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Fluorine in PDB 4i1o: Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3

Protein crystallography data

The structure of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3, PDB code: 4i1o was solved by E.M.Gazdag, A.Streller, I.R.Vetter, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.16 / 2.70
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 124.410, 124.410, 147.470, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 24.9

Other elements in 4i1o:

The structure of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 (pdb code 4i1o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3, PDB code: 4i1o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4i1o

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Fluorine binding site 1 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:38.7
occ:1.00
 F1 A:BEF203 0.0 38.7 1.0
BE A:BEF203 1.5 32.1 1.0
O2B A:GDP202 2.1 35.2 1.0
F3 A:BEF203 2.5 26.9 1.0
F2 A:BEF203 2.5 51.8 1.0
OG A:SER17 2.6 29.6 1.0
NH1 D:ARG444 2.7 24.5 1.0
NH2 D:ARG444 3.0 34.4 1.0
N A:GLY18 3.1 29.0 1.0
CZ D:ARG444 3.3 32.1 1.0
OG A:SER39 3.4 37.2 1.0
PB A:GDP202 3.6 32.9 1.0
CA A:SER17 3.6 29.5 1.0
CB A:SER17 3.6 27.2 1.0
C A:SER17 3.7 29.1 1.0
CA A:GLY18 4.0 29.9 1.0
CB A:SER39 4.1 35.7 1.0
O3A A:GDP202 4.2 23.3 1.0
OE1 A:GLN67 4.3 40.7 1.0
O3B A:GDP202 4.3 28.9 1.0
O1B A:GDP202 4.4 32.2 1.0
CA A:SER39 4.5 33.0 1.0
NE2 A:GLN67 4.5 35.2 1.0
NE D:ARG444 4.6 31.6 1.0
CD A:GLN67 4.7 38.3 1.0
N A:THR40 4.7 34.0 1.0
O A:HOH306 4.8 21.8 1.0
O A:SER17 4.8 29.6 1.0
N A:SER17 5.0 31.4 1.0

Fluorine binding site 2 out of 12 in 4i1o

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Fluorine binding site 2 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:51.8
occ:1.00
 F2 A:BEF203 0.0 51.8 1.0
BE A:BEF203 1.6 32.1 1.0
O2B A:GDP202 2.3 35.2 1.0
F3 A:BEF203 2.4 26.9 1.0
F1 A:BEF203 2.5 38.7 1.0
NZ A:LYS21 2.9 27.7 1.0
N A:GLY66 3.1 29.3 1.0
CA A:SER17 3.3 29.5 1.0
PB A:GDP202 3.3 32.9 1.0
O1B A:GDP202 3.5 32.2 1.0
CE A:LYS21 3.6 26.1 1.0
N A:GLY18 3.7 29.0 1.0
CA A:GLY66 3.8 26.5 1.0
OG A:SER17 3.8 29.6 1.0
CB A:SER17 3.9 27.2 1.0
O3B A:GDP202 4.0 28.9 1.0
C A:ALA65 4.0 29.6 1.0
C A:SER17 4.1 29.1 1.0
CA A:ALA65 4.1 32.9 1.0
O A:ASP16 4.1 28.8 1.0
N A:SER17 4.2 31.4 1.0
O A:THR64 4.2 30.7 1.0
MG A:MG201 4.2 33.0 1.0
OE1 A:GLN67 4.3 40.7 1.0
C A:ASP16 4.5 30.9 1.0
O3A A:GDP202 4.7 23.3 1.0
O A:GLY15 4.7 27.5 1.0
C A:GLY66 4.9 33.3 1.0
CA A:GLY18 4.9 29.9 1.0
CB A:ALA65 4.9 34.1 1.0

Fluorine binding site 3 out of 12 in 4i1o

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Fluorine binding site 3 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:26.9
occ:1.00
 F3 A:BEF203 0.0 26.9 1.0
BE A:BEF203 1.5 32.1 1.0
F2 A:BEF203 2.4 51.8 1.0
F1 A:BEF203 2.5 38.7 1.0
O2B A:GDP202 2.8 35.2 1.0
N A:THR40 3.1 34.0 1.0
CB A:THR40 3.3 25.1 1.0
OG A:SER39 3.3 37.2 1.0
MG A:MG201 3.3 33.0 1.0
OG1 A:THR40 3.4 32.3 1.0
O A:THR40 3.6 37.0 1.0
CA A:THR40 3.6 27.7 1.0
O3B A:GDP202 3.7 28.9 1.0
PB A:GDP202 3.8 32.9 1.0
O A:HOH306 3.9 21.8 1.0
C A:SER39 4.0 33.7 1.0
C A:THR40 4.1 32.7 1.0
CA A:ALA65 4.1 32.9 1.0
CA A:SER39 4.1 33.0 1.0
OE1 A:GLN67 4.2 40.7 1.0
CB A:SER39 4.3 35.7 1.0
NH2 D:ARG444 4.3 34.4 1.0
N A:GLY66 4.4 29.3 1.0
CB A:ALA65 4.5 34.1 1.0
O A:THR64 4.6 30.7 1.0
OG A:SER17 4.6 29.6 1.0
O1B A:GDP202 4.7 32.2 1.0
CG2 A:THR40 4.7 24.9 1.0
NH1 D:ARG444 4.8 24.5 1.0
OG A:SER22 4.8 29.5 1.0
C A:ALA65 4.8 29.6 1.0
CZ D:ARG444 5.0 32.1 1.0
NZ A:LYS21 5.0 27.7 1.0
O3A A:GDP202 5.0 23.3 1.0
CD A:GLN67 5.0 38.3 1.0

Fluorine binding site 4 out of 12 in 4i1o

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Fluorine binding site 4 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:45.8
occ:1.00
 F1 C:BEF203 0.0 45.8 1.0
BE C:BEF203 1.5 47.7 1.0
O2B C:GDP202 2.2 46.8 1.0
F3 C:BEF203 2.5 59.2 1.0
OG C:SER17 2.5 32.2 1.0
F2 C:BEF203 2.5 27.2 1.0
NH1 B:ARG444 2.7 22.7 1.0
NH2 B:ARG444 3.1 32.3 1.0
N C:GLY18 3.2 25.6 1.0
CZ B:ARG444 3.3 30.1 1.0
OG C:SER39 3.4 34.7 1.0
CB C:SER17 3.5 28.3 1.0
CA C:SER17 3.6 29.4 1.0
PB C:GDP202 3.7 32.8 1.0
C C:SER17 3.7 26.8 1.0
CA C:GLY18 4.0 27.4 1.0
O3A C:GDP202 4.2 22.2 1.0
CB C:SER39 4.2 33.6 1.0
OE1 C:GLN67 4.3 43.5 1.0
NE2 C:GLN67 4.5 32.8 1.0
O3B C:GDP202 4.5 29.1 1.0
O1B C:GDP202 4.5 28.8 1.0
CA C:SER39 4.5 31.6 1.0
CD C:GLN67 4.5 39.7 1.0
MG C:MG201 4.6 34.5 1.0
NE B:ARG444 4.6 29.8 1.0
N C:THR40 4.7 34.6 1.0
O C:SER17 4.8 28.1 1.0
N C:SER17 4.9 33.8 1.0

Fluorine binding site 5 out of 12 in 4i1o

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Fluorine binding site 5 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:27.2
occ:1.00
 F2 C:BEF203 0.0 27.2 1.0
BE C:BEF203 1.5 47.7 1.0
F3 C:BEF203 2.5 59.2 1.0
F1 C:BEF203 2.5 45.8 1.0
O2B C:GDP202 2.9 46.8 1.0
N C:THR40 3.1 34.6 1.0
CB C:THR40 3.4 25.8 1.0
O C:HOH304 3.4 24.6 1.0
MG C:MG201 3.4 34.5 1.0
OG C:SER39 3.5 34.7 1.0
OG1 C:THR40 3.5 34.8 1.0
O C:THR40 3.5 38.5 1.0
CA C:THR40 3.7 28.1 1.0
O3B C:GDP202 3.9 29.1 1.0
CA C:ALA65 4.0 32.5 1.0
PB C:GDP202 4.0 32.8 1.0
OE1 C:GLN67 4.0 43.5 1.0
C C:SER39 4.1 34.2 1.0
C C:THR40 4.1 32.8 1.0
CA C:SER39 4.2 31.6 1.0
CB C:ALA65 4.3 32.8 1.0
N C:GLY66 4.3 30.3 1.0
CB C:SER39 4.4 33.6 1.0
O C:THR64 4.4 28.7 1.0
NH2 B:ARG444 4.4 32.3 1.0
OG C:SER17 4.5 32.2 1.0
C C:ALA65 4.7 31.5 1.0
CG2 C:THR40 4.7 23.3 1.0
NH1 B:ARG444 4.8 22.7 1.0
CD C:GLN67 4.8 39.7 1.0
O1B C:GDP202 4.9 28.8 1.0
N C:ALA65 5.0 32.2 1.0
OG C:SER22 5.0 26.1 1.0

Fluorine binding site 6 out of 12 in 4i1o

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Fluorine binding site 6 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:59.2
occ:1.00
 F3 C:BEF203 0.0 59.2 1.0
BE C:BEF203 1.5 47.7 1.0
O2B C:GDP202 1.7 46.8 1.0
F2 C:BEF203 2.5 27.2 1.0
F1 C:BEF203 2.5 45.8 1.0
PB C:GDP202 2.8 32.8 1.0
NZ C:LYS21 2.8 28.6 1.0
O1B C:GDP202 3.1 28.8 1.0
O3B C:GDP202 3.4 29.1 1.0
N C:GLY18 3.4 25.6 1.0
CA C:SER17 3.5 29.4 1.0
CE C:LYS21 3.6 24.9 1.0
O C:HOH304 3.7 24.6 1.0
N C:GLY66 3.8 30.3 1.0
C C:SER17 4.0 26.8 1.0
OG C:SER17 4.0 32.2 1.0
O3A C:GDP202 4.1 22.2 1.0
O C:ASP16 4.1 35.0 1.0
CB C:SER17 4.1 28.3 1.0
MG C:MG201 4.2 34.5 1.0
O C:THR64 4.3 28.7 1.0
N C:SER17 4.4 33.8 1.0
CA C:GLY66 4.5 28.4 1.0
CA C:ALA65 4.5 32.5 1.0
CA C:GLY18 4.5 27.4 1.0
NH2 B:ARG444 4.6 32.3 1.0
C C:ALA65 4.6 31.5 1.0
C C:ASP16 4.6 33.2 1.0
O C:GLY15 4.9 26.7 1.0
CD C:LYS21 4.9 26.2 1.0

Fluorine binding site 7 out of 12 in 4i1o

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Fluorine binding site 7 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F203

b:55.0
occ:1.00
 F1 E:BEF203 0.0 55.0 1.0
BE E:BEF203 1.5 61.5 1.0
O3B E:GDP202 2.2 29.1 1.0
F3 E:BEF203 2.5 66.4 1.0
F2 E:BEF203 2.6 36.5 1.0
NH1 F:ARG444 2.9 22.9 1.0
OG E:SER17 2.9 26.8 1.0
NH2 F:ARG444 3.0 33.1 1.0
OG E:SER39 3.1 38.8 1.0
CZ F:ARG444 3.3 30.6 1.0
PB E:GDP202 3.6 34.4 1.0
N E:GLY18 3.6 28.2 1.0
CB E:SER39 3.8 35.8 1.0
MG E:MG201 4.0 32.6 1.0
CB E:SER17 4.0 24.8 1.0
CA E:SER39 4.0 33.8 1.0
CA E:SER17 4.1 29.6 1.0
N E:THR40 4.1 34.8 1.0
O3A E:GDP202 4.2 26.3 1.0
O1B E:GDP202 4.3 37.5 1.0
OE1 E:GLN67 4.3 45.4 1.0
C E:SER17 4.3 29.7 1.0
CA E:GLY18 4.4 27.4 1.0
O2B E:GDP202 4.5 42.5 1.0
NE2 E:GLN67 4.5 34.2 1.0
NE F:ARG444 4.6 30.1 1.0
C E:SER39 4.6 35.5 1.0
CD E:GLN67 4.7 39.0 1.0
O E:HOH306 4.8 16.8 1.0
OG1 E:THR40 5.0 33.7 1.0
O E:ILE38 5.0 45.2 1.0

Fluorine binding site 8 out of 12 in 4i1o

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Fluorine binding site 8 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


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 the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F203

b:36.5
occ:1.00
 F2 E:BEF203 0.0 36.5 1.0
BE E:BEF203 1.6 61.5 1.0
MG E:MG201 1.7 32.6 1.0
O3B E:GDP202 2.0 29.1 1.0
O E:HOH306 2.2 16.8 1.0
O1B E:GDP202 2.3 37.5 1.0
F3 E:BEF203 2.5 66.4 1.0
F1 E:BEF203 2.6 55.0 1.0
PB E:GDP202 2.7 34.4 1.0
OG1 E:THR40 2.7 33.7 1.0
N E:THR40 3.3 34.8 1.0
CB E:THR40 3.3 27.9 1.0
OG E:SER22 3.4 27.5 1.0
O3A E:GDP202 3.7 26.3 1.0
NH2 F:ARG444 3.8 33.1 1.0
O2B E:GDP202 3.8 42.5 1.0
O2A E:GDP202 3.9 33.2 1.0
CA E:THR40 3.9 30.3 1.0
C E:SER39 4.3 35.5 1.0
CA E:SER39 4.3 33.8 1.0
OG E:SER39 4.4 38.8 1.0
PA E:GDP202 4.4 38.3 1.0
O E:THR64 4.6 30.3 1.0
CB E:SER22 4.7 24.2 1.0
CG2 E:THR40 4.7 27.1 1.0
O E:THR40 4.7 38.5 1.0
CZ F:ARG444 4.7 30.6 1.0
O E:ILE38 4.8 45.2 1.0
NZ E:LYS21 4.8 33.5 1.0
C E:THR40 4.8 33.6 1.0
CE E:LYS21 4.9 31.3 1.0
CB E:SER39 4.9 35.8 1.0
NH1 F:ARG444 4.9 22.9 1.0

Fluorine binding site 9 out of 12 in 4i1o

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Fluorine binding site 9 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F203

b:66.4
occ:1.00
 F3 E:BEF203 0.0 66.4 1.0
BE E:BEF203 1.5 61.5 1.0
F1 E:BEF203 2.5 55.0 1.0
F2 E:BEF203 2.5 36.5 1.0
O3B E:GDP202 2.7 29.1 1.0
N E:GLY66 3.0 28.4 1.0
CA E:ALA65 3.3 30.4 1.0
C E:ALA65 3.7 29.3 1.0
OE1 E:GLN67 3.8 45.4 1.0
O E:HOH306 3.8 16.8 1.0
NZ E:LYS21 3.9 33.5 1.0
PB E:GDP202 3.9 34.4 1.0
O E:THR64 3.9 30.3 1.0
CB E:ALA65 3.9 33.4 1.0
OG E:SER17 4.1 26.8 1.0
CA E:GLY66 4.1 31.9 1.0
O1B E:GDP202 4.2 37.5 1.0
MG E:MG201 4.2 32.6 1.0
CE E:LYS21 4.2 31.3 1.0
CB E:THR40 4.3 27.9 1.0
CA E:SER17 4.3 29.6 1.0
O E:THR40 4.3 38.5 1.0
O2B E:GDP202 4.3 42.5 1.0
OG E:SER39 4.4 38.8 1.0
N E:ALA65 4.4 31.2 1.0
N E:THR40 4.4 34.8 1.0
OG1 E:THR40 4.5 33.7 1.0
CB E:SER17 4.5 24.8 1.0
C E:THR64 4.6 32.1 1.0
N E:GLY18 4.7 28.2 1.0
CD E:GLN67 4.7 39.0 1.0
CA E:THR40 4.8 30.3 1.0
N E:GLN67 4.9 32.8 1.0
O E:ALA65 4.9 30.9 1.0

Fluorine binding site 10 out of 12 in 4i1o

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Fluorine binding site 10 out of 12 in the Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Legionella Pneumophila Gap Domain of Lepb in Complex with RAB1B Bound to Gdp and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F203

b:36.5
occ:1.00
 F1 G:BEF203 0.0 36.5 1.0
BE G:BEF203 1.5 38.5 1.0
F3 G:BEF203 2.5 57.1 1.0
F2 G:BEF203 2.5 0.1 1.0
O2B G:GDP202 2.9 45.7 1.0
OG G:SER39 3.3 35.3 1.0
N G:THR40 3.3 33.1 1.0
O G:THR40 3.4 36.4 1.0
O G:HOH307 3.5 28.9 1.0
CB G:THR40 3.5 26.9 1.0
OG1 G:THR40 3.7 34.7 1.0
MG G:MG201 3.7 35.7 1.0
CA G:ALA65 3.8 32.9 1.0
OE1 G:GLN67 3.8 44.7 1.0
CA G:THR40 3.8 28.1 1.0
O3B G:GDP202 3.9 40.1 1.0
N G:GLY66 4.0 29.8 1.0
PB G:GDP202 4.0 33.4 1.0
CB G:ALA65 4.0 33.4 1.0
C G:THR40 4.1 32.9 1.0
C G:SER39 4.2 33.1 1.0
CB G:SER39 4.4 34.1 1.0
CA G:SER39 4.4 30.7 1.0
OG G:SER17 4.4 29.7 1.0
C G:ALA65 4.4 30.3 1.0
O G:THR64 4.5 28.0 1.0
NH2 H:ARG444 4.6 32.3 1.0
CD G:GLN67 4.7 38.4 1.0
NH1 H:ARG444 4.8 22.2 1.0
NE2 G:GLN67 4.8 34.5 1.0
N G:ALA65 4.9 30.4 1.0
CG2 G:THR40 4.9 24.7 1.0
O1B G:GDP202 4.9 33.8 1.0
O3A G:GDP202 5.0 19.8 1.0

Reference:

E.Mihai Gazdag, A.Streller, I.Haneburger, H.Hilbi, I.R.Vetter, R.S.Goody, A.Itzen. Mechanism of RAB1B Deactivation By the Legionella Pneumophila Gap Lepb. Embo Rep. V. 14 199 2013.
ISSN: ISSN 1469-221X
PubMed: 23288104
DOI: 10.1038/EMBOR.2012.211
Page generated: Sun Dec 13 12:04:10 2020

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