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Fluorine in PDB 5jcp: Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State

Protein crystallography data

The structure of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State, PDB code: 5jcp was solved by H.Bao, F.Li, C.Wang, N.Wang, Y.Jiang, Y.Tang, J.Wu, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.71 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.786, 93.208, 164.283, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Other elements in 5jcp:

The structure of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State 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 Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State (pdb code 5jcp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State, PDB code: 5jcp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5jcp

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Fluorine binding site 1 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1203

b:22.9
occ:1.00
 F1 B:ALF1203 0.0 22.9 1.0
AL B:ALF1203 1.8 26.7 1.0
MG B:MG1202 2.0 26.5 1.0
F3 B:ALF1203 2.5 28.8 1.0
F4 B:ALF1203 2.5 26.0 1.0
O3B B:GDP1201 2.7 22.7 1.0
O B:HOH1320 2.8 23.0 1.0
O B:HOH1304 2.8 19.8 1.0
O2B B:GDP1201 2.9 22.1 1.0
PB B:GDP1201 3.3 21.7 1.0
O B:HOH1312 3.3 25.5 1.0
F2 B:ALF1203 3.5 25.6 1.0
O B:THR60 4.0 21.2 1.0
O1B B:GDP1201 4.0 20.9 1.0
NZ B:LYS18 4.1 17.4 1.0
CA B:ALA61 4.1 22.4 1.0
CE B:LYS18 4.1 16.6 1.0
OG1 B:THR19 4.1 21.0 1.0
N B:GLY62 4.3 23.0 1.0
NH2 B:ARG942 4.6 23.0 1.0
O3A B:GDP1201 4.7 21.7 1.0
CB B:ALA61 4.7 21.1 1.0
C B:ALA61 4.7 23.8 1.0
C B:THR60 4.8 25.3 1.0
N B:ALA61 4.9 24.3 1.0
OE1 B:GLN63 5.0 23.9 1.0

Fluorine binding site 2 out of 8 in 5jcp

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Fluorine binding site 2 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1203

b:25.6
occ:1.00
 F2 B:ALF1203 0.0 25.6 1.0
AL B:ALF1203 1.8 26.7 1.0
F3 B:ALF1203 2.5 28.8 1.0
F4 B:ALF1203 2.5 26.0 1.0
O3B B:GDP1201 2.7 22.7 1.0
O B:HOH1304 2.7 19.8 1.0
NE2 B:GLN63 2.8 19.4 1.0
N B:ALA15 2.9 18.4 1.0
NE B:ARG942 2.9 23.4 1.0
CA B:GLY14 3.4 20.9 1.0
F1 B:ALF1203 3.5 22.9 1.0
C B:GLY14 3.6 24.8 1.0
CD B:GLN63 3.6 26.9 1.0
OE1 B:GLN63 3.6 23.9 1.0
CG B:ARG942 3.6 23.0 1.0
NH2 B:ARG942 3.7 23.0 1.0
CZ B:ARG942 3.8 25.9 1.0
CA B:ALA15 3.8 21.9 1.0
CD B:ARG942 3.8 23.4 1.0
PB B:GDP1201 4.2 21.7 1.0
CB B:ALA15 4.4 20.6 1.0
O1B B:GDP1201 4.7 20.9 1.0
O B:GLY14 4.7 21.2 1.0
N B:GLY14 4.8 18.9 1.0
O B:ARG942 4.8 24.2 1.0
O3A B:GDP1201 4.8 21.7 1.0
N B:GLY62 4.8 23.0 1.0
NZ B:LYS18 4.9 17.4 1.0
O2B B:GDP1201 5.0 22.1 1.0

Fluorine binding site 3 out of 8 in 5jcp

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Fluorine binding site 3 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1203

b:28.8
occ:1.00
 F3 B:ALF1203 0.0 28.8 1.0
AL B:ALF1203 1.8 26.7 1.0
F2 B:ALF1203 2.5 25.6 1.0
F1 B:ALF1203 2.5 22.9 1.0
NH2 B:ARG942 2.6 23.0 1.0
O3B B:GDP1201 2.7 22.7 1.0
O B:HOH1304 2.8 19.8 1.0
O B:HOH1312 3.0 25.5 1.0
NE B:ARG942 3.3 23.4 1.0
CZ B:ARG942 3.3 25.9 1.0
MG B:MG1202 3.4 26.5 1.0
F4 B:ALF1203 3.6 26.0 1.0
PB B:GDP1201 3.8 21.7 1.0
O2B B:GDP1201 3.9 22.1 1.0
O2A B:GDP1201 4.4 30.2 1.0
O3A B:GDP1201 4.5 21.7 1.0
CD B:ARG942 4.6 23.4 1.0
NH1 B:ARG942 4.6 26.6 1.0
N B:ALA15 4.8 18.4 1.0
NE2 B:GLN63 4.8 19.4 1.0
OE1 B:GLN63 4.8 23.9 1.0
O1B B:GDP1201 4.9 20.9 1.0

Fluorine binding site 4 out of 8 in 5jcp

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Fluorine binding site 4 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1203

b:26.0
occ:1.00
 F4 B:ALF1203 0.0 26.0 1.0
AL B:ALF1203 1.8 26.7 1.0
F1 B:ALF1203 2.5 22.9 1.0
F2 B:ALF1203 2.5 25.6 1.0
O B:HOH1304 2.6 19.8 1.0
N B:GLY62 2.8 23.0 1.0
O3B B:GDP1201 2.8 22.7 1.0
NZ B:LYS18 2.9 17.4 1.0
CA B:GLY14 3.3 20.9 1.0
CA B:GLY62 3.3 21.8 1.0
CE B:LYS18 3.5 16.6 1.0
F3 B:ALF1203 3.6 28.8 1.0
N B:ALA15 3.6 18.4 1.0
OE1 B:GLN63 3.7 23.9 1.0
O1B B:GDP1201 3.8 20.9 1.0
PB B:GDP1201 3.8 21.7 1.0
C B:ALA61 3.8 23.8 1.0
NE2 B:GLN63 4.0 19.4 1.0
C B:GLY14 4.0 24.8 1.0
N B:GLY14 4.1 18.9 1.0
CA B:ALA61 4.1 22.4 1.0
O B:ASP13 4.1 16.9 1.0
CD B:GLN63 4.2 26.9 1.0
O2B B:GDP1201 4.3 22.1 1.0
MG B:MG1202 4.4 26.5 1.0
C B:GLY62 4.4 25.8 1.0
C B:ASP13 4.4 22.6 1.0
O B:HOH1320 4.5 23.0 1.0
N B:GLN63 4.5 21.0 1.0
O B:GLY12 4.6 18.8 1.0
O B:THR60 4.6 21.2 1.0
CB B:ALA61 4.8 21.1 1.0
CA B:ALA15 4.8 21.9 1.0
O B:ALA61 4.9 27.4 1.0

Fluorine binding site 5 out of 8 in 5jcp

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Fluorine binding site 5 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:21.8
occ:1.00
 F1 A:ALF1203 0.0 21.8 1.0
AL A:ALF1203 1.8 27.2 1.0
F3 A:ALF1203 2.5 27.8 1.0
F4 A:ALF1203 2.6 26.2 1.0
O3B A:GDP1201 2.6 23.8 1.0
NZ A:LYS18 2.6 20.1 1.0
O A:HOH1305 2.8 25.5 1.0
N A:GLY62 2.9 25.3 1.0
CA A:GLY14 3.3 24.3 1.0
N A:ALA15 3.5 25.8 1.0
CA A:GLY62 3.5 22.9 1.0
CE A:LYS18 3.5 23.4 1.0
F2 A:ALF1203 3.6 29.2 1.0
PB A:GDP1201 3.6 24.6 1.0
O1B A:GDP1201 3.7 22.1 1.0
C A:GLY14 3.9 27.9 1.0
OE1 A:GLN63 3.9 26.8 1.0
C A:ALA61 3.9 25.7 1.0
NE2 A:GLN63 4.0 22.8 1.0
O A:ASP13 4.0 21.2 1.0
N A:GLY14 4.0 24.1 1.0
O2B A:GDP1201 4.1 21.2 1.0
CA A:ALA61 4.1 23.6 1.0
CD A:GLN63 4.3 28.2 1.0
C A:ASP13 4.3 26.3 1.0
MG A:MG1202 4.3 28.9 1.0
C A:GLY62 4.6 29.7 1.0
O A:HOH1307 4.6 23.2 1.0
O A:THR60 4.6 21.2 1.0
O A:GLY12 4.6 23.2 1.0
N A:GLN63 4.7 25.4 1.0
CA A:ALA15 4.7 29.2 1.0
CB A:ALA61 4.8 23.1 1.0
O3A A:GDP1201 5.0 27.0 1.0
CD A:LYS18 5.0 19.9 1.0

Fluorine binding site 6 out of 8 in 5jcp

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Fluorine binding site 6 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:29.2
occ:1.00
 F2 A:ALF1203 0.0 29.2 1.0
AL A:ALF1203 1.8 27.2 1.0
F4 A:ALF1203 2.5 26.2 1.0
F3 A:ALF1203 2.6 27.8 1.0
O A:HOH1305 2.7 25.5 1.0
O3B A:GDP1201 2.7 23.8 1.0
O A:HOH1323 2.7 26.0 1.0
NH2 A:ARG942 2.8 29.4 1.0
NE A:ARG942 3.3 34.6 1.0
CZ A:ARG942 3.4 36.6 1.0
MG A:MG1202 3.4 28.9 1.0
O A:HOH1376 3.5 52.2 1.0
F1 A:ALF1203 3.6 21.8 1.0
PB A:GDP1201 3.9 24.6 1.0
O2B A:GDP1201 3.9 21.2 1.0
O2A A:GDP1201 4.4 25.9 1.0
O3A A:GDP1201 4.5 27.0 1.0
CD A:ARG942 4.6 31.5 1.0
NH1 A:ARG942 4.7 30.2 1.0
N A:ALA15 4.8 25.8 1.0
NE2 A:GLN63 4.8 22.8 1.0
OE1 A:GLN63 4.8 26.8 1.0
CG A:ARG942 4.9 28.5 1.0

Fluorine binding site 7 out of 8 in 5jcp

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Fluorine binding site 7 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:27.8
occ:1.00
 F3 A:ALF1203 0.0 27.8 1.0
AL A:ALF1203 1.8 27.2 1.0
F1 A:ALF1203 2.5 21.8 1.0
F2 A:ALF1203 2.6 29.2 1.0
NE2 A:GLN63 2.7 22.8 1.0
O A:HOH1305 2.7 25.5 1.0
O3B A:GDP1201 2.7 23.8 1.0
N A:ALA15 2.9 25.8 1.0
NE A:ARG942 3.0 34.6 1.0
CA A:GLY14 3.4 24.3 1.0
CG A:ARG942 3.4 28.5 1.0
CD A:GLN63 3.6 28.2 1.0
C A:GLY14 3.6 27.9 1.0
F4 A:ALF1203 3.6 26.2 1.0
OE1 A:GLN63 3.6 26.8 1.0
CD A:ARG942 3.8 31.5 1.0
CA A:ALA15 3.9 29.2 1.0
CZ A:ARG942 3.9 36.6 1.0
NH2 A:ARG942 4.0 29.4 1.0
PB A:GDP1201 4.2 24.6 1.0
O A:HOH1376 4.4 52.2 1.0
CB A:ALA15 4.4 24.7 1.0
O A:ARG942 4.6 27.6 1.0
N A:GLY14 4.7 24.1 1.0
O A:GLY14 4.7 27.1 1.0
N A:GLY62 4.8 25.3 1.0
NZ A:LYS18 4.8 20.1 1.0
O1B A:GDP1201 4.8 22.1 1.0
O3A A:GDP1201 4.9 27.0 1.0
CB A:ARG942 4.9 31.9 1.0
O2B A:GDP1201 4.9 21.2 1.0
O A:HOH1323 5.0 26.0 1.0

Fluorine binding site 8 out of 8 in 5jcp

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Fluorine binding site 8 out of 8 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1203

b:26.2
occ:1.00
 F4 A:ALF1203 0.0 26.2 1.0
AL A:ALF1203 1.8 27.2 1.0
MG A:MG1202 2.0 28.9 1.0
F2 A:ALF1203 2.5 29.2 1.0
F1 A:ALF1203 2.6 21.8 1.0
O3B A:GDP1201 2.7 23.8 1.0
O2B A:GDP1201 2.8 21.2 1.0
O A:HOH1305 2.8 25.5 1.0
O A:HOH1307 2.8 23.2 1.0
O A:HOH1323 3.0 26.0 1.0
PB A:GDP1201 3.3 24.6 1.0
F3 A:ALF1203 3.6 27.8 1.0
NZ A:LYS18 4.0 20.1 1.0
O A:THR60 4.0 21.2 1.0
CA A:ALA61 4.0 23.6 1.0
O1B A:GDP1201 4.1 22.1 1.0
OG1 A:THR19 4.1 27.4 1.0
CE A:LYS18 4.1 23.4 1.0
N A:GLY62 4.4 25.3 1.0
CB A:ALA61 4.6 23.1 1.0
O3A A:GDP1201 4.6 27.0 1.0
NH2 A:ARG942 4.7 29.4 1.0
C A:THR60 4.7 25.8 1.0
C A:ALA61 4.8 25.7 1.0
N A:ALA61 4.8 24.0 1.0

Reference:

H.Bao, F.Li, C.Wang, N.Wang, Y.Jiang, Y.Tang, J.Wu, Y.Shi. Structural Basis For the Specific Recognition of Rhoa By the Dual Gtpase-Activating Protein ARAP3 J.Biol.Chem. V. 291 16709 2016.
ISSN: ESSN 1083-351X
PubMed: 27311713
DOI: 10.1074/JBC.M116.736140
Page generated: Thu Aug 1 10:30:37 2024

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