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Fluorine in PDB 4iru: Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3

Enzymatic activity of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3

All present enzymatic activity of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3, PDB code: 4iru was solved by A.K.Mishra, C.M.Delcampo, R.E.Collins, C.R.Roy, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.01 / 3.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 139.404, 139.404, 384.519, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28.8

Other elements in 4iru:

The structure of Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 3 atoms
Potassium (K) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 (pdb code 4iru). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3, PDB code: 4iru:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4iru

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Fluorine binding site 1 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:32.2
occ:1.00
F1 B:AF3203 0.0 32.2 1.0
AL B:AF3203 1.8 33.4 1.0
MG B:MG201 1.8 32.8 1.0
O B:HOH308 2.5 16.4 1.0
O B:HOH303 2.7 18.3 1.0
N B:THR43 2.7 18.2 1.0
CB B:THR43 2.8 17.3 1.0
O B:HOH302 2.8 22.8 1.0
F3 B:AF3203 3.0 31.7 1.0
F2 B:AF3203 3.1 33.3 1.0
OG1 B:THR43 3.1 17.3 1.0
O1B B:GDP202 3.1 19.9 1.0
CA B:THR43 3.3 17.4 1.0
O3B B:GDP202 3.4 20.2 1.0
O B:THR43 3.7 16.9 1.0
C B:SER42 3.7 18.7 1.0
PB B:GDP202 3.8 19.1 1.0
OG B:SER42 3.9 18.5 1.0
CA B:SER42 3.9 18.9 1.0
C B:THR43 3.9 17.0 1.0
NH2 A:ARG444 4.0 28.0 1.0
CG2 B:THR43 4.1 17.5 1.0
OG B:SER25 4.1 24.1 1.0
O B:THR67 4.4 29.7 1.0
CB B:SER42 4.5 18.4 1.0
CA B:ALA68 4.6 28.6 1.0
O B:ILE41 4.8 22.1 1.0
O B:SER42 4.8 18.6 1.0
O2B B:GDP202 4.8 20.4 1.0
N B:GLY69 4.8 29.2 1.0
O1A B:GDP202 4.9 22.9 1.0
O3A B:GDP202 5.0 21.8 1.0

Fluorine binding site 2 out of 9 in 4iru

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Fluorine binding site 2 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:33.3
occ:1.00
F2 B:AF3203 0.0 33.3 1.0
AL B:AF3203 1.8 33.4 1.0
N B:GLY69 2.8 29.2 1.0
O1B B:GDP202 2.9 19.9 1.0
NZ B:LYS24 2.9 26.8 1.0
F3 B:AF3203 3.0 31.7 1.0
F1 B:AF3203 3.1 32.2 1.0
CE B:LYS24 3.2 26.4 1.0
O B:HOH308 3.2 16.4 1.0
CA B:GLY69 3.5 29.7 1.0
CA B:SER20 3.5 29.0 1.0
PB B:GDP202 3.5 19.1 1.0
O2B B:GDP202 3.6 20.4 1.0
O B:ASP19 3.6 28.6 1.0
N B:GLY21 3.8 29.4 1.0
O B:THR67 3.8 29.7 1.0
C B:ALA68 3.8 28.9 1.0
MG B:MG201 3.9 32.8 1.0
O B:HOH302 4.0 22.8 1.0
OG B:SER20 4.0 28.9 1.0
O3B B:GDP202 4.0 20.2 1.0
CA B:ALA68 4.1 28.6 1.0
CB B:SER20 4.2 28.9 1.0
C B:SER20 4.2 29.5 1.0
C B:ASP19 4.3 29.9 1.0
N B:SER20 4.3 29.7 1.0
OE1 B:GLN70 4.4 29.2 1.0
O B:GLY18 4.6 34.1 1.0
CD B:LYS24 4.7 25.7 1.0
C B:GLY69 4.7 29.6 1.0
C B:THR67 4.8 29.8 1.0
NH2 A:ARG444 4.8 28.0 1.0
O B:ALA68 4.9 30.2 1.0
N B:ALA68 5.0 29.3 1.0
N B:GLN70 5.0 28.8 1.0

Fluorine binding site 3 out of 9 in 4iru

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Fluorine binding site 3 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:31.7
occ:1.00
F3 B:AF3203 0.0 31.7 1.0
AL B:AF3203 1.7 33.4 1.0
O B:HOH308 2.3 16.4 1.0
OG B:SER20 2.4 28.9 1.0
OG B:SER42 2.6 18.5 1.0
F2 B:AF3203 3.0 33.3 1.0
NH1 A:ARG444 3.0 27.2 1.0
O1B B:GDP202 3.0 19.9 1.0
F1 B:AF3203 3.0 32.2 1.0
NH2 A:ARG444 3.0 28.0 1.0
CZ A:ARG444 3.4 27.9 1.0
CB B:SER42 3.5 18.4 1.0
CB B:SER20 3.5 28.9 1.0
OE1 B:GLN70 3.6 29.2 1.0
NE2 B:GLN70 3.7 28.4 1.0
N B:GLY21 3.8 29.4 1.0
CA B:SER20 3.8 29.0 1.0
CD B:GLN70 3.9 28.4 1.0
CA B:SER42 3.9 18.9 1.0
C B:SER20 4.2 29.5 1.0
N B:THR43 4.4 18.2 1.0
MG B:MG201 4.4 32.8 1.0
PB B:GDP202 4.4 19.1 1.0
C B:SER42 4.5 18.7 1.0
CA B:GLY21 4.6 28.2 1.0
N B:GLY69 4.6 29.2 1.0
O B:THR43 4.7 16.9 1.0
NE A:ARG444 4.8 28.5 1.0
O B:HOH303 4.8 18.3 1.0

Fluorine binding site 4 out of 9 in 4iru

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Fluorine binding site 4 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:29.4
occ:1.00
F1 D:AF3203 0.0 29.4 1.0
MG D:MG201 1.8 36.0 1.0
AL D:AF3203 1.8 30.5 1.0
O D:HOH301 2.5 46.6 1.0
N D:THR43 2.6 22.8 1.0
CB D:THR43 2.8 21.4 1.0
O D:HOH302 2.9 18.5 1.0
F3 D:AF3203 3.1 30.2 1.0
F2 D:AF3203 3.1 30.3 1.0
O D:HOH303 3.1 12.9 1.0
OG1 D:THR43 3.1 21.6 1.0
O3B D:GDP202 3.1 23.5 1.0
CA D:THR43 3.2 22.0 1.0
O1B D:GDP202 3.4 23.4 1.0
C D:SER42 3.7 24.2 1.0
O D:THR43 3.7 22.5 1.0
PB D:GDP202 3.7 22.9 1.0
OG D:SER42 3.8 23.9 1.0
NH1 C:ARG444 3.9 24.4 1.0
CA D:SER42 3.9 25.4 1.0
C D:THR43 4.0 22.1 1.0
OG D:SER25 4.0 28.8 1.0
CG2 D:THR43 4.1 21.3 1.0
O D:THR67 4.3 31.0 1.0
CB D:SER42 4.5 24.9 1.0
CA D:ALA68 4.5 29.9 1.0
O2B D:GDP202 4.6 24.0 1.0
O D:ILE41 4.7 28.7 1.0
O D:SER42 4.8 23.6 1.0
CZ C:ARG444 4.8 24.0 1.0
N D:GLY69 4.9 31.7 1.0
O1A D:GDP202 4.9 25.7 1.0
O3A D:GDP202 5.0 24.4 1.0

Fluorine binding site 5 out of 9 in 4iru

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Fluorine binding site 5 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:30.3
occ:1.00
F2 D:AF3203 0.0 30.3 1.0
AL D:AF3203 1.7 30.5 1.0
NZ D:LYS24 2.7 34.6 1.0
O1B D:GDP202 2.9 23.4 1.0
N D:GLY69 3.0 31.7 1.0
F3 D:AF3203 3.0 30.2 1.0
F1 D:AF3203 3.1 29.4 1.0
CE D:LYS24 3.1 33.4 1.0
O D:HOH301 3.2 46.6 1.0
O2B D:GDP202 3.4 24.0 1.0
PB D:GDP202 3.4 22.9 1.0
CA D:SER20 3.4 30.9 1.0
CA D:GLY69 3.6 31.8 1.0
N D:GLY21 3.7 31.6 1.0
O D:ASP19 3.8 29.7 1.0
MG D:MG201 3.8 36.0 1.0
O D:THR67 3.8 31.0 1.0
O3B D:GDP202 3.8 23.5 1.0
C D:ALA68 3.9 31.1 1.0
O D:HOH302 4.0 18.5 1.0
OG D:SER20 4.0 29.7 1.0
CB D:SER20 4.1 31.0 1.0
C D:SER20 4.1 31.6 1.0
CA D:ALA68 4.2 29.9 1.0
N D:SER20 4.3 31.4 1.0
C D:ASP19 4.3 31.9 1.0
OE1 D:GLN70 4.4 30.8 1.0
CD D:LYS24 4.6 33.1 1.0
O D:GLY18 4.6 34.0 1.0
C D:GLY69 4.8 32.4 1.0
C D:THR67 4.8 30.6 1.0
NH1 C:ARG444 4.8 24.4 1.0
CA D:GLY21 4.9 32.6 1.0
O3A D:GDP202 4.9 24.4 1.0
O D:ALA68 5.0 33.7 1.0
N D:ALA68 5.0 30.1 1.0

Fluorine binding site 6 out of 9 in 4iru

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Fluorine binding site 6 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:30.2
occ:1.00
F3 D:AF3203 0.0 30.2 1.0
AL D:AF3203 1.7 30.5 1.0
O D:HOH301 2.3 46.6 1.0
OG D:SER20 2.5 29.7 1.0
OG D:SER42 2.5 23.9 1.0
NH2 C:ARG444 2.8 23.5 1.0
F2 D:AF3203 3.0 30.3 1.0
F1 D:AF3203 3.1 29.4 1.0
O1B D:GDP202 3.1 23.4 1.0
NH1 C:ARG444 3.2 24.4 1.0
CZ C:ARG444 3.4 24.0 1.0
OE1 D:GLN70 3.5 30.8 1.0
CB D:SER20 3.5 31.0 1.0
CB D:SER42 3.5 24.9 1.0
NE2 D:GLN70 3.8 31.2 1.0
N D:GLY21 3.8 31.6 1.0
CD D:GLN70 3.8 31.0 1.0
CA D:SER20 3.9 30.9 1.0
CA D:SER42 4.0 25.4 1.0
C D:SER20 4.2 31.6 1.0
N D:THR43 4.4 22.8 1.0
MG D:MG201 4.4 36.0 1.0
PB D:GDP202 4.4 22.9 1.0
C D:SER42 4.6 24.2 1.0
N D:GLY69 4.6 31.7 1.0
CA D:GLY21 4.7 32.6 1.0
NE C:ARG444 4.7 24.6 1.0
O3B D:GDP202 4.9 23.5 1.0
O D:THR43 4.9 22.5 1.0

Fluorine binding site 7 out of 9 in 4iru

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Fluorine binding site 7 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F202

b:60.3
occ:1.00
F1 F:AF3202 0.0 60.3 1.0
AL F:AF3202 1.8 61.7 1.0
MG F:MG200 2.2 45.2 1.0
O1B F:GDP201 2.4 98.4 1.0
F2 F:AF3202 3.1 66.3 1.0
N F:THR43 3.1 0.7 1.0
OG1 F:THR43 3.2 61.1 1.0
F3 F:AF3202 3.2 56.4 1.0
O3B F:GDP201 3.3 92.9 1.0
PB F:GDP201 3.3 96.9 1.0
CB F:THR43 3.3 79.0 1.0
CA F:THR43 3.7 94.6 1.0
C F:SER42 4.0 0.9 1.0
OG F:SER25 4.0 57.5 1.0
OD1 F:ASP66 4.1 0.9 1.0
O F:THR67 4.1 99.3 1.0
CA F:SER42 4.1 0.9 1.0
O F:THR43 4.1 96.2 1.0
O2B F:GDP201 4.2 90.8 1.0
NH2 E:ARG444 4.3 87.2 1.0
C F:THR43 4.4 99.2 1.0
O1A F:GDP201 4.4 1.0 1.0
CB F:SER25 4.5 57.5 1.0
O3A F:GDP201 4.5 94.8 1.0
O F:ILE41 4.6 0.8 1.0
CB F:SER42 4.8 1.0 1.0
CG2 F:THR43 4.8 75.6 1.0
N F:SER25 4.9 61.2 1.0

Fluorine binding site 8 out of 9 in 4iru

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Fluorine binding site 8 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F202

b:66.3
occ:1.00
F2 F:AF3202 0.0 66.3 1.0
AL F:AF3202 1.8 61.7 1.0
O2B F:GDP201 2.8 90.8 1.0
CE F:LYS24 3.0 88.2 1.0
O1B F:GDP201 3.0 98.4 1.0
F3 F:AF3202 3.1 56.4 1.0
MG F:MG200 3.1 45.2 1.0
F1 F:AF3202 3.1 60.3 1.0
PB F:GDP201 3.2 96.9 1.0
O F:ASP19 3.5 0.7 1.0
O F:THR67 3.5 99.3 1.0
N F:GLY21 3.7 0.9 1.0
O3B F:GDP201 3.7 92.9 1.0
N F:GLY69 3.8 0.5 1.0
CA F:SER20 3.8 0.7 1.0
NZ F:LYS24 4.0 88.1 1.0
CD F:LYS24 4.0 87.2 1.0
CG F:LYS24 4.0 85.3 1.0
CB F:LYS24 4.1 80.3 1.0
C F:ASP19 4.2 0.7 1.0
C F:SER20 4.3 0.5 1.0
N F:SER20 4.4 0.3 1.0
CA F:GLY69 4.5 0.2 1.0
C F:THR67 4.6 98.7 1.0
CA F:ALA68 4.6 0.4 1.0
CA F:GLY21 4.7 0.6 1.0
C F:ALA68 4.7 1.0 1.0
O3A F:GDP201 4.7 94.8 1.0
CB F:SER20 4.8 0.2 1.0
OG F:SER20 4.8 80.2 1.0
OD1 F:ASP66 4.9 0.9 1.0
N F:VAL22 4.9 0.2 1.0

Fluorine binding site 9 out of 9 in 4iru

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Fluorine binding site 9 out of 9 in the Crystal Structure of Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3


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 Lepb Gap Core in A Transition State Mimetic Complex with RAB1A and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F202

b:56.4
occ:1.00
F3 F:AF3202 0.0 56.4 1.0
AL F:AF3202 1.8 61.7 1.0
CD F:GLN70 2.9 0.6 1.0
OG F:SER20 3.0 80.2 1.0
F2 F:AF3202 3.1 66.3 1.0
OE1 F:GLN70 3.1 0.0 1.0
F1 F:AF3202 3.2 60.3 1.0
CG F:GLN70 3.2 1.0 1.0
NE2 F:GLN70 3.3 96.3 1.0
CB F:SER20 3.8 0.2 1.0
O1B F:GDP201 3.8 98.4 1.0
CA F:SER20 3.8 0.7 1.0
CB F:SER42 4.0 1.0 1.0
N F:GLY21 4.1 0.9 1.0
O F:THR43 4.1 96.2 1.0
N F:GLY69 4.2 0.5 1.0
OG F:SER42 4.3 0.3 1.0
CA F:ALA68 4.4 0.4 1.0
CA F:SER42 4.4 0.9 1.0
C F:SER20 4.4 0.5 1.0
N F:GLN70 4.5 0.3 1.0
N F:THR43 4.6 0.7 1.0
CB F:GLN70 4.6 0.8 1.0
C F:SER42 4.7 0.9 1.0
C F:ALA68 4.8 1.0 1.0
NH2 E:ARG444 4.8 87.2 1.0
MG F:MG200 4.9 45.2 1.0
CB F:ALA68 4.9 90.2 1.0
O F:THR67 4.9 99.3 1.0
PB F:GDP201 4.9 96.9 1.0
N F:SER20 5.0 0.3 1.0
NH1 E:ARG444 5.0 84.3 1.0

Reference:

A.K.Mishra, C.M.Del Campo, R.E.Collins, C.R.Roy, D.G.Lambright. The Legionella Pneumophila Gtpase Activating Protein Lepb Accelerates RAB1 Deactivation By A Non-Canonical Hydrolytic Mechanism. J.Biol.Chem. V. 288 24000 2013.
ISSN: ISSN 0021-9258
PubMed: 23821544
DOI: 10.1074/JBC.M113.470625
Page generated: Thu Aug 1 02:33:32 2024

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