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Fluorine in PDB 5irc: P190A Gap Domain Complex with Rhoa

Protein crystallography data

The structure of P190A Gap Domain Complex with Rhoa, PDB code: 5irc was solved by U.Derewenda, Z.Derewenda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.54 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.026, 112.322, 147.611, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.3

Other elements in 5irc:

The structure of P190A Gap Domain Complex with Rhoa also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the P190A Gap Domain Complex with Rhoa (pdb code 5irc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the P190A Gap Domain Complex with Rhoa, PDB code: 5irc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 1 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:11.7
occ:1.00
 F1 F:MGF203 0.0 11.7 1.0
MG F:MGF203 1.8 13.6 1.0
NZ F:LYS18 2.7 15.9 1.0
N F:GLY62 2.7 14.0 1.0
O1B F:GDP201 3.1 15.0 1.0
F3 F:MGF203 3.1 12.1 1.0
O F:HOH308 3.1 13.9 1.0
F2 F:MGF203 3.2 13.4 1.0
CA F:GLY62 3.3 15.9 1.0
CA F:GLY14 3.3 12.5 1.0
CE F:LYS18 3.4 15.1 1.0
C F:ALA61 3.8 16.8 1.0
N F:ALA15 3.9 10.0 1.0
PB F:GDP201 3.9 13.3 1.0
N F:GLY14 4.0 12.2 1.0
O F:ASP13 4.0 11.7 1.0
O3B F:GDP201 4.0 11.0 1.0
O F:THR60 4.0 17.6 1.0
CA F:ALA61 4.0 14.0 1.0
NE2 F:GLN63 4.1 8.6 1.0
OE1 F:GLN63 4.2 12.2 1.0
O F:HOH318 4.2 12.3 1.0
C F:GLY14 4.2 11.8 1.0
C F:ASP13 4.3 10.4 1.0
C F:GLY62 4.3 14.8 1.0
O F:GLY12 4.3 12.3 1.0
O2B F:GDP201 4.4 12.4 1.0
CD F:GLN63 4.5 15.3 1.0
N F:GLN63 4.5 9.6 1.0
MG F:MG202 4.6 15.9 1.0
O F:ALA61 4.9 16.8 1.0
CD F:LYS18 4.9 13.2 1.0
C F:THR60 4.9 17.2 1.0
N F:ALA61 5.0 13.6 1.0

Fluorine binding site 2 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 2 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:13.4
occ:1.00
 F2 F:MGF203 0.0 13.4 1.0
MG F:MGF203 1.8 13.6 1.0
MG F:MG202 2.1 15.9 1.0
N F:THR37 2.8 14.6 1.0
O F:HOH308 2.8 13.9 1.0
O1B F:GDP201 2.9 15.0 1.0
O2B F:GDP201 3.0 12.4 1.0
O F:HOH318 3.0 12.3 1.0
OG1 F:THR37 3.0 15.0 1.0
O F:HOH338 3.0 15.5 1.0
CB F:THR37 3.1 16.2 1.0
F1 F:MGF203 3.2 11.7 1.0
F3 F:MGF203 3.2 12.1 1.0
PB F:GDP201 3.5 13.3 1.0
CA F:THR37 3.5 14.5 1.0
C F:PRO36 3.7 13.3 1.0
NH2 A:ARG1284 3.8 15.6 1.0
CA F:PRO36 3.8 14.1 1.0
O F:THR37 4.0 17.1 1.0
OG1 F:THR19 4.2 14.7 1.0
C F:THR37 4.2 16.9 1.0
O F:THR60 4.3 17.6 1.0
CB F:PRO36 4.5 13.1 1.0
O3B F:GDP201 4.5 11.0 1.0
O F:VAL35 4.5 21.2 1.0
CG2 F:THR37 4.6 18.3 1.0
O3A F:GDP201 4.6 11.1 1.0
CZ A:ARG1284 4.7 14.5 1.0
NZ F:LYS18 4.8 15.9 1.0
O1A F:GDP201 4.8 16.1 1.0
NE A:ARG1284 4.9 13.2 1.0
O F:PRO36 4.9 17.8 1.0
CA F:ALA61 5.0 14.0 1.0

Fluorine binding site 3 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 3 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:12.1
occ:1.00
 F3 F:MGF203 0.0 12.1 1.0
MG F:MGF203 1.8 13.6 1.0
NE A:ARG1284 2.7 13.2 1.0
O1B F:GDP201 2.8 15.0 1.0
NE2 F:GLN63 2.9 8.6 1.0
O F:HOH308 3.0 13.9 1.0
F1 F:MGF203 3.1 11.7 1.0
F2 F:MGF203 3.2 13.4 1.0
NH2 A:ARG1284 3.3 15.6 1.0
CG A:ARG1284 3.4 14.0 1.0
CZ A:ARG1284 3.4 14.5 1.0
N F:ALA15 3.4 10.0 1.0
CB F:PRO36 3.5 13.1 1.0
CD A:ARG1284 3.6 12.1 1.0
CA F:GLY14 3.8 12.5 1.0
CD F:GLN63 3.8 15.3 1.0
CA F:PRO36 3.8 14.1 1.0
OE1 F:GLN63 3.9 12.2 1.0
C F:GLY14 4.0 11.8 1.0
CA F:ALA15 4.2 14.5 1.0
PB F:GDP201 4.3 13.3 1.0
N F:THR37 4.6 14.6 1.0
O A:ARG1284 4.6 13.2 1.0
CB F:ALA15 4.7 15.1 1.0
NH1 A:ARG1284 4.7 17.4 1.0
C F:PRO36 4.7 13.3 1.0
CG F:PRO36 4.8 16.5 1.0
CB A:ARG1284 4.9 10.2 1.0
N F:PRO36 4.9 18.3 1.0
O2B F:GDP201 4.9 12.4 1.0
O3A F:GDP201 4.9 11.1 1.0

Fluorine binding site 4 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 4 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:14.2
occ:1.00
 F1 D:MGF203 0.0 14.2 1.0
MG D:MGF203 1.8 15.8 1.0
NZ D:LYS18 2.6 16.4 1.0
N D:GLY62 2.7 14.1 1.0
F3 D:MGF203 3.1 16.5 1.0
O2B D:GDP201 3.1 18.5 1.0
O D:HOH301 3.2 18.3 1.0
F2 D:MGF203 3.2 16.2 1.0
CA D:GLY62 3.3 13.6 1.0
CA D:GLY14 3.3 12.1 1.0
CE D:LYS18 3.4 14.7 1.0
C D:ALA61 3.7 14.3 1.0
N D:ALA15 3.9 13.5 1.0
O1B D:GDP201 3.9 15.7 1.0
O D:ASP13 3.9 14.1 1.0
CA D:ALA61 4.0 14.7 1.0
N D:GLY14 4.0 11.6 1.0
PB D:GDP201 4.0 16.0 1.0
O D:THR60 4.0 19.0 1.0
O D:HOH339 4.1 17.7 1.0
NE2 D:GLN63 4.1 12.6 1.0
C D:GLY14 4.2 12.6 1.0
OE1 D:GLN63 4.2 16.3 1.0
C D:ASP13 4.3 12.8 1.0
O3B D:GDP201 4.3 18.2 1.0
C D:GLY62 4.4 13.7 1.0
O D:GLY12 4.4 14.2 1.0
CD D:GLN63 4.5 14.2 1.0
MG D:MG202 4.5 17.7 1.0
N D:GLN63 4.5 13.9 1.0
O D:ALA61 4.8 16.7 1.0
CD D:LYS18 4.8 17.1 1.0
C D:THR60 4.9 19.5 1.0
N D:ALA61 4.9 19.2 1.0

Fluorine binding site 5 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 5 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:16.2
occ:1.00
 F2 D:MGF203 0.0 16.2 1.0
MG D:MGF203 1.8 15.8 1.0
MG D:MG202 2.0 17.7 1.0
N D:THR37 2.8 17.4 1.0
O3B D:GDP201 2.9 18.2 1.0
O2B D:GDP201 2.9 18.5 1.0
O D:HOH339 2.9 17.7 1.0
O D:HOH301 2.9 18.3 1.0
OG1 D:THR37 3.0 22.0 1.0
O D:HOH302 3.0 19.9 1.0
F3 D:MGF203 3.2 16.5 1.0
F1 D:MGF203 3.2 14.2 1.0
CB D:THR37 3.2 20.2 1.0
PB D:GDP201 3.4 16.0 1.0
CA D:THR37 3.6 18.4 1.0
NH2 B:ARG1284 3.7 19.6 1.0
C D:PRO36 3.8 20.9 1.0
CA D:PRO36 3.8 16.7 1.0
OG1 D:THR19 4.1 20.1 1.0
O D:THR37 4.1 20.8 1.0
O D:THR60 4.3 19.0 1.0
C D:THR37 4.3 21.8 1.0
O1B D:GDP201 4.4 15.7 1.0
O D:VAL35 4.4 24.1 1.0
O3A D:GDP201 4.6 16.4 1.0
CB D:PRO36 4.6 19.8 1.0
CG2 D:THR37 4.6 22.6 1.0
CZ B:ARG1284 4.7 18.8 1.0
NZ D:LYS18 4.7 16.4 1.0
O2A D:GDP201 4.8 20.5 1.0
NE B:ARG1284 4.8 16.6 1.0
CE D:LYS18 5.0 14.7 1.0
O D:PRO36 5.0 21.9 1.0
N D:PRO36 5.0 23.0 1.0

Fluorine binding site 6 out of 6 in 5irc

Go back to Fluorine Binding Sites List in 5irc
Fluorine binding site 6 out of 6 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P190A Gap Domain Complex with Rhoa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:16.5
occ:1.00
 F3 D:MGF203 0.0 16.5 1.0
MG D:MGF203 1.8 15.8 1.0
NE B:ARG1284 2.6 16.6 1.0
O2B D:GDP201 2.8 18.5 1.0
NE2 D:GLN63 2.9 12.6 1.0
F1 D:MGF203 3.1 14.2 1.0
O D:HOH301 3.1 18.3 1.0
F2 D:MGF203 3.2 16.2 1.0
N D:ALA15 3.3 13.5 1.0
NH2 B:ARG1284 3.3 19.6 1.0
CZ B:ARG1284 3.4 18.8 1.0
CG B:ARG1284 3.4 13.3 1.0
CD B:ARG1284 3.6 14.2 1.0
CB D:PRO36 3.7 19.8 1.0
CA D:GLY14 3.7 12.1 1.0
CD D:GLN63 3.8 14.2 1.0
CA D:PRO36 3.9 16.7 1.0
OE1 D:GLN63 3.9 16.3 1.0
C D:GLY14 3.9 12.6 1.0
CA D:ALA15 4.1 18.4 1.0
PB D:GDP201 4.3 16.0 1.0
CB D:ALA15 4.6 16.6 1.0
O B:ARG1284 4.6 13.3 1.0
N D:THR37 4.6 17.4 1.0
NH1 B:ARG1284 4.7 16.7 1.0
C D:PRO36 4.8 20.9 1.0
O3B D:GDP201 4.8 18.2 1.0
CB B:ARG1284 4.9 11.1 1.0
MG D:MG202 4.9 17.7 1.0
O3A D:GDP201 5.0 16.4 1.0
N D:PRO36 5.0 23.0 1.0
CG D:PRO36 5.0 19.2 1.0

Reference:

E.Amin, M.Jaiswal, U.Derewenda, K.Reis, K.Nouri, K.T.Koessmeier, P.Aspenstrom, A.V.Somlyo, R.Dvorsky, M.R.Ahmadian. Deciphering the Molecular and Functional Basis of Rhogap Family Proteins: A Systematic Approach Toward Selective Inactivation of Rho Family Proteins. J.Biol.Chem. V. 291 20353 2016.
ISSN: ESSN 1083-351X
PubMed: 27481945
DOI: 10.1074/JBC.M116.736967
Page generated: Thu Aug 1 10:16:19 2024

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