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Fluorine in PDB 5m6x: Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human

Protein crystallography data

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human, PDB code: 5m6x was solved by E.Pellegrini, M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.55 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.470, 66.690, 76.890, 90.00, 95.41, 90.00
R / Rfree (%) 22.4 / 27.2

Other elements in 5m6x:

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human (pdb code 5m6x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human, PDB code: 5m6x:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5m6x

Go back to Fluorine Binding Sites List in 5m6x
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:11.8
occ:1.00
F1 B:MGF203 0.0 11.8 1.0
MG B:MGF203 1.9 11.7 1.0
O B:HOH309 2.6 12.6 1.0
NZ B:LYS18 2.7 14.7 1.0
N B:GLY62 2.7 16.8 1.0
O3B B:GDP202 3.1 13.4 1.0
CA B:GLY62 3.2 17.2 1.0
F3 B:MGF203 3.3 11.5 1.0
F2 B:MGF203 3.3 11.6 1.0
CE B:LYS18 3.3 14.8 1.0
CA B:GLY14 3.5 16.0 1.0
NE2 B:GLN63 3.8 18.1 1.0
O1B B:GDP202 3.8 13.4 1.0
C B:ALA61 3.8 16.5 1.0
PB B:GDP202 3.9 13.3 1.0
OE1 B:GLN63 3.9 18.2 1.0
N B:ALA15 3.9 15.6 1.0
CD B:GLN63 4.1 18.1 1.0
O B:ASP13 4.1 16.1 1.0
C B:GLY62 4.2 17.4 1.0
N B:GLY14 4.2 16.0 1.0
CA B:ALA61 4.2 16.5 1.0
O B:HOH306 4.2 10.6 1.0
C B:GLY14 4.2 15.7 1.0
O B:THR60 4.3 16.5 1.0
N B:GLN63 4.4 17.7 1.0
C B:ASP13 4.4 16.0 1.0
O2B B:GDP202 4.5 13.3 1.0
MG B:MG201 4.6 15.4 1.0
O B:GLY12 4.6 16.2 1.0
CD B:LYS18 4.8 14.8 1.0
O B:ALA61 4.9 16.2 1.0

Fluorine binding site 2 out of 6 in 5m6x

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:11.6
occ:1.00
F2 B:MGF203 0.0 11.6 1.0
MG B:MG201 1.9 15.4 1.0
MG B:MGF203 1.9 11.7 1.0
O B:HOH309 2.6 12.6 1.0
N B:THR37 2.7 17.3 1.0
O B:HOH306 2.7 10.6 1.0
O3B B:GDP202 2.9 13.4 1.0
OG1 B:THR37 2.9 17.1 1.0
O B:HOH301 3.0 20.4 1.0
O2B B:GDP202 3.1 13.3 1.0
CB B:THR37 3.1 17.3 1.0
F1 B:MGF203 3.3 11.8 1.0
F3 B:MGF203 3.3 11.5 1.0
CA B:THR37 3.4 17.5 1.0
PB B:GDP202 3.5 13.3 1.0
C B:PRO36 3.7 17.5 1.0
CA B:PRO36 3.8 17.7 1.0
O B:THR37 3.9 17.4 1.0
OG1 B:THR19 3.9 15.9 1.0
C B:THR37 4.1 17.7 1.0
O B:VAL35 4.3 18.5 1.0
O B:THR60 4.4 16.5 1.0
O1B B:GDP202 4.5 13.4 1.0
O2A B:GDP202 4.5 13.4 1.0
CG2 B:THR37 4.6 17.4 1.0
CB B:PRO36 4.7 17.6 1.0
O3A B:GDP202 4.8 13.4 1.0
O B:PRO36 4.9 17.4 1.0
CE B:LYS18 4.9 14.8 1.0
NZ B:LYS18 4.9 14.7 1.0
N B:PRO36 4.9 18.0 1.0
CA B:ALA61 5.0 16.5 1.0

Fluorine binding site 3 out of 6 in 5m6x

Go back to Fluorine Binding Sites List in 5m6x
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:11.5
occ:1.00
F3 B:MGF203 0.0 11.5 1.0
MG B:MGF203 1.9 11.7 1.0
OH B:TYR34 2.5 19.9 1.0
NE2 B:GLN63 2.7 18.1 1.0
O B:HOH309 2.7 12.6 1.0
O3B B:GDP202 2.8 13.4 1.0
F1 B:MGF203 3.3 11.8 1.0
F2 B:MGF203 3.3 11.6 1.0
CB B:PRO36 3.4 17.6 1.0
CA B:PRO36 3.5 17.7 1.0
CZ B:TYR34 3.5 20.1 1.0
CE1 B:TYR34 3.7 20.1 1.0
N B:ALA15 3.7 15.6 1.0
CD B:GLN63 3.8 18.1 1.0
OE1 B:GLN63 4.1 18.2 1.0
PB B:GDP202 4.3 13.3 1.0
CA B:GLY14 4.3 16.0 1.0
N B:THR37 4.4 17.3 1.0
N B:PRO36 4.4 18.0 1.0
CG B:PRO36 4.4 17.7 1.0
C B:GLY14 4.4 15.7 1.0
CA B:ALA15 4.4 15.7 1.0
C B:PRO36 4.4 17.5 1.0
O A:ALA85 4.7 21.1 1.0
CE2 B:TYR34 4.7 20.3 1.0
CB A:ALA85 4.8 20.4 1.0
MG B:MG201 4.8 15.4 1.0
CB B:ALA15 4.8 15.6 1.0
CD B:PRO36 4.9 17.9 1.0
O B:HOH301 5.0 20.4 1.0
O2B B:GDP202 5.0 13.3 1.0

Fluorine binding site 4 out of 6 in 5m6x

Go back to Fluorine Binding Sites List in 5m6x
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:12.6
occ:1.00
F1 I:MGF203 0.0 12.6 1.0
MG I:MGF203 1.9 12.8 1.0
O I:HOH311 2.6 16.0 1.0
N I:GLY62 2.7 14.3 1.0
NZ I:LYS18 2.7 17.4 1.0
O3B I:GDP202 3.0 17.7 1.0
CA I:GLY62 3.1 14.5 1.0
F3 I:MGF203 3.3 13.0 1.0
F2 I:MGF203 3.3 12.8 1.0
CE I:LYS18 3.4 17.4 1.0
CA I:GLY14 3.5 19.5 1.0
N I:ALA15 3.8 19.2 1.0
C I:ALA61 3.8 14.1 1.0
PB I:GDP202 3.8 17.7 1.0
O2B I:GDP202 3.8 17.6 1.0
OE1 I:GLN63 3.9 15.4 1.0
NE2 I:GLN63 3.9 15.3 1.0
O I:HOH314 4.0 15.3 1.0
C I:GLY62 4.1 14.7 1.0
CD I:GLN63 4.1 15.2 1.0
O I:ASP13 4.2 20.2 1.0
CA I:ALA61 4.2 14.1 1.0
C I:GLY14 4.2 19.3 1.0
N I:GLY14 4.2 19.7 1.0
N I:GLN63 4.3 14.9 1.0
O I:THR60 4.3 14.1 1.0
MG I:MG201 4.3 13.3 1.0
O1B I:GDP202 4.5 17.4 1.0
C I:ASP13 4.5 19.9 1.0
O I:GLY12 4.6 19.2 1.0
CD I:LYS18 4.9 17.5 1.0
O I:ALA61 4.9 14.0 1.0
CA I:ALA15 5.0 19.1 1.0

Fluorine binding site 5 out of 6 in 5m6x

Go back to Fluorine Binding Sites List in 5m6x
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:12.8
occ:1.00
F2 I:MGF203 0.0 12.8 1.0
MG I:MGF203 1.9 12.8 1.0
OH I:TYR34 2.5 19.5 1.0
NE2 I:GLN63 2.7 15.3 1.0
O3B I:GDP202 2.7 17.7 1.0
O I:HOH311 3.0 16.0 1.0
F3 I:MGF203 3.3 13.0 1.0
F1 I:MGF203 3.3 12.6 1.0
CB I:PRO36 3.4 17.4 1.0
CZ I:TYR34 3.5 20.1 1.0
CA I:PRO36 3.5 17.5 1.0
N I:ALA15 3.5 19.2 1.0
CE1 I:TYR34 3.6 20.0 1.0
CD I:GLN63 3.8 15.2 1.0
CA I:ALA15 4.2 19.1 1.0
OE1 I:GLN63 4.2 15.4 1.0
PB I:GDP202 4.2 17.7 1.0
C I:GLY14 4.3 19.3 1.0
CA I:GLY14 4.3 19.5 1.0
N I:THR37 4.4 17.3 1.0
CB I:ALA15 4.4 18.9 1.0
C I:PRO36 4.5 17.4 1.0
O H:ALA85 4.5 21.2 1.0
N I:PRO36 4.5 17.5 1.0
CG I:PRO36 4.5 17.4 1.0
MG I:MG201 4.7 13.3 1.0
CE2 I:TYR34 4.8 20.1 1.0
CB H:ALA85 4.8 21.1 1.0
CD1 I:TYR34 4.9 20.1 1.0
O3A I:GDP202 4.9 17.7 1.0
O1B I:GDP202 5.0 17.4 1.0
O I:HOH306 5.0 11.0 1.0
CD I:PRO36 5.0 17.5 1.0

Fluorine binding site 6 out of 6 in 5m6x

Go back to Fluorine Binding Sites List in 5m6x
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:13.0
occ:1.00
F3 I:MGF203 0.0 13.0 1.0
MG I:MG201 1.8 13.3 1.0
MG I:MGF203 1.9 12.8 1.0
O I:HOH311 2.5 16.0 1.0
N I:THR37 2.6 17.3 1.0
O I:HOH314 2.6 15.3 1.0
OG1 I:THR37 2.7 17.2 1.0
O3B I:GDP202 2.9 17.7 1.0
O I:HOH306 2.9 11.0 1.0
CB I:THR37 3.0 17.4 1.0
O1B I:GDP202 3.2 17.4 1.0
F1 I:MGF203 3.3 12.6 1.0
F2 I:MGF203 3.3 12.8 1.0
CA I:THR37 3.4 17.4 1.0
PB I:GDP202 3.5 17.7 1.0
C I:PRO36 3.6 17.4 1.0
CA I:PRO36 3.7 17.5 1.0
OG1 I:THR19 4.0 17.6 1.0
O I:THR37 4.1 17.5 1.0
C I:THR37 4.2 17.5 1.0
O I:VAL35 4.3 17.6 1.0
CG2 I:THR37 4.5 17.4 1.0
O I:THR60 4.5 14.1 1.0
CB I:PRO36 4.6 17.4 1.0
O2B I:GDP202 4.6 17.6 1.0
O2A I:GDP202 4.6 17.5 1.0
O I:PRO36 4.7 17.5 1.0
O3A I:GDP202 4.8 17.7 1.0
N I:PRO36 4.8 17.5 1.0
NZ I:LYS18 4.9 17.4 1.0
C I:VAL35 5.0 17.8 1.0
CE1 I:TYR34 5.0 20.0 1.0

Reference:

Y.Jin, R.W.Molt, E.Pellegrini, M.J.Cliff, M.W.Bowler, N.G.J.Richards, G.M.Blackburn, J.P.Waltho. Assessing the Influence of Mutation on Gtpase Transition States By Using X-Ray Crystallography, (19) F uc(Nmr), and Dft Approaches. Angew. Chem. Int. Ed. Engl. V. 56 9732 2017.
ISSN: ESSN 1521-3773
PubMed: 28498638
DOI: 10.1002/ANIE.201703074
Page generated: Tue Jul 15 05:10:59 2025

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