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:
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
|