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Fluorine in PDB 5hpy: Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain

Protein crystallography data

The structure of Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain, PDB code: 5hpy was solved by F.S.Yi, J.Q.Ren, W.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.055, 90.762, 93.582, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.6

Other elements in 5hpy:

The structure of Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain (pdb code 5hpy). 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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain, PDB code: 5hpy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5hpy

Go back to Fluorine Binding Sites List in 5hpy
Fluorine binding site 1 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:37.9
occ:1.00
 F1 B:MGF201 0.0 37.9 1.0
MG B:MGF201 1.8 40.7 1.0
NE A:ARG235 2.6 43.0 1.0
O2B B:GDP203 2.8 36.4 1.0
NE2 B:GLN63 2.9 40.3 1.0
F2 B:MGF201 3.1 39.0 1.0
NH2 A:ARG235 3.1 41.8 1.0
F3 B:MGF201 3.2 38.1 1.0
O B:HOH318 3.2 33.0 1.0
CZ A:ARG235 3.3 43.9 1.0
N B:ALA15 3.3 40.8 1.0
CG A:ARG235 3.6 42.1 1.0
CB B:PRO36 3.6 40.0 1.0
CA B:GLY14 3.6 36.2 1.0
CD A:ARG235 3.7 43.4 1.0
CA B:PRO36 3.9 38.9 1.0
C B:GLY14 3.9 39.3 1.0
CD B:GLN63 3.9 39.6 1.0
OE1 B:GLN63 4.1 36.5 1.0
CA B:ALA15 4.2 43.7 1.0
PB B:GDP203 4.3 42.7 1.0
NH1 A:ARG235 4.6 42.5 1.0
CB B:ALA15 4.6 43.9 1.0
N B:THR37 4.7 39.5 1.0
CG B:PRO36 4.8 43.9 1.0
O A:ARG235 4.8 42.6 1.0
C B:PRO36 4.9 37.9 1.0
N B:PRO36 4.9 43.2 1.0
O1B B:GDP203 4.9 39.2 1.0
O3B B:GDP203 5.0 34.7 1.0
O B:HOH319 5.0 37.0 1.0
MG B:MG202 5.0 38.0 1.0
N B:GLY14 5.0 35.8 1.0
O3A B:GDP203 5.0 50.3 1.0

Fluorine binding site 2 out of 6 in 5hpy

Go back to Fluorine Binding Sites List in 5hpy
Fluorine binding site 2 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:39.0
occ:1.00
 F2 B:MGF201 0.0 39.0 1.0
MG B:MGF201 1.8 40.7 1.0
MG B:MG202 2.0 38.0 1.0
O2B B:GDP203 2.6 36.4 1.0
O B:HOH319 2.8 37.0 1.0
N B:THR37 2.9 39.5 1.0
O B:HOH318 2.9 33.0 1.0
O3B B:GDP203 3.0 34.7 1.0
F1 B:MGF201 3.1 37.9 1.0
F3 B:MGF201 3.1 38.1 1.0
O B:HOH305 3.2 35.7 1.0
CB B:THR37 3.3 37.0 1.0
OG1 B:THR37 3.3 37.2 1.0
PB B:GDP203 3.4 42.7 1.0
CA B:THR37 3.6 39.2 1.0
NH2 A:ARG235 3.6 41.8 1.0
CA B:PRO36 3.8 38.9 1.0
C B:PRO36 3.8 37.9 1.0
O B:THR37 4.1 35.7 1.0
OG1 B:THR19 4.2 38.5 1.0
O B:THR60 4.3 35.1 1.0
O1B B:GDP203 4.3 39.2 1.0
C B:THR37 4.4 39.1 1.0
CB B:PRO36 4.4 40.0 1.0
O B:VAL35 4.5 42.7 1.0
O3A B:GDP203 4.6 50.3 1.0
CZ A:ARG235 4.6 43.9 1.0
CG2 B:THR37 4.7 35.7 1.0
NZ B:LYS18 4.7 38.8 1.0
O2A B:GDP203 4.7 34.9 1.0
CE B:LYS18 4.8 37.6 1.0
NE A:ARG235 4.8 43.0 1.0
O B:PRO36 5.0 40.1 1.0
N B:PRO36 5.0 43.2 1.0

Fluorine binding site 3 out of 6 in 5hpy

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Fluorine binding site 3 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:38.1
occ:1.00
 F3 B:MGF201 0.0 38.1 1.0
MG B:MGF201 1.8 40.7 1.0
NZ B:LYS18 2.6 38.8 1.0
N B:GLY62 2.7 34.4 1.0
O B:HOH318 3.0 33.0 1.0
F2 B:MGF201 3.1 39.0 1.0
F1 B:MGF201 3.2 37.9 1.0
CE B:LYS18 3.2 37.6 1.0
CA B:GLY14 3.3 36.2 1.0
CA B:GLY62 3.3 34.7 1.0
O2B B:GDP203 3.4 36.4 1.0
C B:ALA61 3.8 36.5 1.0
O1B B:GDP203 3.9 39.2 1.0
OE1 B:GLN63 3.9 36.5 1.0
O B:THR60 4.0 35.1 1.0
CA B:ALA61 4.0 35.0 1.0
N B:GLY14 4.0 35.8 1.0
N B:ALA15 4.0 40.8 1.0
PB B:GDP203 4.0 42.7 1.0
O B:ASP13 4.1 34.3 1.0
C B:GLY14 4.2 39.3 1.0
NE2 B:GLN63 4.2 40.3 1.0
O B:HOH305 4.2 35.7 1.0
O B:GLY12 4.3 34.4 1.0
C B:ASP13 4.3 37.3 1.0
C B:GLY62 4.4 37.3 1.0
CD B:GLN63 4.4 39.6 1.0
O3B B:GDP203 4.4 34.7 1.0
MG B:MG202 4.5 38.0 1.0
N B:GLN63 4.6 37.6 1.0
CD B:LYS18 4.7 40.0 1.0
C B:THR60 4.8 34.4 1.0
O B:ALA61 4.9 36.9 1.0
N B:ALA61 4.9 33.8 1.0

Fluorine binding site 4 out of 6 in 5hpy

Go back to Fluorine Binding Sites List in 5hpy
Fluorine binding site 4 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:40.6
occ:1.00
 F1 F:MGF201 0.0 40.6 1.0
MG F:MGF201 1.8 41.9 1.0
NZ F:LYS18 2.5 44.5 1.0
N F:GLY62 2.7 39.7 1.0
F3 F:MGF201 3.1 47.1 1.0
F2 F:MGF201 3.1 36.9 1.0
O F:HOH314 3.1 38.4 1.0
CE F:LYS18 3.2 42.7 1.0
CA F:GLY62 3.3 39.4 1.0
CA F:GLY14 3.3 44.7 1.0
O1B F:GDP202 3.5 52.8 1.0
O3B F:GDP202 3.7 39.8 1.0
C F:ALA61 3.8 42.0 1.0
O F:ASP13 3.9 47.3 1.0
N F:GLY14 3.9 41.3 1.0
OE1 F:GLN63 4.0 40.3 1.0
CA F:ALA61 4.0 40.0 1.0
N F:ALA15 4.0 45.1 1.0
PB F:GDP202 4.1 43.6 1.0
O F:THR60 4.2 39.5 1.0
C F:ASP13 4.2 46.3 1.0
NE2 F:GLN63 4.2 42.4 1.0
O F:HOH307 4.2 39.3 1.0
C F:GLY14 4.2 47.6 1.0
O F:GLY12 4.3 43.7 1.0
O2B F:GDP202 4.4 41.0 1.0
C F:GLY62 4.4 42.4 1.0
CD F:GLN63 4.5 42.7 1.0
MG F:MG203 4.5 42.7 1.0
N F:GLN63 4.6 40.4 1.0
CD F:LYS18 4.6 43.4 1.0
O F:ALA61 4.9 41.1 1.0
N F:ALA61 5.0 39.8 1.0
C F:THR60 5.0 40.1 1.0

Fluorine binding site 5 out of 6 in 5hpy

Go back to Fluorine Binding Sites List in 5hpy
Fluorine binding site 5 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:36.9
occ:1.00
 F2 F:MGF201 0.0 36.9 1.0
MG F:MGF201 1.8 41.9 1.0
NE D:ARG235 2.7 47.5 1.0
NE2 F:GLN63 2.9 42.4 1.0
O3B F:GDP202 3.1 39.8 1.0
O F:HOH314 3.1 38.4 1.0
F3 F:MGF201 3.1 47.1 1.0
F1 F:MGF201 3.1 40.6 1.0
NH2 D:ARG235 3.2 47.7 1.0
N F:ALA15 3.3 45.1 1.0
CZ D:ARG235 3.4 49.8 1.0
CB F:PRO36 3.5 40.0 1.0
CG D:ARG235 3.6 43.9 1.0
CA F:GLY14 3.6 44.7 1.0
CA F:PRO36 3.7 41.8 1.0
CD D:ARG235 3.7 45.0 1.0
CD F:GLN63 3.9 42.7 1.0
C F:GLY14 3.9 47.6 1.0
OE1 F:GLN63 4.0 40.3 1.0
CA F:ALA15 4.3 48.9 1.0
PB F:GDP202 4.4 43.6 1.0
NH1 D:ARG235 4.6 50.0 1.0
N F:PRO36 4.7 46.8 1.0
N F:THR37 4.7 43.0 1.0
CG F:PRO36 4.7 44.0 1.0
O D:ARG235 4.7 45.3 1.0
C F:PRO36 4.7 43.7 1.0
CB F:ALA15 4.7 47.6 1.0
O1B F:GDP202 4.8 52.8 1.0
MG F:MG203 4.9 42.7 1.0
O2B F:GDP202 4.9 41.0 1.0
N F:GLY14 5.0 41.3 1.0

Fluorine binding site 6 out of 6 in 5hpy

Go back to Fluorine Binding Sites List in 5hpy
Fluorine binding site 6 out of 6 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:47.1
occ:1.00
 F3 F:MGF201 0.0 47.1 1.0
MG F:MGF201 1.8 41.9 1.0
MG F:MG203 2.0 42.7 1.0
N F:THR37 2.9 43.0 1.0
O2B F:GDP202 2.9 41.0 1.0
O3B F:GDP202 2.9 39.8 1.0
O F:HOH314 3.0 38.4 1.0
O F:HOH307 3.1 39.3 1.0
O F:HOH315 3.1 38.9 1.0
F1 F:MGF201 3.1 40.6 1.0
F2 F:MGF201 3.1 36.9 1.0
OG1 F:THR37 3.2 42.8 1.0
CB F:THR37 3.3 39.8 1.0
PB F:GDP202 3.4 43.6 1.0
CA F:THR37 3.7 42.9 1.0
CA F:PRO36 3.7 41.8 1.0
C F:PRO36 3.8 43.7 1.0
NH2 D:ARG235 3.8 47.7 1.0
OG1 F:THR19 4.0 41.3 1.0
O1B F:GDP202 4.1 52.8 1.0
O F:THR37 4.1 36.4 1.0
O F:THR60 4.3 39.5 1.0
C F:THR37 4.4 40.7 1.0
CB F:PRO36 4.4 40.0 1.0
O2A F:GDP202 4.4 45.0 1.0
O F:VAL35 4.6 44.9 1.0
NZ F:LYS18 4.6 44.5 1.0
CG2 F:THR37 4.8 39.9 1.0
CE F:LYS18 4.8 42.7 1.0
CZ D:ARG235 4.8 49.8 1.0
O3A F:GDP202 4.8 57.0 1.0
N F:PRO36 4.9 46.8 1.0
NE D:ARG235 5.0 47.5 1.0
O F:PRO36 5.0 45.4 1.0

Reference:

F.Yi, R.Kong, J.Ren, L.Zhu, J.Lou, J.Y.Wu, W.Feng. Noncanonical MYO9B-Rhogap Accelerates Rhoa Gtp Hydrolysis By A Dual-Arginine-Finger Mechanism J.Mol.Biol. V. 428 3043 2016.
ISSN: ESSN 1089-8638
PubMed: 27363609
DOI: 10.1016/J.JMB.2016.06.014
Page generated: Thu Aug 1 09:57:35 2024

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