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Fluorine in PDB 3brw: Structure of the Rap-Rapgap Complex

Protein crystallography data

The structure of Structure of the Rap-Rapgap Complex, PDB code: 3brw was solved by A.Scrima, C.Thomas, D.Deaconescu, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.08 / 3.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.723, 209.723, 108.217, 90.00, 90.00, 120.00
R / Rfree (%) 23.4 / 28

Other elements in 3brw:

The structure of Structure of the Rap-Rapgap Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Rap-Rapgap Complex (pdb code 3brw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Rap-Rapgap Complex, PDB code: 3brw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3brw

Go back to Fluorine Binding Sites List in 3brw
Fluorine binding site 1 out of 3 in the Structure of the Rap-Rapgap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Rap-Rapgap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F170

b:65.3
occ:1.00
F1 D:BEF170 0.0 65.3 1.0
BE D:BEF170 1.5 64.5 1.0
MG D:MG172 2.2 68.5 1.0
F3 D:BEF170 2.4 64.8 1.0
F2 D:BEF170 2.4 64.6 1.0
O3B D:GDP171 2.7 63.8 1.0
OG1 D:THR35 2.9 73.5 1.0
N D:THR35 2.9 75.5 1.0
O D:HOH175 3.1 68.1 1.0
O2B D:GDP171 3.2 63.7 1.0
O D:HOH174 3.2 68.3 1.0
PB D:GDP171 3.5 63.4 1.0
CA D:PRO34 3.6 76.2 1.0
C D:PRO34 3.7 75.9 1.0
CA D:THR35 3.8 75.1 1.0
CB D:THR35 3.9 75.0 1.0
O D:THR35 3.9 75.1 1.0
O1B D:GDP171 4.3 62.7 1.0
OG D:SER17 4.3 67.8 1.0
C D:THR35 4.3 75.2 1.0
N D:GLY60 4.4 73.0 1.0
CB D:PRO34 4.4 76.2 1.0
CG2 D:THR35 4.5 74.9 1.0
CE1 D:TYR32 4.5 77.3 1.0
OD1 B:ASN290 4.6 75.1 1.0
O D:THR58 4.7 74.9 1.0
OH D:TYR32 4.7 77.3 1.0
N D:PRO34 4.7 76.5 1.0
O D:ASP33 4.8 76.9 1.0
O3A D:GDP171 4.8 63.5 1.0
NZ D:LYS16 4.8 67.3 1.0
O1A D:GDP171 4.9 62.9 1.0
O D:PRO34 4.9 75.9 1.0
CA D:ALA59 5.0 73.7 1.0
ND2 B:ASN290 5.0 75.5 1.0

Fluorine binding site 2 out of 3 in 3brw

Go back to Fluorine Binding Sites List in 3brw
Fluorine binding site 2 out of 3 in the Structure of the Rap-Rapgap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Rap-Rapgap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F170

b:64.6
occ:1.00
F2 D:BEF170 0.0 64.6 1.0
BE D:BEF170 1.5 64.5 1.0
F3 D:BEF170 2.4 64.8 1.0
F1 D:BEF170 2.4 65.3 1.0
NZ D:LYS16 2.6 67.3 1.0
O3B D:GDP171 2.7 63.8 1.0
O1B D:GDP171 3.1 62.7 1.0
N D:GLY60 3.1 73.0 1.0
PB D:GDP171 3.2 63.4 1.0
O D:HOH175 3.3 68.1 1.0
CA D:GLY60 3.3 72.6 1.0
CE D:LYS16 3.3 67.0 1.0
O2B D:GDP171 3.7 63.7 1.0
MG D:MG172 3.7 68.5 1.0
CA D:GLY12 3.8 66.0 1.0
N D:GLY13 4.0 66.1 1.0
O D:SER11 4.0 65.9 1.0
C D:ALA59 4.1 73.4 1.0
N D:GLY12 4.3 65.9 1.0
C D:SER11 4.3 65.9 1.0
O D:THR58 4.3 74.9 1.0
C D:GLY12 4.4 66.1 1.0
OG1 D:THR35 4.5 73.5 1.0
O D:GLY10 4.6 66.4 1.0
CA D:ALA59 4.7 73.7 1.0
C D:GLY60 4.7 72.4 1.0
O3A D:GDP171 4.7 63.5 1.0
CD D:LYS16 4.8 67.3 1.0
ND2 B:ASN290 4.8 75.5 1.0
O D:ALA59 4.9 73.2 1.0

Fluorine binding site 3 out of 3 in 3brw

Go back to Fluorine Binding Sites List in 3brw
Fluorine binding site 3 out of 3 in the Structure of the Rap-Rapgap Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Rap-Rapgap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F170

b:64.8
occ:1.00
F3 D:BEF170 0.0 64.8 1.0
BE D:BEF170 1.5 64.5 1.0
F2 D:BEF170 2.4 64.6 1.0
F1 D:BEF170 2.4 65.3 1.0
O3B D:GDP171 2.8 63.8 1.0
OH D:TYR32 2.9 77.3 1.0
ND2 B:ASN290 2.9 75.5 1.0
CA D:GLY12 3.5 66.0 1.0
OD1 B:ASN290 3.5 75.1 1.0
CG B:ASN290 3.6 75.2 1.0
N D:GLY13 3.6 66.1 1.0
CE1 D:TYR32 3.8 77.3 1.0
CZ D:TYR32 3.8 77.2 1.0
C D:GLY12 4.1 66.1 1.0
CA D:PRO34 4.1 76.2 1.0
N D:GLY60 4.2 73.0 1.0
CB D:PRO34 4.2 76.2 1.0
PB D:GDP171 4.2 63.4 1.0
CA D:GLY60 4.2 72.6 1.0
MG D:MG172 4.4 68.5 1.0
N D:THR35 4.5 75.5 1.0
N D:GLY12 4.5 65.9 1.0
O1B D:GDP171 4.6 62.7 1.0
O2B D:GDP171 4.7 63.7 1.0
CA D:GLY13 4.8 66.2 1.0
CG D:PRO34 4.8 76.2 1.0
C D:PRO34 4.8 75.9 1.0
NZ D:LYS16 4.9 67.3 1.0
O D:HOH174 5.0 68.3 1.0

Reference:

A.Scrima, C.Thomas, D.Deaconescu, A.Wittinghofer. The Rap-Rapgap Complex: Gtp Hydrolysis Without Catalytic Glutamine and Arginine Residues Embo J. V. 27 1145 2008.
ISSN: ISSN 0261-4189
PubMed: 18309292
DOI: 10.1038/EMBOJ.2008.30
Page generated: Wed Jul 31 17:18:28 2024

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