Atomistry » Fluorine » PDB 1udb-1w5y » 1vfx
Atomistry »
  Fluorine »
    PDB 1udb-1w5y »
      1vfx »

Fluorine in PDB 1vfx: Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx

Protein crystallography data

The structure of Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx, PDB code: 1vfx was solved by R.Nitta, M.Kikkawa, Y.Okada, N.Hirokawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.18 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.934, 54.649, 156.784, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 29.4

Other elements in 1vfx:

The structure of Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx (pdb code 1vfx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx, PDB code: 1vfx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1vfx

Go back to Fluorine Binding Sites List in 1vfx
Fluorine binding site 1 out of 3 in the Crystal Structure of the KIF1A Motor Domain 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 Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:81.8
occ:1.00
F1 A:AF3400 0.0 81.8 1.0
AL A:AF3400 1.9 76.3 1.0
MG A:MG501 2.1 54.4 1.0
O3B A:ADP500 2.9 42.8 1.0
F2 A:AF3400 3.2 65.7 1.0
F3 A:AF3400 3.2 62.0 1.0
OG A:SER215 3.6 77.3 1.0
CG2 A:THR213 3.8 87.8 1.0
O2A A:ADP500 3.8 51.4 1.0
OG A:SER104 3.9 37.0 1.0
O A:THR213 4.2 87.9 1.0
CB A:SER215 4.2 81.8 1.0
PB A:ADP500 4.3 44.1 1.0
CB A:SER104 4.5 26.9 1.0
PA A:ADP500 5.0 52.7 1.0

Fluorine binding site 2 out of 3 in 1vfx

Go back to Fluorine Binding Sites List in 1vfx
Fluorine binding site 2 out of 3 in the Crystal Structure of the KIF1A Motor Domain 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 Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:65.7
occ:1.00
F2 A:AF3400 0.0 65.7 1.0
AL A:AF3400 1.8 76.3 1.0
O3B A:ADP500 2.5 42.8 1.0
O A:HOH504 3.1 45.7 1.0
F1 A:AF3400 3.2 81.8 1.0
F3 A:AF3400 3.2 62.0 1.0
CB A:THR99 3.3 44.1 1.0
CB A:SER215 3.3 81.8 1.0
OG1 A:THR99 3.5 36.4 1.0
OG A:SER215 3.6 77.3 1.0
PB A:ADP500 3.7 44.1 1.0
O1B A:ADP500 3.7 50.0 1.0
CA A:THR99 3.8 38.2 1.0
N A:GLY100 4.1 33.0 1.0
MG A:MG501 4.2 54.4 1.0
O A:HOH519 4.4 47.2 1.0
C A:THR99 4.4 36.5 1.0
NZ A:LYS103 4.4 13.3 1.0
O2B A:ADP500 4.5 57.9 1.0
CG2 A:THR99 4.6 35.4 1.0
CA A:SER215 4.8 79.6 1.0
O3A A:ADP500 4.9 50.1 1.0
CE A:LYS103 5.0 22.5 1.0

Fluorine binding site 3 out of 3 in 1vfx

Go back to Fluorine Binding Sites List in 1vfx
Fluorine binding site 3 out of 3 in the Crystal Structure of the KIF1A Motor Domain 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 Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-Alfx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:62.0
occ:1.00
F3 A:AF3400 0.0 62.0 1.0
AL A:AF3400 1.9 76.3 1.0
OG A:SER215 2.7 77.3 1.0
MG A:MG501 3.0 54.4 1.0
OD1 A:ASP248 3.0 29.7 1.0
O3B A:ADP500 3.2 42.8 1.0
F2 A:AF3400 3.2 65.7 1.0
F1 A:AF3400 3.2 81.8 1.0
O A:HOH504 3.5 45.7 1.0
CB A:SER215 3.6 81.8 1.0
CE A:LYS103 3.7 22.5 1.0
OD2 A:ASP248 3.8 49.4 1.0
CG A:ASP248 3.8 42.7 1.0
OG A:SER104 4.0 37.0 1.0
O2B A:ADP500 4.1 57.9 1.0
NZ A:LYS103 4.2 13.3 1.0
PB A:ADP500 4.2 44.1 1.0
O A:LEU249 4.2 40.1 1.0
CB A:LYS103 4.5 29.7 1.0
CD A:LYS103 4.9 22.2 1.0
N A:SER104 4.9 33.7 1.0
O A:ASP248 4.9 38.3 1.0
CA A:SER215 4.9 79.6 1.0
CB A:SER104 4.9 26.9 1.0

Reference:

R.Nitta, M.Kikkawa, Y.Okada, N.Hirokawa. KIF1A Alternately Uses Two Loops to Bind Microtubules Science V. 305 678 2004.
ISSN: ISSN 0036-8075
PubMed: 15286375
DOI: 10.1126/SCIENCE.1096621
Page generated: Wed Jul 31 13:08:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy