Fluorine in PDB 8cnj: Hras(1-166) in Complex with Gdp and BEF3-
Enzymatic activity of Hras(1-166) in Complex with Gdp and BEF3-
All present enzymatic activity of Hras(1-166) in Complex with Gdp and BEF3-:
3.6.5.2;
Protein crystallography data
The structure of Hras(1-166) in Complex with Gdp and BEF3-, PDB code: 8cnj
was solved by
P.Baumann,
Y.Jin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.59 /
1.35
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.433,
51.957,
136.149,
90,
90,
90
|
|
R / Rfree (%)
|
14.3 /
17.9
|
Other elements in 8cnj:
The structure of Hras(1-166) in Complex with Gdp and BEF3- also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Hras(1-166) in Complex with Gdp and BEF3-
(pdb code 8cnj). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Hras(1-166) in Complex with Gdp and BEF3-, PDB code: 8cnj:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 1 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:12.1
occ:1.00
|
F1
|
A:BEF202
|
0.0
|
12.1
|
1.0
|
|
BE
|
A:BEF202
|
1.6
|
11.6
|
1.0
|
|
F2
|
A:BEF202
|
2.6
|
11.6
|
1.0
|
|
NZ
|
A:LYS16
|
2.6
|
11.7
|
1.0
|
|
F3
|
A:BEF202
|
2.6
|
11.5
|
1.0
|
|
O3B
|
A:GDP201
|
2.6
|
9.8
|
1.0
|
|
N
|
A:GLY60
|
2.7
|
12.6
|
1.0
|
|
CA
|
A:GLY60
|
3.1
|
13.9
|
1.0
|
|
O
|
A:HOH383
|
3.4
|
12.5
|
1.0
|
|
CE
|
A:LYS16
|
3.4
|
11.9
|
1.0
|
|
CA
|
A:GLY12
|
3.4
|
12.2
|
1.0
|
|
PB
|
A:GDP201
|
3.6
|
10.4
|
1.0
|
|
N
|
A:GLN61
|
3.8
|
16.2
|
1.0
|
|
C
|
A:GLY60
|
3.8
|
15.4
|
1.0
|
|
O2B
|
A:GDP201
|
3.9
|
10.5
|
1.0
|
|
C
|
A:ALA59
|
3.9
|
12.5
|
1.0
|
|
O
|
A:HOH315
|
4.0
|
11.5
|
1.0
|
|
O
|
A:THR58
|
4.0
|
11.4
|
1.0
|
|
O
|
A:ALA11
|
4.0
|
12.4
|
1.0
|
|
N
|
A:GLY13
|
4.0
|
11.4
|
1.0
|
|
N
|
A:GLY12
|
4.1
|
12.5
|
1.0
|
|
O1B
|
A:GDP201
|
4.1
|
10.4
|
1.0
|
|
MG
|
A:MG203
|
4.1
|
11.2
|
1.0
|
|
C
|
A:GLY12
|
4.3
|
12.6
|
1.0
|
|
CA
|
A:ALA59
|
4.3
|
12.7
|
1.0
|
|
C
|
A:ALA11
|
4.3
|
12.0
|
1.0
|
|
O
|
A:GLY10
|
4.5
|
12.2
|
1.0
|
|
OH
|
A:TYR32
|
4.5
|
12.9
|
1.0
|
|
O
|
A:GLY60
|
4.8
|
17.1
|
1.0
|
|
CD
|
A:LYS16
|
4.8
|
11.5
|
1.0
|
|
N
|
A:THR35
|
4.9
|
11.8
|
1.0
|
|
O
|
A:ALA59
|
4.9
|
15.9
|
1.0
|
|
CG
|
A:GLN61
|
5.0
|
20.0
|
1.0
|
|
C
|
A:THR58
|
5.0
|
11.3
|
1.0
|
|
O3A
|
A:GDP201
|
5.0
|
10.1
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 2 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:11.6
occ:1.00
|
F2
|
A:BEF202
|
0.0
|
11.6
|
1.0
|
|
BE
|
A:BEF202
|
1.6
|
11.6
|
1.0
|
|
OH
|
A:TYR32
|
2.5
|
12.9
|
1.0
|
|
F1
|
A:BEF202
|
2.6
|
12.1
|
1.0
|
|
F3
|
A:BEF202
|
2.6
|
11.5
|
1.0
|
|
O3B
|
A:GDP201
|
2.6
|
9.8
|
1.0
|
|
O
|
A:HOH383
|
2.8
|
12.5
|
1.0
|
|
CE1
|
A:TYR32
|
3.3
|
12.0
|
1.0
|
|
CZ
|
A:TYR32
|
3.3
|
12.6
|
1.0
|
|
CA
|
A:PRO34
|
3.4
|
11.1
|
1.0
|
|
CB
|
A:PRO34
|
3.6
|
11.9
|
1.0
|
|
CG
|
A:GLN61
|
3.6
|
20.0
|
1.0
|
|
N
|
A:THR35
|
3.7
|
11.8
|
1.0
|
|
CA
|
A:GLY12
|
3.9
|
12.2
|
1.0
|
|
N
|
A:GLY13
|
4.0
|
11.4
|
1.0
|
|
C
|
A:PRO34
|
4.0
|
11.7
|
1.0
|
|
PB
|
A:GDP201
|
4.1
|
10.4
|
1.0
|
|
O
|
A:HOH342
|
4.3
|
11.6
|
1.0
|
|
N
|
A:GLN61
|
4.3
|
16.2
|
1.0
|
|
MG
|
A:MG203
|
4.3
|
11.2
|
1.0
|
|
CG
|
A:PRO34
|
4.4
|
12.8
|
1.0
|
|
CB
|
A:GLN61
|
4.5
|
18.3
|
1.0
|
|
C
|
A:GLY12
|
4.5
|
12.6
|
1.0
|
|
N
|
A:GLY60
|
4.5
|
12.6
|
1.0
|
|
NE2
|
A:GLN61
|
4.5
|
20.1
|
1.0
|
|
N
|
A:PRO34
|
4.5
|
11.7
|
1.0
|
|
CD1
|
A:TYR32
|
4.6
|
11.6
|
1.0
|
|
O1B
|
A:GDP201
|
4.6
|
10.4
|
1.0
|
|
CE2
|
A:TYR32
|
4.6
|
13.4
|
1.0
|
|
CD
|
A:GLN61
|
4.6
|
21.2
|
1.0
|
|
CA
|
A:THR35
|
4.8
|
11.9
|
1.0
|
|
O3A
|
A:GDP201
|
4.9
|
10.1
|
1.0
|
|
O
|
A:THR35
|
4.9
|
12.7
|
1.0
|
|
CA
|
A:GLY60
|
5.0
|
13.9
|
1.0
|
|
NZ
|
A:LYS16
|
5.0
|
11.7
|
1.0
|
|
CA
|
A:GLY13
|
5.0
|
11.3
|
1.0
|
|
CA
|
A:GLN61
|
5.0
|
18.4
|
1.0
|
|
C
|
A:GLY60
|
5.0
|
15.4
|
1.0
|
|
OG1
|
A:THR35
|
5.0
|
12.5
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 3 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:11.5
occ:1.00
|
F3
|
A:BEF202
|
0.0
|
11.5
|
1.0
|
|
BE
|
A:BEF202
|
1.6
|
11.6
|
1.0
|
|
MG
|
A:MG203
|
1.9
|
11.2
|
1.0
|
|
F2
|
A:BEF202
|
2.6
|
11.6
|
1.0
|
|
F1
|
A:BEF202
|
2.6
|
12.1
|
1.0
|
|
O3B
|
A:GDP201
|
2.6
|
9.8
|
1.0
|
|
OG1
|
A:THR35
|
2.7
|
12.5
|
1.0
|
|
O
|
A:HOH342
|
2.8
|
11.6
|
1.0
|
|
O
|
A:HOH315
|
2.8
|
11.5
|
1.0
|
|
N
|
A:THR35
|
2.9
|
11.8
|
1.0
|
|
O1B
|
A:GDP201
|
2.9
|
10.4
|
1.0
|
|
CB
|
A:THR35
|
3.0
|
12.3
|
1.0
|
|
PB
|
A:GDP201
|
3.3
|
10.4
|
1.0
|
|
CA
|
A:THR35
|
3.5
|
11.9
|
1.0
|
|
O
|
A:HOH383
|
3.7
|
12.5
|
1.0
|
|
C
|
A:PRO34
|
3.9
|
11.7
|
1.0
|
|
OG
|
A:SER17
|
3.9
|
10.5
|
1.0
|
|
CA
|
A:PRO34
|
4.0
|
11.1
|
1.0
|
|
O
|
A:THR58
|
4.1
|
11.4
|
1.0
|
|
NZ
|
A:LYS16
|
4.4
|
11.7
|
1.0
|
|
O2B
|
A:GDP201
|
4.4
|
10.5
|
1.0
|
|
CG2
|
A:THR35
|
4.4
|
12.0
|
1.0
|
|
O
|
A:ASP33
|
4.4
|
11.7
|
1.0
|
|
O3A
|
A:GDP201
|
4.4
|
10.1
|
1.0
|
|
O
|
A:THR35
|
4.5
|
12.7
|
1.0
|
|
CE1
|
A:TYR32
|
4.5
|
12.0
|
1.0
|
|
C
|
A:THR35
|
4.5
|
12.4
|
1.0
|
|
N
|
A:GLY60
|
4.6
|
12.6
|
1.0
|
|
CE
|
A:LYS16
|
4.6
|
11.9
|
1.0
|
|
O1A
|
A:GDP201
|
4.8
|
11.1
|
1.0
|
|
OH
|
A:TYR32
|
4.8
|
12.9
|
1.0
|
|
CA
|
A:ALA59
|
4.9
|
12.7
|
1.0
|
|
CB
|
A:SER17
|
5.0
|
10.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 4 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F202
b:14.1
occ:1.00
|
F1
|
B:BEF202
|
0.0
|
14.1
|
1.0
|
|
BE
|
B:BEF202
|
1.6
|
13.7
|
1.0
|
|
OH
|
B:TYR32
|
2.5
|
15.4
|
1.0
|
|
F3
|
B:BEF202
|
2.5
|
14.3
|
1.0
|
|
F2
|
B:BEF202
|
2.6
|
14.1
|
1.0
|
|
O2B
|
B:GDP201
|
2.6
|
12.4
|
1.0
|
|
O
|
B:HOH359
|
2.8
|
15.4
|
1.0
|
|
CE1
|
B:TYR32
|
3.3
|
15.3
|
1.0
|
|
CA
|
B:PRO34
|
3.3
|
15.5
|
1.0
|
|
CZ
|
B:TYR32
|
3.3
|
15.0
|
1.0
|
|
CB
|
B:PRO34
|
3.4
|
16.7
|
1.0
|
|
N
|
B:THR35
|
3.7
|
14.5
|
1.0
|
|
CG
|
B:GLN61
|
3.8
|
27.4
|
1.0
|
|
CA
|
B:GLY12
|
3.9
|
14.3
|
1.0
|
|
N
|
B:GLY13
|
4.0
|
13.9
|
1.0
|
|
C
|
B:PRO34
|
4.0
|
14.8
|
1.0
|
|
PB
|
B:GDP201
|
4.1
|
13.1
|
1.0
|
|
CG
|
B:PRO34
|
4.2
|
18.1
|
1.0
|
|
O
|
B:HOH325
|
4.3
|
13.9
|
1.0
|
|
MG
|
B:MG204
|
4.3
|
13.0
|
1.0
|
|
N
|
B:GLN61
|
4.4
|
21.5
|
1.0
|
|
N
|
B:PRO34
|
4.4
|
14.8
|
1.0
|
|
C
|
B:GLY12
|
4.4
|
14.7
|
1.0
|
|
NE2
|
B:GLN61
|
4.4
|
31.6
|
1.0
|
|
N
|
B:GLY60
|
4.5
|
16.7
|
1.0
|
|
CD1
|
B:TYR32
|
4.6
|
15.4
|
1.0
|
|
O3B
|
B:GDP201
|
4.6
|
12.8
|
1.0
|
|
CE2
|
B:TYR32
|
4.6
|
16.2
|
1.0
|
|
CD
|
B:GLN61
|
4.7
|
29.6
|
1.0
|
|
CB
|
B:GLN61
|
4.7
|
25.5
|
1.0
|
|
CA
|
B:GLY60
|
4.9
|
18.2
|
1.0
|
|
CA
|
B:THR35
|
4.9
|
13.8
|
1.0
|
|
O
|
B:THR35
|
4.9
|
15.0
|
1.0
|
|
O3A
|
B:GDP201
|
4.9
|
12.4
|
1.0
|
|
CA
|
B:GLY13
|
4.9
|
14.3
|
1.0
|
|
NZ
|
B:LYS16
|
5.0
|
13.8
|
1.0
|
|
C
|
B:GLY60
|
5.0
|
20.9
|
1.0
|
|
O1B
|
B:GDP201
|
5.0
|
13.7
|
1.0
|
|
O
|
B:ASP33
|
5.0
|
15.0
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 5 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F202
b:14.1
occ:1.00
|
F2
|
B:BEF202
|
0.0
|
14.1
|
1.0
|
|
BE
|
B:BEF202
|
1.6
|
13.7
|
1.0
|
|
MG
|
B:MG204
|
1.9
|
13.0
|
1.0
|
|
F1
|
B:BEF202
|
2.6
|
14.1
|
1.0
|
|
F3
|
B:BEF202
|
2.6
|
14.3
|
1.0
|
|
O2B
|
B:GDP201
|
2.7
|
12.4
|
1.0
|
|
OG1
|
B:THR35
|
2.7
|
13.4
|
1.0
|
|
O
|
B:HOH325
|
2.8
|
13.9
|
1.0
|
|
O
|
B:HOH313
|
2.8
|
13.6
|
1.0
|
|
N
|
B:THR35
|
2.9
|
14.5
|
1.0
|
|
O3B
|
B:GDP201
|
2.9
|
12.8
|
1.0
|
|
CB
|
B:THR35
|
3.0
|
14.2
|
1.0
|
|
PB
|
B:GDP201
|
3.3
|
13.1
|
1.0
|
|
CA
|
B:THR35
|
3.5
|
13.8
|
1.0
|
|
O
|
B:HOH359
|
3.6
|
15.4
|
1.0
|
|
C
|
B:PRO34
|
3.9
|
14.8
|
1.0
|
|
OG
|
B:SER17
|
3.9
|
12.7
|
1.0
|
|
CA
|
B:PRO34
|
4.0
|
15.5
|
1.0
|
|
O
|
B:THR58
|
4.0
|
14.1
|
1.0
|
|
O1B
|
B:GDP201
|
4.3
|
13.7
|
1.0
|
|
NZ
|
B:LYS16
|
4.3
|
13.8
|
1.0
|
|
O
|
B:THR35
|
4.4
|
15.0
|
1.0
|
|
CG2
|
B:THR35
|
4.4
|
14.1
|
1.0
|
|
C
|
B:THR35
|
4.4
|
14.3
|
1.0
|
|
N
|
B:GLY60
|
4.5
|
16.7
|
1.0
|
|
O3A
|
B:GDP201
|
4.5
|
12.4
|
1.0
|
|
O
|
B:ASP33
|
4.5
|
15.0
|
1.0
|
|
CE1
|
B:TYR32
|
4.6
|
15.3
|
1.0
|
|
CE
|
B:LYS16
|
4.6
|
14.0
|
1.0
|
|
O2A
|
B:GDP201
|
4.7
|
14.0
|
1.0
|
|
CB
|
B:PRO34
|
4.9
|
16.7
|
1.0
|
|
CA
|
B:ALA59
|
4.9
|
15.3
|
1.0
|
|
OH
|
B:TYR32
|
4.9
|
15.4
|
1.0
|
|
CB
|
B:SER17
|
5.0
|
12.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8cnj
Go back to
Fluorine Binding Sites List in 8cnj
Fluorine binding site 6 out
of 6 in the Hras(1-166) in Complex with Gdp and BEF3-
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Hras(1-166) in Complex with Gdp and BEF3- within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F202
b:14.3
occ:1.00
|
F3
|
B:BEF202
|
0.0
|
14.3
|
1.0
|
|
BE
|
B:BEF202
|
1.6
|
13.7
|
1.0
|
|
F1
|
B:BEF202
|
2.5
|
14.1
|
1.0
|
|
NZ
|
B:LYS16
|
2.6
|
13.8
|
1.0
|
|
F2
|
B:BEF202
|
2.6
|
14.1
|
1.0
|
|
N
|
B:GLY60
|
2.7
|
16.7
|
1.0
|
|
O2B
|
B:GDP201
|
2.7
|
12.4
|
1.0
|
|
CA
|
B:GLY60
|
3.0
|
18.2
|
1.0
|
|
O
|
B:HOH359
|
3.2
|
15.4
|
1.0
|
|
CA
|
B:GLY12
|
3.4
|
14.3
|
1.0
|
|
CE
|
B:LYS16
|
3.4
|
14.0
|
1.0
|
|
PB
|
B:GDP201
|
3.6
|
13.1
|
1.0
|
|
C
|
B:ALA59
|
3.8
|
15.9
|
1.0
|
|
O1B
|
B:GDP201
|
3.8
|
13.7
|
1.0
|
|
C
|
B:GLY60
|
3.9
|
20.9
|
1.0
|
|
N
|
B:GLN61
|
3.9
|
21.5
|
1.0
|
|
O
|
B:ALA11
|
4.0
|
14.9
|
1.0
|
|
N
|
B:GLY13
|
4.0
|
13.9
|
1.0
|
|
N
|
B:GLY12
|
4.0
|
14.8
|
1.0
|
|
O
|
B:HOH313
|
4.1
|
13.6
|
1.0
|
|
O
|
B:THR58
|
4.1
|
14.1
|
1.0
|
|
O3B
|
B:GDP201
|
4.1
|
12.8
|
1.0
|
|
MG
|
B:MG204
|
4.1
|
13.0
|
1.0
|
|
C
|
B:GLY12
|
4.2
|
14.7
|
1.0
|
|
C
|
B:ALA11
|
4.3
|
14.5
|
1.0
|
|
CA
|
B:ALA59
|
4.3
|
15.3
|
1.0
|
|
O
|
B:GLY10
|
4.5
|
14.6
|
1.0
|
|
OH
|
B:TYR32
|
4.5
|
15.4
|
1.0
|
|
O
|
B:ALA59
|
4.8
|
17.7
|
1.0
|
|
O
|
B:GLY60
|
4.9
|
22.3
|
1.0
|
|
N
|
B:THR35
|
4.9
|
14.5
|
1.0
|
|
CD
|
B:LYS16
|
4.9
|
13.3
|
1.0
|
|
Reference:
P.Baumann,
Y.Jin.
Hras(1-166) in Complex with Gdp and BEF3- To Be Published.
Page generated: Fri Aug 2 17:14:03 2024
|
