Phosphorus in PDB 1a4r: G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
Protein crystallography data
The structure of G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form, PDB code: 1a4r
was solved by
M.G.Rudolph,
I.R.Vetter,
A.Wittinghofer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.50
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.650,
98.650,
104.160,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.8 /
28
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
(pdb code 1a4r). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the
G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form, PDB code: 1a4r:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
Phosphorus binding site 1 out
of 4 in 1a4r
Go back to
Phosphorus Binding Sites List in 1a4r
Phosphorus binding site 1 out
of 4 in the G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P200
b:39.0
occ:1.00
|
PB
|
A:GDP200
|
0.0
|
39.0
|
1.0
|
O1B
|
A:GDP200
|
1.5
|
37.2
|
1.0
|
O2B
|
A:GDP200
|
1.5
|
38.9
|
1.0
|
O3B
|
A:GDP200
|
1.5
|
36.1
|
1.0
|
O3A
|
A:GDP200
|
1.6
|
33.4
|
1.0
|
PA
|
A:GDP200
|
2.9
|
31.7
|
1.0
|
MG
|
A:MG199
|
3.2
|
40.0
|
1.0
|
N
|
A:ALA13
|
3.4
|
39.2
|
1.0
|
O1A
|
A:GDP200
|
3.4
|
33.2
|
1.0
|
N
|
A:LYS16
|
3.5
|
31.7
|
1.0
|
O2A
|
A:GDP200
|
3.5
|
23.7
|
1.0
|
N
|
A:GLY15
|
3.5
|
31.9
|
1.0
|
O
|
A:HOH1002
|
3.7
|
30.3
|
1.0
|
NZ
|
A:LYS16
|
3.7
|
34.9
|
1.0
|
CA
|
A:ALA13
|
3.8
|
34.6
|
1.0
|
CA
|
A:GLY15
|
3.9
|
34.1
|
1.0
|
O5'
|
A:GDP200
|
3.9
|
27.3
|
1.0
|
N
|
A:VAL14
|
4.0
|
32.5
|
1.0
|
O
|
A:HOH1003
|
4.0
|
56.0
|
1.0
|
C
|
A:GLY15
|
4.0
|
31.8
|
1.0
|
O
|
A:HOH1006
|
4.1
|
52.9
|
1.0
|
C
|
A:ALA13
|
4.1
|
34.4
|
1.0
|
O
|
A:HOH1001
|
4.1
|
58.1
|
1.0
|
N
|
A:THR17
|
4.3
|
28.9
|
1.0
|
CB
|
A:LYS16
|
4.3
|
28.5
|
1.0
|
O
|
A:HOH1032
|
4.4
|
54.7
|
1.0
|
C5'
|
A:GDP200
|
4.4
|
32.1
|
1.0
|
CA
|
A:LYS16
|
4.4
|
26.3
|
1.0
|
C
|
A:VAL12
|
4.5
|
42.9
|
1.0
|
CG
|
A:LYS16
|
4.6
|
20.5
|
1.0
|
OG1
|
A:THR17
|
4.6
|
32.9
|
1.0
|
C
|
A:VAL14
|
4.7
|
30.4
|
1.0
|
CE
|
A:LYS16
|
4.8
|
20.8
|
1.0
|
CA
|
A:VAL12
|
4.8
|
41.4
|
1.0
|
O
|
A:ASP11
|
4.9
|
43.5
|
1.0
|
C
|
A:LYS16
|
4.9
|
27.2
|
1.0
|
CA
|
A:VAL14
|
4.9
|
26.7
|
1.0
|
O
|
A:ALA13
|
5.0
|
39.1
|
1.0
|
|
Phosphorus binding site 2 out
of 4 in 1a4r
Go back to
Phosphorus Binding Sites List in 1a4r
Phosphorus binding site 2 out
of 4 in the G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P200
b:31.7
occ:1.00
|
PA
|
A:GDP200
|
0.0
|
31.7
|
1.0
|
O1A
|
A:GDP200
|
1.5
|
33.2
|
1.0
|
O2A
|
A:GDP200
|
1.5
|
23.7
|
1.0
|
O5'
|
A:GDP200
|
1.6
|
27.3
|
1.0
|
O3A
|
A:GDP200
|
1.6
|
33.4
|
1.0
|
C5'
|
A:GDP200
|
2.7
|
32.1
|
1.0
|
PB
|
A:GDP200
|
2.9
|
39.0
|
1.0
|
O3B
|
A:GDP200
|
3.1
|
36.1
|
1.0
|
O1B
|
A:GDP200
|
3.5
|
37.2
|
1.0
|
CA
|
A:GLY15
|
3.6
|
34.1
|
1.0
|
C4'
|
A:GDP200
|
3.9
|
34.4
|
1.0
|
SG
|
A:CYS18
|
4.0
|
39.2
|
1.0
|
N
|
A:GLY15
|
4.0
|
31.9
|
1.0
|
O2B
|
A:GDP200
|
4.0
|
38.9
|
1.0
|
C
|
A:GLY15
|
4.1
|
31.8
|
1.0
|
O
|
A:HOH1003
|
4.2
|
56.0
|
1.0
|
O4'
|
A:GDP200
|
4.3
|
41.2
|
1.0
|
O
|
A:HOH1006
|
4.3
|
52.9
|
1.0
|
N
|
A:CYS18
|
4.4
|
34.3
|
1.0
|
C3'
|
A:GDP200
|
4.4
|
34.5
|
1.0
|
N
|
A:LYS16
|
4.4
|
31.7
|
1.0
|
C2'
|
A:GDP200
|
4.5
|
33.2
|
1.0
|
N
|
A:THR17
|
4.6
|
28.9
|
1.0
|
CB
|
A:THR17
|
4.6
|
32.4
|
1.0
|
C8
|
A:GDP200
|
4.6
|
29.1
|
1.0
|
MG
|
A:MG199
|
4.6
|
40.0
|
1.0
|
CB
|
A:CYS18
|
4.6
|
25.3
|
1.0
|
CG1
|
A:VAL33
|
4.7
|
36.6
|
1.0
|
CA
|
A:ALA13
|
4.8
|
34.6
|
1.0
|
O
|
A:GLY15
|
4.8
|
36.0
|
1.0
|
C
|
A:ALA13
|
4.9
|
34.4
|
1.0
|
C1'
|
A:GDP200
|
4.9
|
32.3
|
1.0
|
OG1
|
A:THR17
|
5.0
|
32.9
|
1.0
|
|
Phosphorus binding site 3 out
of 4 in 1a4r
Go back to
Phosphorus Binding Sites List in 1a4r
Phosphorus binding site 3 out
of 4 in the G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P400
b:80.0
occ:1.00
|
PB
|
B:GNH400
|
0.0
|
80.0
|
1.0
|
N3B
|
B:GNH400
|
1.5
|
74.9
|
1.0
|
O2B
|
B:GNH400
|
1.5
|
83.7
|
1.0
|
O1B
|
B:GNH400
|
1.5
|
81.2
|
1.0
|
O3A
|
B:GNH400
|
1.6
|
75.9
|
1.0
|
PA
|
B:GNH400
|
2.9
|
74.6
|
1.0
|
O1A
|
B:GNH400
|
3.5
|
75.4
|
1.0
|
N
|
B:ALA213
|
3.5
|
67.0
|
1.0
|
O2A
|
B:GNH400
|
3.5
|
78.7
|
1.0
|
NZ
|
B:LYS216
|
3.8
|
72.0
|
1.0
|
N
|
B:LYS216
|
3.9
|
55.0
|
1.0
|
CA
|
B:ALA213
|
3.9
|
65.6
|
1.0
|
O5'
|
B:GNH400
|
3.9
|
68.0
|
1.0
|
N
|
B:GLY215
|
4.1
|
63.5
|
1.0
|
OG1
|
B:THR217
|
4.3
|
66.7
|
1.0
|
N
|
B:THR217
|
4.4
|
59.5
|
1.0
|
CB
|
B:LYS216
|
4.4
|
57.4
|
1.0
|
C
|
B:ALA213
|
4.4
|
65.8
|
1.0
|
N
|
B:VAL214
|
4.4
|
66.8
|
1.0
|
C5'
|
B:GNH400
|
4.5
|
63.2
|
1.0
|
CA
|
B:GLY215
|
4.5
|
59.8
|
1.0
|
C
|
B:VAL212
|
4.6
|
64.8
|
1.0
|
C
|
B:GLY215
|
4.6
|
57.4
|
1.0
|
CA
|
B:LYS216
|
4.6
|
57.8
|
1.0
|
CA
|
B:VAL212
|
4.8
|
64.2
|
1.0
|
CG
|
B:LYS216
|
4.8
|
56.2
|
1.0
|
CG1
|
B:VAL212
|
4.8
|
66.5
|
1.0
|
CB
|
B:THR217
|
4.9
|
62.4
|
1.0
|
|
Phosphorus binding site 4 out
of 4 in 1a4r
Go back to
Phosphorus Binding Sites List in 1a4r
Phosphorus binding site 4 out
of 4 in the G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P400
b:74.6
occ:1.00
|
PA
|
B:GNH400
|
0.0
|
74.6
|
1.0
|
O1A
|
B:GNH400
|
1.5
|
75.4
|
1.0
|
O2A
|
B:GNH400
|
1.5
|
78.7
|
1.0
|
O5'
|
B:GNH400
|
1.6
|
68.0
|
1.0
|
O3A
|
B:GNH400
|
1.6
|
75.9
|
1.0
|
C5'
|
B:GNH400
|
2.7
|
63.2
|
1.0
|
PB
|
B:GNH400
|
2.9
|
80.0
|
1.0
|
O1B
|
B:GNH400
|
3.1
|
81.2
|
1.0
|
N3B
|
B:GNH400
|
3.7
|
74.9
|
1.0
|
C4'
|
B:GNH400
|
3.9
|
64.6
|
1.0
|
CA
|
B:GLY215
|
3.9
|
59.8
|
1.0
|
O2B
|
B:GNH400
|
4.0
|
83.7
|
1.0
|
C3'
|
B:GNH400
|
4.1
|
67.5
|
1.0
|
SG
|
B:CYS218
|
4.2
|
58.1
|
1.0
|
N
|
B:GLY215
|
4.3
|
63.5
|
1.0
|
C
|
B:GLY215
|
4.5
|
57.4
|
1.0
|
C2'
|
B:GNH400
|
4.5
|
70.2
|
1.0
|
CB
|
B:THR217
|
4.5
|
62.4
|
1.0
|
O4'
|
B:GNH400
|
4.5
|
66.2
|
1.0
|
N
|
B:LYS216
|
4.5
|
55.0
|
1.0
|
N
|
B:CYS218
|
4.5
|
50.1
|
1.0
|
N
|
B:THR217
|
4.6
|
59.5
|
1.0
|
OG1
|
B:THR217
|
4.7
|
66.7
|
1.0
|
CA
|
B:ALA213
|
4.7
|
65.6
|
1.0
|
C8
|
B:GNH400
|
4.8
|
53.8
|
1.0
|
CB
|
B:CYS218
|
4.9
|
48.8
|
1.0
|
C
|
B:ALA213
|
5.0
|
65.8
|
1.0
|
|
Reference:
M.G.Rudolph,
A.Wittinghofer,
I.R.Vetter.
Nucleotide Binding to the G12V-Mutant of CDC42 Investigated By X-Ray Diffraction and Fluorescence Spectroscopy: Two Different Nucleotide States in One Crystal. Protein Sci. V. 8 778 1999.
ISSN: ISSN 0961-8368
PubMed: 10211824
Page generated: Fri Sep 25 12:12:23 2020
|