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Fluorine in PDB 5m70: Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human

Protein crystallography data

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human, PDB code: 5m70 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) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.554, 66.063, 76.759, 90.00, 96.07, 90.00
R / Rfree (%) 23.8 / 27.7

Other elements in 5m70:

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human (pdb code 5m70). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human, PDB code: 5m70:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:24.9
occ:1.00
 F1 B:ALF203 0.0 24.9 1.0
AL B:ALF203 1.8 25.6 1.0
F3 B:ALF203 2.5 26.7 1.0
O B:HOH303 2.6 25.7 1.0
F4 B:ALF203 2.6 25.8 1.0
OH B:TYR34 2.6 31.1 1.0
O3B B:GDP202 2.6 33.1 1.0
NE2 B:GLN63 2.8 30.6 1.0
CZ B:TYR34 3.6 31.4 1.0
CA B:PRO36 3.6 30.4 1.0
F2 B:ALF203 3.6 27.6 1.0
CE1 B:TYR34 3.7 31.1 1.0
N B:ALA15 3.7 31.2 1.0
CD B:GLN63 3.8 30.7 1.0
CB B:PRO36 3.8 30.3 1.0
OE1 B:GLN63 3.9 30.9 1.0
PB B:GDP202 4.0 31.8 1.0
N B:THR37 4.1 29.7 1.0
MG B:MG201 4.2 28.4 1.0
CA B:ALA15 4.2 31.9 1.0
C B:PRO36 4.4 29.9 1.0
O3A B:GDP202 4.4 32.4 1.0
CG B:PRO36 4.5 30.2 1.0
O B:HOH309 4.6 27.8 1.0
O1B B:GDP202 4.6 30.4 1.0
N B:PRO36 4.6 31.0 1.0
C B:GLY14 4.7 31.4 1.0
O A:ALA85 4.7 35.5 1.0
CB B:ALA15 4.7 32.1 1.0
CA B:GLY14 4.8 32.1 1.0
CE2 B:TYR34 4.9 32.2 1.0
O B:VAL35 5.0 32.3 1.0

Fluorine binding site 2 out of 8 in 5m70

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:27.6
occ:1.00
 F2 B:ALF203 0.0 27.6 1.0
AL B:ALF203 1.8 25.6 1.0
F4 B:ALF203 2.5 25.8 1.0
O B:HOH317 2.5 30.2 1.0
O B:HOH303 2.5 25.7 1.0
F3 B:ALF203 2.6 26.7 1.0
NZ B:LYS18 2.9 33.2 1.0
O3B B:GDP202 2.9 33.1 1.0
N B:GLY62 3.0 30.8 1.0
O B:THR60 3.1 29.9 1.0
CE B:LYS18 3.2 34.1 1.0
MG B:MG201 3.2 28.4 1.0
O1B B:GDP202 3.6 30.4 1.0
PB B:GDP202 3.6 31.8 1.0
CA B:ALA61 3.6 31.9 1.0
F1 B:ALF203 3.6 24.9 1.0
C B:ALA61 3.7 31.5 1.0
CA B:GLY62 3.9 31.2 1.0
C B:THR60 4.0 31.2 1.0
O2B B:GDP202 4.1 33.0 1.0
CB B:THR37 4.2 29.5 1.0
N B:ALA61 4.2 31.9 1.0
OG1 B:THR37 4.4 30.6 1.0
O B:THR37 4.5 28.9 1.0
CD B:LYS18 4.6 34.2 1.0
N B:THR37 4.6 29.7 1.0
CB B:ALA61 4.7 31.8 1.0
OE1 B:GLN63 4.8 30.9 1.0
O B:ALA61 4.8 32.1 1.0
CA B:THR37 4.9 29.9 1.0
CB B:LYS18 4.9 35.5 1.0
OG1 B:THR19 4.9 31.3 1.0

Fluorine binding site 3 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:26.7
occ:1.00
 F3 B:ALF203 0.0 26.7 1.0
AL B:ALF203 1.8 25.6 1.0
MG B:MG201 2.0 28.4 1.0
F1 B:ALF203 2.5 24.9 1.0
O B:HOH303 2.6 25.7 1.0
F2 B:ALF203 2.6 27.6 1.0
N B:THR37 2.6 29.7 1.0
O3B B:GDP202 2.9 33.1 1.0
OG1 B:THR37 3.0 30.6 1.0
O B:HOH309 3.0 27.8 1.0
O B:HOH317 3.2 30.2 1.0
CB B:THR37 3.2 29.5 1.0
O1B B:GDP202 3.3 30.4 1.0
CA B:THR37 3.4 29.9 1.0
C B:PRO36 3.5 29.9 1.0
F4 B:ALF203 3.6 25.8 1.0
CA B:PRO36 3.6 30.4 1.0
PB B:GDP202 3.6 31.8 1.0
O B:THR37 3.9 28.9 1.0
OG1 B:THR19 4.1 31.3 1.0
O B:VAL35 4.1 32.3 1.0
C B:THR37 4.2 29.4 1.0
O3A B:GDP202 4.5 32.4 1.0
CB B:PRO36 4.5 30.3 1.0
CE1 B:TYR34 4.6 31.1 1.0
OH B:TYR34 4.6 31.1 1.0
CG2 B:THR37 4.7 29.2 1.0
O B:PRO36 4.7 30.1 1.0
N B:PRO36 4.7 31.0 1.0
O2A B:GDP202 4.8 33.7 1.0
C B:VAL35 4.9 31.9 1.0
O2B B:GDP202 4.9 33.0 1.0
NE2 B:GLN63 4.9 30.6 1.0

Fluorine binding site 4 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:25.8
occ:1.00
 F4 B:ALF203 0.0 25.8 1.0
AL B:ALF203 1.8 25.6 1.0
F2 B:ALF203 2.5 27.6 1.0
O B:HOH303 2.5 25.7 1.0
O3B B:GDP202 2.6 33.1 1.0
F1 B:ALF203 2.6 24.9 1.0
N B:GLY62 2.9 30.8 1.0
CA B:GLY62 3.1 31.2 1.0
N B:ALA15 3.2 31.2 1.0
NZ B:LYS18 3.2 33.2 1.0
CA B:GLY14 3.3 32.1 1.0
NE2 B:GLN63 3.3 30.6 1.0
OE1 B:GLN63 3.5 30.9 1.0
F3 B:ALF203 3.6 26.7 1.0
CD B:GLN63 3.6 30.7 1.0
C B:GLY14 3.7 31.4 1.0
O B:ASP13 3.8 31.8 1.0
C B:GLY62 3.9 31.3 1.0
N B:GLN63 3.9 30.6 1.0
PB B:GDP202 4.0 31.8 1.0
N B:GLY14 4.0 32.3 1.0
C B:ALA61 4.1 31.5 1.0
C B:ASP13 4.2 32.1 1.0
CE B:LYS18 4.3 34.1 1.0
CA B:ALA15 4.4 31.9 1.0
O2B B:GDP202 4.4 33.0 1.0
CA B:ALA61 4.6 31.9 1.0
CG B:GLN63 4.7 30.1 1.0
O1B B:GDP202 4.8 30.4 1.0
O A:ALA85 4.8 35.5 1.0
O B:GLY12 4.8 30.6 1.0
OH B:TYR34 4.9 31.1 1.0
MG B:MG201 4.9 28.4 1.0
O B:HOH317 4.9 30.2 1.0
O B:GLY62 4.9 31.3 1.0
O B:GLY14 4.9 32.0 1.0

Fluorine binding site 5 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F203

b:25.7
occ:1.00
 F1 G:ALF203 0.0 25.7 1.0
AL G:ALF203 1.8 26.3 1.0
O G:HOH303 2.5 24.3 1.0
F4 G:ALF203 2.5 27.0 1.0
F3 G:ALF203 2.5 22.2 1.0
N G:GLY62 2.9 28.9 1.0
O3B G:GDP202 3.0 33.6 1.0
OE1 G:GLN63 3.1 31.0 1.0
NE2 G:GLN63 3.1 30.9 1.0
CA G:GLY14 3.1 31.7 1.0
CA G:GLY62 3.1 29.5 1.0
N G:ALA15 3.2 33.9 1.0
CD G:GLN63 3.2 30.5 1.0
NZ G:LYS18 3.4 30.6 1.0
F2 G:ALF203 3.6 25.6 1.0
C G:GLY14 3.7 32.8 1.0
N G:GLN63 3.8 29.6 1.0
C G:GLY62 3.8 29.7 1.0
O G:ASP13 3.8 31.0 1.0
N G:GLY14 3.9 31.9 1.0
C G:ALA61 4.2 30.1 1.0
C G:ASP13 4.2 30.5 1.0
PB G:GDP202 4.2 31.8 1.0
CA G:ALA15 4.4 34.6 1.0
CG G:GLN63 4.4 29.7 1.0
O1B G:GDP202 4.5 31.5 1.0
CE G:LYS18 4.5 31.0 1.0
CA G:ALA61 4.6 30.3 1.0
O F:ALA85 4.7 38.7 1.0
OH G:TYR34 4.8 31.7 1.0
O G:GLY62 4.8 30.1 1.0
CA G:GLN63 4.8 30.3 1.0
O G:GLY14 4.9 33.9 1.0

Fluorine binding site 6 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- 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 Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F203

b:25.6
occ:1.00
 F2 G:ALF203 0.0 25.6 1.0
AL G:ALF203 1.8 26.3 1.0
MG G:MG201 2.0 28.5 1.0
F4 G:ALF203 2.5 27.0 1.0
F3 G:ALF203 2.5 22.2 1.0
O3B G:GDP202 2.6 33.6 1.0
O G:HOH303 2.6 24.3 1.0
N G:THR37 2.9 31.5 1.0
O G:HOH305 2.9 27.4 1.0
OG1 G:THR37 3.0 30.7 1.0
O2B G:GDP202 3.1 29.4 1.0
CB G:THR37 3.3 31.4 1.0
PB G:GDP202 3.3 31.8 1.0
O G:HOH306 3.4 28.0 1.0
F1 G:ALF203 3.6 25.7 1.0
CA G:THR37 3.6 31.9 1.0
C G:PRO36 3.9 32.0 1.0
CA G:PRO36 3.9 31.9 1.0
OG1 G:THR19 4.1 30.4 1.0
O G:THR37 4.2 32.4 1.0
O G:VAL35 4.3 33.2 1.0
O3A G:GDP202 4.4 32.7 1.0
C G:THR37 4.4 32.4 1.0
O1B G:GDP202 4.5 31.5 1.0
O2A G:GDP202 4.6 33.5 1.0
CE1 G:TYR34 4.6 33.1 1.0
OH G:TYR34 4.7 31.7 1.0
O G:THR60 4.8 31.9 1.0
CG2 G:THR37 4.8 31.7 1.0
NZ G:LYS18 4.8 30.6 1.0
CB G:PRO36 4.9 32.2 1.0
N G:PRO36 5.0 32.6 1.0
CB G:THR19 5.0 30.4 1.0

Fluorine binding site 7 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human


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 Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F203

b:22.2
occ:1.00
 F3 G:ALF203 0.0 22.2 1.0
AL G:ALF203 1.8 26.3 1.0
O G:HOH303 2.5 24.3 1.0
F2 G:ALF203 2.5 25.6 1.0
F1 G:ALF203 2.5 25.7 1.0
O3B G:GDP202 2.6 33.6 1.0
OH G:TYR34 2.6 31.7 1.0
NE2 G:GLN63 2.9 30.9 1.0
CA G:PRO36 3.6 31.9 1.0
CZ G:TYR34 3.6 33.5 1.0
F4 G:ALF203 3.6 27.0 1.0
N G:ALA15 3.7 33.9 1.0
CE1 G:TYR34 3.7 33.1 1.0
CD G:GLN63 3.7 30.5 1.0
OE1 G:GLN63 3.8 31.0 1.0
CB G:PRO36 3.9 32.2 1.0
N G:THR37 4.1 31.5 1.0
PB G:GDP202 4.1 31.8 1.0
CA G:ALA15 4.2 34.6 1.0
MG G:MG201 4.3 28.5 1.0
C G:PRO36 4.4 32.0 1.0
CG G:PRO36 4.5 32.0 1.0
N G:PRO36 4.6 32.6 1.0
C G:GLY14 4.7 32.8 1.0
CB G:ALA15 4.7 34.7 1.0
O2B G:GDP202 4.7 29.4 1.0
O3A G:GDP202 4.7 32.7 1.0
CA G:GLY14 4.8 31.7 1.0
O F:ALA85 4.8 38.7 1.0
CE2 G:TYR34 4.9 34.5 1.0
O G:HOH306 4.9 28.0 1.0
O G:VAL35 5.0 33.2 1.0

Fluorine binding site 8 out of 8 in 5m70

Go back to Fluorine Binding Sites List in 5m70
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human


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 Human Rhogap Mutated in Its Arginin Finger (R85A) in Complex with Rhoa.Gdp.ALF4- Human within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F203

b:27.0
occ:1.00
 F4 G:ALF203 0.0 27.0 1.0
AL G:ALF203 1.8 26.3 1.0
F2 G:ALF203 2.5 25.6 1.0
F1 G:ALF203 2.5 25.7 1.0
O G:HOH303 2.6 24.3 1.0
NZ G:LYS18 2.7 30.6 1.0
O G:HOH305 2.8 27.4 1.0
O G:THR60 2.9 31.9 1.0
N G:GLY62 3.0 28.9 1.0
O3B G:GDP202 3.0 33.6 1.0
CE G:LYS18 3.0 31.0 1.0
PB G:GDP202 3.5 31.8 1.0
F3 G:ALF203 3.6 22.2 1.0
MG G:MG201 3.6 28.5 1.0
O2B G:GDP202 3.6 29.4 1.0
C G:ALA61 3.7 30.1 1.0
CA G:ALA61 3.7 30.3 1.0
CA G:GLY62 3.8 29.5 1.0
O1B G:GDP202 3.8 31.5 1.0
C G:THR60 3.9 30.3 1.0
N G:ALA61 4.3 30.6 1.0
CB G:THR37 4.5 31.4 1.0
CD G:LYS18 4.5 31.3 1.0
OE1 G:GLN63 4.6 31.0 1.0
OG1 G:THR37 4.7 30.7 1.0
O G:THR37 4.7 32.4 1.0
O G:ALA61 4.8 31.2 1.0
O G:ASP13 4.8 31.0 1.0
CB G:LYS18 4.8 32.1 1.0
N G:THR37 4.8 31.5 1.0
OD1 G:ASP59 4.9 33.5 1.0
N G:ALA15 4.9 33.9 1.0
CB G:ALA61 5.0 29.6 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: Thu Aug 1 11:37:56 2024

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