Fluorine in PDB 4jvs: Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3

The structure of Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3, PDB code: 4jvs was solved by Q.Yu, Q.Yao, D.-C.Wang, F.Shao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.78
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.561, 95.561, 197.724, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.5

The structure of Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3 (pdb code 4jvs). 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 Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3, PDB code: 4jvs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp 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 Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:34.8 occ:1.00 F1 B:AF3401 0.0 34.8 1.0 AL B:AF3401 1.7 35.1 1.0 O1B B:GDP400 2.5 38.7 1.0 O B:HOH502 2.6 41.3 1.0 F2 B:AF3401 2.8 35.7 1.0 F3 B:AF3401 2.9 34.9 1.0 CA B:SER20 3.0 31.6 1.0 N B:GLY69 3.0 35.0 1.0 OE1 B:GLN70 3.2 34.9 1.0 NZ B:LYS24 3.4 32.8 1.0 CB B:SER20 3.4 30.3 1.0 OG B:SER20 3.5 31.8 1.0 CA B:GLY69 3.7 31.8 1.0 MG B:MG402 3.7 36.2 1.0 N B:GLY21 3.8 31.5 1.0 N B:SER20 3.8 34.1 1.0 PB B:GDP400 3.9 34.3 1.0 C B:SER20 3.9 31.4 1.0 C B:ALA68 3.9 35.2 1.0 CA B:ALA68 4.0 35.4 1.0 O B:ASP19 4.0 33.5 1.0 CE B:LYS24 4.1 32.6 1.0 CD B:GLN70 4.1 37.5 1.0 NE2 B:GLN70 4.1 33.7 1.0 C B:ASP19 4.2 33.6 1.0 O2B B:GDP400 4.3 36.2 1.0 N B:GLN70 4.4 34.0 1.0 O3B B:GDP400 4.5 29.2 1.0 OG B:SER42 4.5 41.5 1.0 C B:GLY69 4.5 34.6 1.0 CB B:ALA68 4.6 37.6 1.0 O B:THR67 4.7 37.7 1.0 O B:GLY18 4.9 36.8 1.0 NH2 A:ARG447 4.9 35.8 1.0 O3A B:GDP400 5.0 35.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp 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 Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:35.7 occ:1.00 F2 B:AF3401 0.0 35.7 1.0 AL B:AF3401 1.7 35.1 1.0 O1B B:GDP400 1.9 38.7 1.0 MG B:MG402 1.9 36.2 1.0 O2B B:GDP400 2.2 36.2 1.0 O B:HOH502 2.4 41.3 1.0 PB B:GDP400 2.5 34.3 1.0 F1 B:AF3401 2.8 34.8 1.0 OG1 B:THR43 2.8 38.9 1.0 F3 B:AF3401 2.9 34.9 1.0 O3A B:GDP400 3.4 35.7 1.0 N B:THR43 3.4 34.9 1.0 NH2 A:ARG447 3.5 35.8 1.0 CB B:THR43 3.7 39.6 1.0 OG B:SER25 3.7 36.9 1.0 O3B B:GDP400 3.8 29.2 1.0 OG B:SER42 4.0 41.5 1.0 NZ B:LYS24 4.1 32.8 1.0 CA B:THR43 4.1 33.6 1.0 CA B:SER42 4.3 32.3 1.0 C B:SER42 4.3 34.0 1.0 N B:GLY21 4.6 31.5 1.0 CZ A:ARG447 4.6 31.8 1.0 O B:THR43 4.6 36.3 1.0 PA B:GDP400 4.6 38.0 1.0 O B:THR67 4.6 37.7 1.0 CE B:LYS24 4.7 32.6 1.0 CB B:SER42 4.8 33.5 1.0 OE1 B:GLN70 4.8 34.9 1.0 O1A B:GDP400 4.9 37.3 1.0 CA B:ALA68 4.9 35.4 1.0 C B:THR43 4.9 35.4 1.0 NH1 A:ARG447 4.9 32.7 1.0 CB B:SER25 5.0 32.3 1.0 O2A B:GDP400 5.0 34.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Lepb Gap Domain From Legionella Drancourtii in Complex with RAB1-Gdp 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 Domain From Legionella Drancourtii in Complex with RAB1-Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:34.9 occ:1.00 F3 B:AF3401 0.0 34.9 1.0 AL B:AF3401 1.7 35.1 1.0 OG B:SER42 2.1 41.5 1.0 NH1 A:ARG447 2.7 32.7 1.0 O B:HOH502 2.8 41.3 1.0 OG B:SER20 2.8 31.8 1.0 NH2 A:ARG447 2.9 35.8 1.0 F2 B:AF3401 2.9 35.7 1.0 F1 B:AF3401 2.9 34.8 1.0 O1B B:GDP400 3.0 38.7 1.0 CZ A:ARG447 3.1 31.8 1.0 CB B:SER42 3.3 33.5 1.0 NE2 B:GLN70 3.4 33.7 1.0 CA B:SER42 3.6 32.3 1.0 OE1 B:GLN70 3.7 34.9 1.0 N B:GLY21 3.9 31.5 1.0 CB B:SER20 3.9 30.3 1.0 CA B:SER20 4.1 31.6 1.0 CD B:GLN70 4.1 37.5 1.0 N B:THR43 4.2 34.9 1.0 PB B:GDP400 4.3 34.3 1.0 NE A:ARG447 4.4 32.5 1.0 C B:SER42 4.4 34.0 1.0 C B:SER20 4.4 31.4 1.0 O3A B:GDP400 4.4 35.7 1.0 MG B:MG402 4.7 36.2 1.0 CA B:GLY21 4.7 32.5 1.0 O2B B:GDP400 4.8 36.2 1.0 N B:SER42 4.8 34.5 1.0

Q.Yu, L.Hu, Q.Yao, Y.Zhu, N.Dong, D.-C.Wang, F.Shao. Structural Analyses of Legionella Lepb Reveal A New Gap Fold That Catalytically Mimics Eukaryotic Rasgap Cell Res. V. 23 775 2013.
ISSN: ISSN 1001-0602
PubMed: 23588383
DOI: 10.1038/CR.2013.54