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Fluorine in PDB 3w6p: Crystal Structure of Human DLP1 in Complex with Gdp.ALF4

Enzymatic activity of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4

All present enzymatic activity of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4:
3.6.5.5;

Protein crystallography data

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p was solved by H.Kishida, S.Sugio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.410, 109.130, 128.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.4

Other elements in 3w6p:

The structure of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 (pdb code 3w6p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4, PDB code: 3w6p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 1 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


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 Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:14.7
occ:1.00
F1 A:ALF802 0.0 14.7 1.0
AL A:ALF802 1.8 8.2 1.0
F3 A:ALF802 2.5 11.9 1.0
F4 A:ALF802 2.6 11.9 1.0
O3B A:GDP801 2.7 5.0 1.0
O A:HOH1103 2.7 6.8 1.0
NA A:NA804 2.8 8.0 1.0
N A:THR59 2.8 7.0 1.0
N A:VAL58 2.8 8.0 1.0
O A:HOH1101 3.1 8.2 1.0
CB A:VAL58 3.2 7.9 1.0
CA A:VAL58 3.3 7.7 1.0
MG A:MG803 3.4 3.1 1.0
C A:VAL58 3.5 7.6 1.0
F2 A:ALF802 3.6 9.4 1.0
OG1 A:THR59 3.7 6.3 1.0
CA A:THR59 3.9 7.3 1.0
PB A:GDP801 3.9 6.3 1.0
CB A:THR59 3.9 6.9 1.0
O2B A:GDP801 3.9 6.7 1.0
C A:ILE57 4.0 9.1 1.0
O A:GLY56 4.0 9.3 1.0
CG2 A:VAL58 4.1 7.6 1.0
CG1 A:VAL58 4.2 7.9 1.0
CA A:ILE57 4.3 9.1 1.0
O A:THR59 4.3 6.6 1.0
O1A A:GDP801 4.4 7.3 1.0
O A:GLY54 4.4 10.3 1.0
C A:THR59 4.6 7.1 1.0
O A:VAL58 4.7 7.1 1.0
O3A A:GDP801 4.7 5.8 1.0
OG A:SER35 5.0 5.7 1.0
C A:GLY56 5.0 9.9 1.0
CG1 A:ILE57 5.0 8.7 1.0

Fluorine binding site 2 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 2 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


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 Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:9.4
occ:1.00
F2 A:ALF802 0.0 9.4 1.0
AL A:ALF802 1.8 8.2 1.0
F4 A:ALF802 2.5 11.9 1.0
F3 A:ALF802 2.5 11.9 1.0
O A:HOH1103 2.6 6.8 1.0
NZ A:LYS38 2.6 7.0 1.0
O3B A:GDP801 2.7 5.0 1.0
N A:GLY149 3.0 5.5 1.0
N A:SER35 3.2 5.2 1.0
CA A:GLN34 3.3 5.2 1.0
CA A:GLY149 3.3 5.4 1.0
O1B A:GDP801 3.5 4.9 1.0
CE A:LYS38 3.5 7.2 1.0
F1 A:ALF802 3.6 14.7 1.0
PB A:GDP801 3.6 6.3 1.0
O A:HOH915 3.6 5.2 1.0
C A:GLN34 3.8 5.4 1.0
CG A:GLN34 4.0 7.1 1.0
CB A:GLN34 4.0 5.6 1.0
C A:PRO148 4.1 6.0 1.0
O A:THR33 4.1 5.9 1.0
O2B A:GDP801 4.1 6.7 1.0
N A:GLN34 4.2 5.3 1.0
CA A:SER35 4.3 6.0 1.0
MG A:MG803 4.3 3.1 1.0
C A:GLY149 4.4 5.9 1.0
NA A:NA804 4.5 8.0 1.0
CA A:PRO148 4.5 6.0 1.0
C A:THR33 4.5 5.5 1.0
O A:HOH1102 4.6 5.5 1.0
O A:LEU147 4.7 6.6 1.0
O A:GLY149 4.7 6.0 1.0
O3A A:GDP801 4.9 5.8 1.0
CD A:LYS38 5.0 5.0 1.0

Fluorine binding site 3 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 3 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


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 Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:11.9
occ:1.00
F3 A:ALF802 0.0 11.9 1.0
AL A:ALF802 1.8 8.2 1.0
NA A:NA804 2.4 8.0 1.0
F1 A:ALF802 2.5 14.7 1.0
F2 A:ALF802 2.5 9.4 1.0
O3B A:GDP801 2.7 5.0 1.0
O A:HOH1103 2.7 6.8 1.0
CG A:GLN34 2.9 7.1 1.0
O A:GLY56 3.2 9.3 1.0
N A:SER35 3.2 5.2 1.0
OG A:SER35 3.4 5.7 1.0
F4 A:ALF802 3.6 11.9 1.0
CA A:ILE57 3.8 9.1 1.0
N A:VAL58 3.8 8.0 1.0
O A:HOH915 3.9 5.2 1.0
CD A:GLN34 3.9 6.7 1.0
CA A:SER35 3.9 6.0 1.0
CA A:GLN34 3.9 5.2 1.0
C A:GLN34 3.9 5.4 1.0
CB A:GLN34 3.9 5.6 1.0
C A:GLY56 4.0 9.9 1.0
PB A:GDP801 4.2 6.3 1.0
CB A:SER35 4.2 6.2 1.0
N A:ILE57 4.3 9.4 1.0
C A:ILE57 4.3 9.1 1.0
OE1 A:GLN34 4.4 7.7 1.0
OD2 B:ASP190 4.5 9.2 1.0
NE2 A:GLN34 4.5 7.8 1.0
CG1 A:ILE57 4.6 8.7 1.0
O A:GLY54 4.6 10.3 1.0
CB A:ILE57 4.6 8.8 1.0
O1B A:GDP801 4.7 4.9 1.0
N A:THR59 4.9 7.0 1.0
O3A A:GDP801 4.9 5.8 1.0
NZ A:LYS38 4.9 7.0 1.0
O2B A:GDP801 4.9 6.7 1.0
CA A:VAL58 5.0 7.7 1.0
N A:GLY149 5.0 5.5 1.0

Fluorine binding site 4 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 4 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:11.9
occ:1.00
F4 A:ALF802 0.0 11.9 1.0
AL A:ALF802 1.8 8.2 1.0
MG A:MG803 2.0 3.1 1.0
F2 A:ALF802 2.5 9.4 1.0
F1 A:ALF802 2.6 14.7 1.0
O A:HOH1103 2.7 6.8 1.0
O3B A:GDP801 2.7 5.0 1.0
O A:HOH1102 2.7 5.5 1.0
O2B A:GDP801 2.8 6.7 1.0
OG1 A:THR59 3.0 6.3 1.0
CB A:THR59 3.1 6.9 1.0
PB A:GDP801 3.2 6.3 1.0
F3 A:ALF802 3.6 11.9 1.0
O A:HOH1101 3.6 8.2 1.0
O A:LEU147 3.8 6.6 1.0
NZ A:LYS38 3.8 7.0 1.0
N A:THR59 3.8 7.0 1.0
O1B A:GDP801 3.9 4.9 1.0
CA A:THR59 4.0 7.3 1.0
CE A:LYS38 4.0 7.2 1.0
OG A:SER39 4.1 4.3 1.0
N A:GLY149 4.1 5.5 1.0
CA A:PRO148 4.2 6.0 1.0
O A:THR59 4.3 6.6 1.0
CG2 A:THR59 4.3 8.1 1.0
C A:PRO148 4.6 6.0 1.0
C A:THR59 4.6 7.1 1.0
C A:LEU147 4.7 6.7 1.0
O3A A:GDP801 4.7 5.8 1.0
NA A:NA804 4.7 8.0 1.0
N A:PRO148 4.9 6.4 1.0

Fluorine binding site 5 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 5 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:16.6
occ:1.00
F1 B:ALF802 0.0 16.6 1.0
AL B:ALF802 1.8 9.3 1.0
F3 B:ALF802 2.5 14.0 1.0
F4 B:ALF802 2.6 13.1 1.0
O B:HOH1135 2.7 5.0 1.0
O3B B:GDP801 2.7 6.1 1.0
N B:VAL58 2.8 8.8 1.0
N B:THR59 2.8 7.3 1.0
NA B:NA804 2.8 10.5 1.0
CB B:VAL58 3.1 8.6 1.0
CA B:VAL58 3.2 8.3 1.0
O B:HOH1134 3.2 7.9 1.0
MG B:MG803 3.4 3.0 1.0
C B:VAL58 3.5 8.1 1.0
F2 B:ALF802 3.5 10.6 1.0
OG1 B:THR59 3.8 6.4 1.0
C B:ILE57 3.9 10.3 1.0
CA B:THR59 3.9 6.6 1.0
CB B:THR59 3.9 6.8 1.0
O B:GLY56 4.0 11.9 1.0
PB B:GDP801 4.0 5.8 1.0
CG2 B:VAL58 4.0 8.3 1.0
O2B B:GDP801 4.0 6.6 1.0
CA B:ILE57 4.2 10.6 1.0
CG1 B:VAL58 4.3 8.0 1.0
O B:THR59 4.3 6.9 1.0
O B:GLY54 4.4 13.2 1.0
O1A B:GDP801 4.4 7.0 1.0
C B:THR59 4.6 6.7 1.0
O B:VAL58 4.7 8.4 1.0
O3A B:GDP801 4.8 5.0 1.0
C B:GLY56 4.9 12.4 1.0
CG1 B:ILE57 5.0 10.0 1.0
O B:ILE57 5.0 11.3 1.0
OG B:SER35 5.0 7.7 1.0

Fluorine binding site 6 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 6 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:10.6
occ:1.00
F2 B:ALF802 0.0 10.6 1.0
AL B:ALF802 1.8 9.3 1.0
F4 B:ALF802 2.5 13.1 1.0
F3 B:ALF802 2.5 14.0 1.0
NZ B:LYS38 2.6 5.0 1.0
O B:HOH1135 2.6 5.0 1.0
O3B B:GDP801 2.7 6.1 1.0
N B:GLY149 2.9 6.0 1.0
N B:SER35 3.2 6.1 1.0
CA B:GLY149 3.2 5.8 1.0
CA B:GLN34 3.3 5.8 1.0
O1B B:GDP801 3.5 5.0 1.0
CE B:LYS38 3.5 7.2 1.0
PB B:GDP801 3.5 5.8 1.0
F1 B:ALF802 3.5 16.6 1.0
O B:HOH951 3.7 7.4 1.0
C B:GLN34 3.8 5.7 1.0
CG B:GLN34 4.0 8.6 1.0
CB B:GLN34 4.0 5.7 1.0
C B:PRO148 4.1 6.4 1.0
O2B B:GDP801 4.1 6.6 1.0
O B:THR33 4.2 5.9 1.0
N B:GLN34 4.2 5.0 1.0
MG B:MG803 4.3 3.0 1.0
CA B:SER35 4.4 6.8 1.0
C B:GLY149 4.4 5.7 1.0
NA B:NA804 4.5 10.5 1.0
CA B:PRO148 4.5 6.2 1.0
O B:HOH1136 4.5 7.3 1.0
C B:THR33 4.6 5.4 1.0
O B:LEU147 4.7 7.1 1.0
O B:GLY149 4.7 5.7 1.0
O3A B:GDP801 4.9 5.0 1.0
CD B:LYS38 4.9 5.2 1.0

Fluorine binding site 7 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 7 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:14.0
occ:1.00
F3 B:ALF802 0.0 14.0 1.0
AL B:ALF802 1.8 9.3 1.0
NA B:NA804 2.4 10.5 1.0
F1 B:ALF802 2.5 16.6 1.0
F2 B:ALF802 2.5 10.6 1.0
O3B B:GDP801 2.7 6.1 1.0
O B:HOH1135 2.7 5.0 1.0
CG B:GLN34 2.8 8.6 1.0
N B:SER35 3.2 6.1 1.0
O B:GLY56 3.2 11.9 1.0
OG B:SER35 3.4 7.7 1.0
F4 B:ALF802 3.6 13.1 1.0
CA B:ILE57 3.7 10.6 1.0
CD B:GLN34 3.8 8.6 1.0
CA B:GLN34 3.8 5.8 1.0
N B:VAL58 3.8 8.8 1.0
CB B:GLN34 3.8 5.7 1.0
O B:HOH951 3.8 7.4 1.0
C B:GLN34 3.9 5.7 1.0
CA B:SER35 3.9 6.8 1.0
C B:GLY56 4.1 12.4 1.0
PB B:GDP801 4.2 5.8 1.0
CB B:SER35 4.2 7.1 1.0
N B:ILE57 4.3 11.5 1.0
C B:ILE57 4.3 10.3 1.0
OE1 B:GLN34 4.4 9.4 1.0
NE2 B:GLN34 4.5 10.2 1.0
OD2 A:ASP190 4.5 9.8 1.0
CB B:ILE57 4.6 10.3 1.0
O B:GLY54 4.6 13.2 1.0
CG1 B:ILE57 4.7 10.0 1.0
O1B B:GDP801 4.7 5.0 1.0
N B:THR59 4.9 7.3 1.0
N B:GLY149 4.9 6.0 1.0
NZ B:LYS38 4.9 5.0 1.0
CA B:VAL58 4.9 8.3 1.0
O3A B:GDP801 4.9 5.0 1.0
O2B B:GDP801 5.0 6.6 1.0

Fluorine binding site 8 out of 8 in 3w6p

Go back to Fluorine Binding Sites List in 3w6p
Fluorine binding site 8 out of 8 in the Crystal Structure of Human DLP1 in Complex with Gdp.ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human DLP1 in Complex with Gdp.ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:13.1
occ:1.00
F4 B:ALF802 0.0 13.1 1.0
AL B:ALF802 1.8 9.3 1.0
MG B:MG803 2.0 3.0 1.0
F2 B:ALF802 2.5 10.6 1.0
F1 B:ALF802 2.6 16.6 1.0
O B:HOH1135 2.6 5.0 1.0
O3B B:GDP801 2.7 6.1 1.0
O B:HOH1136 2.8 7.3 1.0
O2B B:GDP801 2.8 6.6 1.0
OG1 B:THR59 3.0 6.4 1.0
CB B:THR59 3.0 6.8 1.0
PB B:GDP801 3.2 5.8 1.0
F3 B:ALF802 3.6 14.0 1.0
O B:HOH1134 3.6 7.9 1.0
N B:THR59 3.7 7.3 1.0
O B:LEU147 3.9 7.1 1.0
NZ B:LYS38 3.9 5.0 1.0
O1B B:GDP801 3.9 5.0 1.0
CA B:THR59 4.0 6.6 1.0
OG B:SER39 4.1 5.9 1.0
N B:GLY149 4.1 6.0 1.0
CE B:LYS38 4.1 7.2 1.0
CG2 B:THR59 4.2 6.1 1.0
O B:THR59 4.3 6.9 1.0
CA B:PRO148 4.3 6.2 1.0
C B:PRO148 4.6 6.4 1.0
C B:THR59 4.6 6.7 1.0
O3A B:GDP801 4.6 5.0 1.0
NA B:NA804 4.7 10.5 1.0
C B:LEU147 4.7 6.1 1.0
N B:PRO148 4.9 6.2 1.0
C B:VAL58 5.0 8.1 1.0
CA B:GLY149 5.0 5.8 1.0

Reference:

H.Kishida, S.Sugio. Crystal Structure of Gtpase Domain Fused with Minimal Stalks From Human Dynamin-1-Like Protein (DLP1) in Complex with Several Nucleotide Analogues Curr Top Pept Protein Res. V. 14 67 2013.
ISSN: ISSN 0972-4524
Page generated: Sun Dec 13 11:57:38 2020

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