Fluorine in PDB 5c2j: Complex Structure of the Gap Domain of Mgcracgap and CDC42

The structure of Complex Structure of the Gap Domain of Mgcracgap and CDC42, PDB code: 5c2j was solved by K.Murayama, M.Kato-Murayama, T.Hosaka, T.Kitamura, S.Yokoyama, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.39 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.324, 74.237, 55.423, 90.00, 96.67, 90.00
R / Rfree (%)	19.8 / 26.3

The structure of Complex Structure of the Gap Domain of Mgcracgap and CDC42 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Complex Structure of the Gap Domain of Mgcracgap and CDC42 (pdb code 5c2j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Complex Structure of the Gap Domain of Mgcracgap and CDC42, PDB code: 5c2j:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Complex Structure of the Gap Domain of Mgcracgap and CDC42


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex Structure of the Gap Domain of Mgcracgap and CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.9 occ:1.00 F1 B:AF3502 0.0 30.9 1.0 AL B:AF3502 1.7 32.8 1.0 O3B B:GDP501 2.4 17.2 1.0 NE A:ARG385 2.9 18.0 1.0 NE2 B:GLN61 2.9 17.5 1.0 F3 B:AF3502 3.0 30.0 1.0 F2 B:AF3502 3.0 30.1 1.0 O B:HOH613 3.0 24.1 1.0 N B:ALA13 3.1 16.9 1.0 NH2 A:ARG385 3.2 18.7 1.0 CA B:GLY12 3.3 18.4 1.0 CZ A:ARG385 3.5 20.6 1.0 C B:GLY12 3.7 18.2 1.0 CG A:ARG385 3.8 22.3 1.0 CD B:GLN61 3.9 16.2 1.0 CD A:ARG385 4.0 19.5 1.0 OE1 B:GLN61 4.0 15.2 1.0 PB B:GDP501 4.0 19.8 1.0 CA B:PRO34 4.1 31.3 1.0 CA B:ALA13 4.2 16.8 1.0 CB B:PRO34 4.4 30.3 1.0 O A:ARG385 4.5 24.1 1.0 N B:THR35 4.6 32.7 1.0 O2B B:GDP501 4.6 16.0 1.0 O1B B:GDP501 4.6 21.6 1.0 N B:GLY12 4.7 19.8 1.0 CB B:ALA13 4.8 14.7 1.0 NH1 A:ARG385 4.8 21.8 1.0 O B:GLY12 4.8 18.5 1.0 CG B:PRO34 4.8 30.9 1.0 NZ B:LYS16 4.9 20.2 1.0 C B:PRO34 5.0 32.1 1.0 O3A B:GDP501 5.0 22.6 1.0

Fluorine binding site 2 out of 3 in the Complex Structure of the Gap Domain of Mgcracgap and CDC42


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex Structure of the Gap Domain of Mgcracgap and CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.1 occ:1.00 F2 B:AF3502 0.0 30.1 1.0 AL B:AF3502 1.7 32.8 1.0 NZ B:LYS16 2.6 20.2 1.0 N B:GLY60 2.7 25.3 1.0 O B:HOH613 2.7 24.1 1.0 F3 B:AF3502 3.0 30.0 1.0 F1 B:AF3502 3.0 30.9 1.0 CE B:LYS16 3.1 22.3 1.0 O3B B:GDP501 3.3 17.2 1.0 CA B:GLY12 3.3 18.4 1.0 CA B:GLY60 3.4 25.6 1.0 O1B B:GDP501 3.7 21.6 1.0 C B:ALA59 3.7 26.7 1.0 O B:THR58 3.8 31.6 1.0 CA B:ALA59 3.9 27.5 1.0 PB B:GDP501 4.0 19.8 1.0 O B:ASP11 4.0 20.4 1.0 OE1 B:GLN61 4.0 15.2 1.0 O B:HOH602 4.0 14.3 1.0 N B:GLY12 4.0 19.8 1.0 NE2 B:GLN61 4.1 17.5 1.0 O B:GLY10 4.2 22.0 1.0 N B:ALA13 4.2 16.9 1.0 C B:ASP11 4.3 20.9 1.0 C B:GLY12 4.3 18.2 1.0 O2B B:GDP501 4.4 16.0 1.0 CD B:GLN61 4.4 16.2 1.0 C B:GLY60 4.5 26.7 1.0 N B:GLN61 4.5 26.5 1.0 CD B:LYS16 4.6 21.3 1.0 C B:THR58 4.7 30.4 1.0 MG B:MG500 4.8 23.0 1.0 N B:ALA59 4.8 28.2 1.0 O B:ALA59 4.9 26.1 1.0 CB B:ALA59 5.0 26.2 1.0

Fluorine binding site 3 out of 3 in the Complex Structure of the Gap Domain of Mgcracgap and CDC42


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex Structure of the Gap Domain of Mgcracgap and CDC42 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:30.0 occ:1.00 F3 B:AF3502 0.0 30.0 1.0 AL B:AF3502 1.7 32.8 1.0 MG B:MG500 2.3 23.0 1.0 O3B B:GDP501 2.6 17.2 1.0 O2B B:GDP501 2.7 16.0 1.0 O B:HOH613 2.8 24.1 1.0 O B:HOH602 2.8 14.3 1.0 F1 B:AF3502 3.0 30.9 1.0 F2 B:AF3502 3.0 30.1 1.0 N B:THR35 3.0 32.7 1.0 O B:HOH618 3.0 27.8 1.0 OG1 B:THR35 3.2 32.2 1.0 PB B:GDP501 3.2 19.8 1.0 CB B:THR35 3.2 32.9 1.0 CA B:THR35 3.7 32.3 1.0 NH2 A:ARG385 3.8 18.7 1.0 O1B B:GDP501 3.9 21.6 1.0 C B:PRO34 3.9 32.1 1.0 CA B:PRO34 4.1 31.3 1.0 OG1 B:THR17 4.1 16.7 1.0 O2A B:GDP501 4.3 21.1 1.0 O B:THR35 4.3 35.3 1.0 O B:THR58 4.4 31.6 1.0 C B:THR35 4.5 33.5 1.0 NZ B:LYS16 4.5 20.2 1.0 O3A B:GDP501 4.5 22.6 1.0 CE B:LYS16 4.6 22.3 1.0 CG2 B:THR35 4.6 30.2 1.0 O B:VAL33 4.6 28.8 1.0 CZ A:ARG385 4.8 20.6 1.0 NE A:ARG385 5.0 18.0 1.0

K.Murayama, M.Kato-Murayama, T.Hosaka, T.Kawashima, T.Kitamura, S.Yokoyama, M.Shirouzu. Structural Basis of G-Protein Target Alternation of Mgcracgap By Phospholylation To Be Published.