Atomistry » Fluorine » PDB 5xd5-5y5r » 5xjb
Atomistry »
  Fluorine »
    PDB 5xd5-5y5r »
      5xjb »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy