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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: Sun Dec 13 11:33:30 2020

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