Fluorine in PDB 2g77: Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3

The structure of Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3, PDB code: 2g77 was solved by X.Pan, S.Eathiraj, M.Munson, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.200, 94.526, 102.561, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.4

The structure of Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to 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 GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3 (pdb code 2g77). 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 GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3, PDB code: 2g77:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to 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 GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:44.0 occ:1.00 F1 B:AF3502 0.0 44.0 1.0 AL B:AF3502 1.7 41.5 1.0 MG B:MG503 2.4 13.3 1.0 N B:THR65 2.6 27.0 1.0 O B:HOH550 2.6 58.1 1.0 F3 B:AF3502 2.9 33.3 1.0 F2 B:AF3502 2.9 33.3 1.0 CB B:THR65 2.9 25.9 1.0 OG1 B:THR65 2.9 24.6 1.0 O1B B:GDP501 3.1 27.1 1.0 O B:HOH632 3.2 22.7 1.0 O B:HOH504 3.2 26.0 1.0 CA B:THR65 3.2 25.9 1.0 O3B B:GDP501 3.5 22.5 1.0 C B:ALA64 3.6 28.7 1.0 O B:THR65 3.7 25.8 1.0 PB B:GDP501 3.8 28.0 1.0 NH1 A:ARG343 3.9 23.1 1.0 CA B:ALA64 3.9 29.4 1.0 C B:THR65 4.0 26.9 1.0 CG2 B:THR65 4.3 25.4 1.0 O B:GLU63 4.4 31.3 1.0 OG1 B:THR47 4.4 32.9 1.0 O B:THR89 4.6 33.4 1.0 CA B:ALA90 4.6 32.9 1.0 CB B:ALA64 4.7 28.4 1.0 O B:ALA64 4.8 29.7 1.0 O2B B:GDP501 4.8 26.7 1.0 CZ A:ARG343 4.8 28.1 1.0 O1A B:GDP501 4.9 30.2 1.0 O3A B:GDP501 4.9 29.7 1.0 OE1 A:GLN378 4.9 22.1 1.0 NE2 A:GLN378 5.0 20.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to 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 GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.3 occ:1.00 F2 B:AF3502 0.0 33.3 1.0 AL B:AF3502 1.7 41.5 1.0 N B:GLY91 2.7 34.2 1.0 NZ B:LYS46 2.8 22.8 1.0 F1 B:AF3502 2.9 44.0 1.0 F3 B:AF3502 2.9 33.3 1.0 O B:HOH550 2.9 58.1 1.0 O1B B:GDP501 3.1 27.1 1.0 CE B:LYS46 3.2 25.5 1.0 CA B:GLY91 3.4 35.2 1.0 C B:ALA90 3.5 33.8 1.0 CA B:ALA90 3.5 32.9 1.0 O B:THR89 3.5 33.4 1.0 O B:HOH504 3.7 26.0 1.0 CA B:SER42 3.8 27.2 1.0 PB B:GDP501 4.0 28.0 1.0 O2B B:GDP501 4.0 26.7 1.0 MG B:MG503 4.3 13.3 1.0 O3B B:GDP501 4.3 22.5 1.0 C B:THR89 4.3 33.3 1.0 N B:SER42 4.4 27.2 1.0 N B:ALA90 4.4 31.7 1.0 O B:ASP41 4.4 28.2 1.0 C B:GLY91 4.4 36.2 1.0 OE1 A:GLN378 4.5 22.1 1.0 CB B:SER42 4.5 25.8 1.0 N B:ASN43 4.5 26.9 1.0 CB B:ALA90 4.5 31.2 1.0 O B:ALA90 4.6 33.6 1.0 N B:GLN92 4.7 36.5 1.0 C B:SER42 4.7 26.7 1.0 OG B:SER42 4.7 28.6 1.0 C B:ASP41 4.7 27.2 1.0 O B:GLY40 4.8 25.7 1.0 CD B:LYS46 4.8 26.9 1.0 CB B:THR65 4.9 25.9 1.0 O B:THR65 5.0 25.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to 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 GYP1 Tbc Domain in Complex with RAB33 Gtpase Bound to Gdp and ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.3 occ:1.00 F3 B:AF3502 0.0 33.3 1.0 AL B:AF3502 1.7 41.5 1.0 O1B B:GDP501 2.5 27.1 1.0 F1 B:AF3502 2.9 44.0 1.0 OG B:SER42 2.9 28.6 1.0 F2 B:AF3502 2.9 33.3 1.0 O B:HOH550 3.0 58.1 1.0 NH2 A:ARG343 3.1 23.1 1.0 NH1 A:ARG343 3.1 23.1 1.0 NE2 A:GLN378 3.2 20.1 1.0 CZ A:ARG343 3.5 28.1 1.0 N B:ASN43 3.5 26.9 1.0 CA B:SER42 3.5 27.2 1.0 CB B:SER42 3.6 25.8 1.0 OE1 A:GLN378 3.9 22.1 1.0 C B:SER42 4.0 26.7 1.0 CD A:GLN378 4.0 27.3 1.0 PB B:GDP501 4.0 28.0 1.0 CA B:ASN43 4.5 26.8 1.0 CA B:ALA64 4.5 29.4 1.0 CB B:ALA64 4.6 28.4 1.0 N B:THR65 4.6 27.0 1.0 O3B B:GDP501 4.7 22.5 1.0 O3A B:GDP501 4.7 29.7 1.0 O2B B:GDP501 4.8 26.7 1.0 OD1 A:ASP340 4.8 23.7 1.0 NE A:ARG343 4.8 26.3 1.0 N B:GLY91 4.9 34.2 1.0 MG B:MG503 4.9 13.3 1.0 N B:SER42 4.9 27.2 1.0 NZ B:LYS46 4.9 22.8 1.0 NE2 A:GLN336 5.0 32.2 1.0

X.Pan, S.Eathiraj, M.Munson, D.G.Lambright. Tbc-Domain Gaps For Rab Gtpases Accelerate Gtp Hydrolysis By A Dual-Finger Mechanism. Nature V. 442 303 2006.
ISSN: ISSN 0028-0836
PubMed: 16855591
DOI: 10.1038/NATURE04847