464 3.9 0.2 1.0
CA B:ALA490 4.0 51.5 1.0
N B:GLY491 4.1 55.4 1.0
C B:LEU489 4.1 53.3 1.0
O1B B:ADP601 4.1 75.2 1.0
C B:ALA490 4.3 54.7 1.0
C B:SER464 4.3 0.0 1.0
CD B:LYS350 4.4 68.3 1.0
N B:ALA490 4.5 54.0 1.0
OG1 B:THR351 4.6 56.1 1.0
O3B B:ADP601 4.6 68.0 1.0
PB B:ADP601 4.6 68.8 1.0
O B:SER466 4.6 67.0 1.0
O B:SER464 4.6 0.7 1.0
O2B B:ADP601 4.8 69.2 1.0
CG B:ASP488 4.8 59.9 1.0
OG B:SER463 4.8 0.9 1.0
C B:SER463 4.9 0.1 1.0
CB B:LYS350 4.9 60.1 1.0
CA B:GLY491 4.9 58.8 1.0

Fluorine binding site 5 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.4
occ:1.00
 F2 B:BEF602 0.0 0.4 1.0
BE B:BEF602 1.8 1.0 1.0
O B:ASP488 2.5 55.0 1.0
OD1 B:ASP488 2.6 60.8 1.0
O B:LEU489 2.8 56.4 1.0
CG B:ASP488 2.9 59.9 1.0
F3 B:BEF602 3.0 0.5 1.0
NH2 B:ARG452 3.1 0.0 1.0
F1 B:BEF602 3.1 0.5 1.0
C B:ASP488 3.3 54.0 1.0
OD2 B:ASP488 3.3 65.6 1.0
O B:SER466 3.3 67.0 1.0
CB B:ASP488 3.6 57.4 1.0
C B:LEU489 3.6 53.3 1.0
NH1 B:ARG452 3.6 0.9 1.0
CZ B:ARG452 3.8 0.7 1.0
CA B:ASP488 4.0 55.1 1.0
N B:LEU489 4.1 50.4 1.0
N B:ALA468 4.1 57.4 1.0
OG B:SER463 4.2 0.9 1.0
MG B:MG603 4.2 62.7 1.0
CA B:LEU489 4.3 50.0 1.0
N B:ALA490 4.4 54.0 1.0
C B:SER466 4.5 63.7 1.0
OG1 B:THR351 4.5 56.1 1.0
CA B:SER464 4.5 0.0 1.0
OG B:SER464 4.6 0.7 1.0
CA B:HIS467 4.6 54.6 1.0
CA B:ALA490 4.6 51.5 1.0
N B:SER464 4.6 0.2 1.0
CB B:ALA468 4.7 59.5 1.0
C B:HIS467 4.8 55.1 1.0
CE B:LYS350 4.9 70.5 1.0

Fluorine binding site 6 out of 6 in 5xjb

Go back to Fluorine Binding Sites List in 5xjb
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-Befx


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-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:0.5
occ:1.00
 F3 B:BEF602 0.0 0.5 1.0
OG B:SER463 1.8 0.9 1.0
BE B:BEF602 1.8 1.0 1.0
N B:SER464 1.8 0.2 1.0
CA B:SER464 2.4 0.0 1.0
CB B:SER463 2.8 0.1 1.0
C B:SER463 2.8 0.1 1.0
OG B:SER464 2.9 0.7 1.0
F2 B:BEF602 3.0 0.4 1.0
NH2 B:ARG452 3.0 0.0 1.0
F1 B:BEF602 3.1 0.5 1.0
CB B:SER464 3.2 0.3 1.0
NH1 B:ARG452 3.3 0.9 1.0
MG B:MG603 3.4 62.7 1.0
CA B:SER463 3.4 0.4 1.0
CZ B:ARG452 3.4 0.7 1.0
O B:SER466 3.5 67.0 1.0
C B:SER464 3.7 0.0 1.0
O B:SER463 3.8 95.0 1.0
N B:ARG465 4.0 0.4 1.0
OG B:SER466 4.3 70.5 1.0
NE B:ARG452 4.4 92.3 1.0
N B:SER463 4.5 0.3 1.0
C B:SER466 4.6 63.7 1.0
N B:SER466 4.6 75.6 1.0
O B:SER464 4.7 0.7 1.0
O B:LEU489 4.8 56.4 1.0
OG1 B:THR351 4.9 56.1 1.0

Reference:

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
Page generated: Thu Aug 1 16:54:38 2024

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