Phosphorus in PDB 1a2k: Gdpran-NTF2 Complex
Protein crystallography data
The structure of Gdpran-NTF2 Complex, PDB code: 1a2k
was solved by
M.Stewart,
H.M.Kent,
A.J.Mccoy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
7.00 /
2.50
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
155.150,
120.540,
108.920,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
21.5 /
27.3
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Gdpran-NTF2 Complex
(pdb code 1a2k). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the
Gdpran-NTF2 Complex, PDB code: 1a2k:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
Phosphorus binding site 1 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 1 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P220
b:29.6
occ:1.00
|
PB
|
C:GDP220
|
0.0
|
29.6
|
1.0
|
|
O3B
|
C:GDP220
|
1.4
|
30.0
|
1.0
|
|
O2B
|
C:GDP220
|
1.5
|
36.4
|
1.0
|
|
O1B
|
C:GDP220
|
1.5
|
26.6
|
1.0
|
|
O3A
|
C:GDP220
|
1.6
|
33.3
|
1.0
|
|
PA
|
C:GDP220
|
3.0
|
33.4
|
1.0
|
|
MG
|
C:MG221
|
3.1
|
22.6
|
1.0
|
|
O5'
|
C:GDP220
|
3.3
|
32.0
|
1.0
|
|
O
|
C:HOH246
|
3.3
|
29.8
|
1.0
|
|
N
|
C:GLY20
|
3.5
|
20.6
|
1.0
|
|
O
|
C:HOH247
|
3.6
|
19.0
|
1.0
|
|
O1A
|
C:GDP220
|
3.7
|
35.2
|
1.0
|
|
N
|
C:LYS23
|
3.8
|
18.9
|
1.0
|
|
CA
|
C:GLY20
|
3.8
|
22.4
|
1.0
|
|
O2A
|
C:GDP220
|
4.0
|
40.0
|
1.0
|
|
N
|
C:GLY22
|
4.0
|
24.7
|
1.0
|
|
N
|
C:THR21
|
4.0
|
25.1
|
1.0
|
|
C5'
|
C:GDP220
|
4.1
|
31.8
|
1.0
|
|
NZ
|
C:LYS23
|
4.1
|
29.7
|
1.0
|
|
N
|
C:THR24
|
4.2
|
27.4
|
1.0
|
|
C
|
C:GLY20
|
4.2
|
26.0
|
1.0
|
|
O
|
C:HOH249
|
4.2
|
13.7
|
1.0
|
|
CA
|
C:GLY22
|
4.4
|
20.7
|
1.0
|
|
CB
|
C:LYS23
|
4.5
|
28.1
|
1.0
|
|
OE2
|
C:GLU70
|
4.5
|
25.0
|
1.0
|
|
C
|
C:GLY22
|
4.5
|
22.8
|
1.0
|
|
CA
|
C:LYS23
|
4.5
|
25.1
|
1.0
|
|
C
|
C:GLY19
|
4.6
|
23.4
|
1.0
|
|
OG1
|
C:THR24
|
4.7
|
22.6
|
1.0
|
|
CG
|
C:LYS23
|
4.8
|
26.9
|
1.0
|
|
CB
|
C:THR24
|
4.8
|
24.2
|
1.0
|
|
CA
|
C:GLY19
|
4.9
|
20.1
|
1.0
|
|
C
|
C:LYS23
|
4.9
|
29.5
|
1.0
|
|
CE
|
C:LYS23
|
4.9
|
26.1
|
1.0
|
|
O
|
C:ASP18
|
5.0
|
31.8
|
1.0
|
|
C
|
C:THR21
|
5.0
|
27.8
|
1.0
|
|
Phosphorus binding site 2 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 2 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P220
b:33.4
occ:1.00
|
PA
|
C:GDP220
|
0.0
|
33.4
|
1.0
|
|
O1A
|
C:GDP220
|
1.5
|
35.2
|
1.0
|
|
O2A
|
C:GDP220
|
1.5
|
40.0
|
1.0
|
|
O5'
|
C:GDP220
|
1.6
|
32.0
|
1.0
|
|
O3A
|
C:GDP220
|
1.6
|
33.3
|
1.0
|
|
C5'
|
C:GDP220
|
2.6
|
31.8
|
1.0
|
|
PB
|
C:GDP220
|
3.0
|
29.6
|
1.0
|
|
O3B
|
C:GDP220
|
3.4
|
30.0
|
1.0
|
|
OG1
|
C:THR25
|
3.5
|
25.1
|
1.0
|
|
O1B
|
C:GDP220
|
3.7
|
26.6
|
1.0
|
|
C4'
|
C:GDP220
|
3.7
|
34.0
|
1.0
|
|
O
|
C:HOH247
|
3.8
|
19.0
|
1.0
|
|
CA
|
C:GLY22
|
4.0
|
20.7
|
1.0
|
|
O2B
|
C:GDP220
|
4.1
|
36.4
|
1.0
|
|
C3'
|
C:GDP220
|
4.1
|
37.9
|
1.0
|
|
N
|
C:THR25
|
4.2
|
21.8
|
1.0
|
|
N
|
C:THR24
|
4.2
|
27.4
|
1.0
|
|
C
|
C:GLY22
|
4.3
|
22.8
|
1.0
|
|
CB
|
C:THR24
|
4.3
|
24.2
|
1.0
|
|
N
|
C:GLY22
|
4.3
|
24.7
|
1.0
|
|
O4'
|
C:GDP220
|
4.4
|
33.5
|
1.0
|
|
N
|
C:LYS23
|
4.4
|
18.9
|
1.0
|
|
C2'
|
C:GDP220
|
4.4
|
37.3
|
1.0
|
|
CB
|
C:THR25
|
4.6
|
21.6
|
1.0
|
|
MG
|
C:MG221
|
4.6
|
22.6
|
1.0
|
|
CA
|
C:THR24
|
4.7
|
28.9
|
1.0
|
|
C8
|
C:GDP220
|
4.8
|
35.7
|
1.0
|
|
C
|
C:THR24
|
4.9
|
26.0
|
1.0
|
|
O
|
C:GLY22
|
4.9
|
27.3
|
1.0
|
|
CA
|
C:GLY20
|
5.0
|
22.4
|
1.0
|
|
C1'
|
C:GDP220
|
5.0
|
35.2
|
1.0
|
|
CA
|
C:THR25
|
5.0
|
26.0
|
1.0
|
|
Phosphorus binding site 3 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 3 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:P220
b:32.3
occ:1.00
|
PB
|
D:GDP220
|
0.0
|
32.3
|
1.0
|
|
O3B
|
D:GDP220
|
1.4
|
32.6
|
1.0
|
|
O2B
|
D:GDP220
|
1.5
|
35.9
|
1.0
|
|
O1B
|
D:GDP220
|
1.5
|
30.9
|
1.0
|
|
O3A
|
D:GDP220
|
1.6
|
33.4
|
1.0
|
|
PA
|
D:GDP220
|
3.0
|
35.1
|
1.0
|
|
MG
|
D:MG221
|
3.2
|
26.5
|
1.0
|
|
O
|
D:HOH346
|
3.3
|
29.0
|
1.0
|
|
O5'
|
D:GDP220
|
3.3
|
37.6
|
1.0
|
|
O
|
D:HOH347
|
3.5
|
22.4
|
1.0
|
|
O
|
D:HOH355
|
3.6
|
27.0
|
1.0
|
|
N
|
D:GLY20
|
3.6
|
21.4
|
1.0
|
|
NZ
|
D:LYS23
|
3.7
|
21.7
|
1.0
|
|
O1A
|
D:GDP220
|
3.8
|
37.5
|
1.0
|
|
N
|
D:GLY22
|
3.8
|
25.8
|
1.0
|
|
N
|
D:LYS23
|
3.9
|
15.8
|
1.0
|
|
O2A
|
D:GDP220
|
4.0
|
42.3
|
1.0
|
|
CA
|
D:GLY20
|
4.0
|
15.3
|
1.0
|
|
N
|
D:THR21
|
4.1
|
14.7
|
1.0
|
|
C5'
|
D:GDP220
|
4.2
|
36.9
|
1.0
|
|
N
|
D:THR24
|
4.3
|
25.5
|
1.0
|
|
O
|
D:HOH349
|
4.3
|
16.5
|
1.0
|
|
C
|
D:GLY20
|
4.3
|
13.2
|
1.0
|
|
CA
|
D:GLY22
|
4.3
|
22.5
|
1.0
|
|
CB
|
D:LYS23
|
4.3
|
15.2
|
1.0
|
|
C
|
D:GLY22
|
4.4
|
20.7
|
1.0
|
|
CA
|
D:LYS23
|
4.5
|
21.4
|
1.0
|
|
C
|
D:GLY19
|
4.6
|
23.6
|
1.0
|
|
OE2
|
D:GLU70
|
4.7
|
17.1
|
1.0
|
|
CE
|
D:LYS23
|
4.7
|
18.7
|
1.0
|
|
OG1
|
D:THR24
|
4.8
|
27.5
|
1.0
|
|
CG
|
D:LYS23
|
4.8
|
20.1
|
1.0
|
|
CA
|
D:GLY19
|
4.8
|
21.9
|
1.0
|
|
C
|
D:THR21
|
4.9
|
26.1
|
1.0
|
|
C
|
D:LYS23
|
4.9
|
26.3
|
1.0
|
|
CB
|
D:THR24
|
4.9
|
31.2
|
1.0
|
|
OG1
|
D:THR21
|
4.9
|
34.4
|
1.0
|
|
CA
|
D:THR21
|
5.0
|
23.2
|
1.0
|
|
Phosphorus binding site 4 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 4 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:P220
b:35.1
occ:1.00
|
PA
|
D:GDP220
|
0.0
|
35.1
|
1.0
|
|
O1A
|
D:GDP220
|
1.5
|
37.5
|
1.0
|
|
O2A
|
D:GDP220
|
1.5
|
42.3
|
1.0
|
|
O3A
|
D:GDP220
|
1.6
|
33.4
|
1.0
|
|
O5'
|
D:GDP220
|
1.6
|
37.6
|
1.0
|
|
C5'
|
D:GDP220
|
2.5
|
36.9
|
1.0
|
|
PB
|
D:GDP220
|
3.0
|
32.3
|
1.0
|
|
O3B
|
D:GDP220
|
3.4
|
32.6
|
1.0
|
|
C4'
|
D:GDP220
|
3.7
|
32.8
|
1.0
|
|
O1B
|
D:GDP220
|
3.7
|
30.9
|
1.0
|
|
OG1
|
D:THR25
|
3.7
|
30.3
|
1.0
|
|
O
|
D:HOH347
|
3.8
|
22.4
|
1.0
|
|
O
|
D:HOH355
|
3.9
|
27.0
|
1.0
|
|
CA
|
D:GLY22
|
4.0
|
22.5
|
1.0
|
|
O2B
|
D:GDP220
|
4.1
|
35.9
|
1.0
|
|
C3'
|
D:GDP220
|
4.1
|
36.2
|
1.0
|
|
O4'
|
D:GDP220
|
4.2
|
30.8
|
1.0
|
|
N
|
D:THR25
|
4.2
|
24.4
|
1.0
|
|
N
|
D:GLY22
|
4.2
|
25.8
|
1.0
|
|
C2'
|
D:GDP220
|
4.4
|
34.3
|
1.0
|
|
C
|
D:GLY22
|
4.4
|
20.7
|
1.0
|
|
CB
|
D:THR24
|
4.5
|
31.2
|
1.0
|
|
CB
|
D:THR25
|
4.6
|
23.1
|
1.0
|
|
N
|
D:THR24
|
4.6
|
25.5
|
1.0
|
|
MG
|
D:MG221
|
4.6
|
26.5
|
1.0
|
|
N
|
D:LYS23
|
4.7
|
15.8
|
1.0
|
|
C8
|
D:GDP220
|
4.8
|
29.9
|
1.0
|
|
C1'
|
D:GDP220
|
4.9
|
32.0
|
1.0
|
|
CA
|
D:THR24
|
5.0
|
27.2
|
1.0
|
|
Phosphorus binding site 5 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 5 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:P220
b:33.0
occ:1.00
|
PB
|
E:GDP220
|
0.0
|
33.0
|
1.0
|
|
O3B
|
E:GDP220
|
1.4
|
28.1
|
1.0
|
|
O2B
|
E:GDP220
|
1.5
|
33.5
|
1.0
|
|
O1B
|
E:GDP220
|
1.5
|
31.7
|
1.0
|
|
O3A
|
E:GDP220
|
1.6
|
38.4
|
1.0
|
|
PA
|
E:GDP220
|
3.0
|
32.5
|
1.0
|
|
MG
|
E:MG221
|
3.1
|
25.3
|
1.0
|
|
O5'
|
E:GDP220
|
3.3
|
37.8
|
1.0
|
|
O
|
E:HOH446
|
3.4
|
22.3
|
1.0
|
|
O
|
E:HOH447
|
3.4
|
27.1
|
1.0
|
|
N
|
E:LYS23
|
3.6
|
29.9
|
1.0
|
|
NZ
|
E:LYS23
|
3.6
|
15.9
|
1.0
|
|
N
|
E:GLY20
|
3.8
|
27.8
|
1.0
|
|
O1A
|
E:GDP220
|
3.8
|
36.8
|
1.0
|
|
N
|
E:GLY22
|
3.9
|
29.6
|
1.0
|
|
O2A
|
E:GDP220
|
3.9
|
38.3
|
1.0
|
|
N
|
E:THR24
|
4.0
|
26.9
|
1.0
|
|
CB
|
E:LYS23
|
4.0
|
25.4
|
1.0
|
|
N
|
E:THR21
|
4.1
|
28.1
|
1.0
|
|
CA
|
E:GLY20
|
4.2
|
22.6
|
1.0
|
|
O
|
E:HOH449
|
4.2
|
35.1
|
1.0
|
|
CA
|
E:GLY22
|
4.3
|
33.2
|
1.0
|
|
CA
|
E:LYS23
|
4.3
|
30.0
|
1.0
|
|
C
|
E:GLY22
|
4.3
|
30.2
|
1.0
|
|
OE2
|
E:GLU70
|
4.4
|
20.6
|
1.0
|
|
C5'
|
E:GDP220
|
4.4
|
38.5
|
1.0
|
|
C
|
E:GLY20
|
4.4
|
25.1
|
1.0
|
|
OG1
|
E:THR24
|
4.5
|
24.5
|
1.0
|
|
CE
|
E:LYS23
|
4.5
|
10.1
|
1.0
|
|
CG
|
E:LYS23
|
4.6
|
24.7
|
1.0
|
|
C
|
E:LYS23
|
4.7
|
29.4
|
1.0
|
|
CB
|
E:THR24
|
4.7
|
28.3
|
1.0
|
|
OG1
|
E:THR21
|
4.8
|
34.8
|
1.0
|
|
C
|
E:GLY19
|
4.8
|
31.2
|
1.0
|
|
C
|
E:THR21
|
4.9
|
30.7
|
1.0
|
|
CA
|
E:THR24
|
4.9
|
28.9
|
1.0
|
|
CA
|
E:THR21
|
5.0
|
30.9
|
1.0
|
|
Phosphorus binding site 6 out
of 6 in 1a2k
Go back to
Phosphorus Binding Sites List in 1a2k
Phosphorus binding site 6 out
of 6 in the Gdpran-NTF2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Gdpran-NTF2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:P220
b:32.5
occ:1.00
|
PA
|
E:GDP220
|
0.0
|
32.5
|
1.0
|
|
O1A
|
E:GDP220
|
1.5
|
36.8
|
1.0
|
|
O2A
|
E:GDP220
|
1.5
|
38.3
|
1.0
|
|
O3A
|
E:GDP220
|
1.5
|
38.4
|
1.0
|
|
O5'
|
E:GDP220
|
1.6
|
37.8
|
1.0
|
|
C5'
|
E:GDP220
|
2.5
|
38.5
|
1.0
|
|
PB
|
E:GDP220
|
3.0
|
33.0
|
1.0
|
|
O3B
|
E:GDP220
|
3.5
|
28.1
|
1.0
|
|
O
|
E:HOH447
|
3.5
|
27.1
|
1.0
|
|
C4'
|
E:GDP220
|
3.7
|
35.9
|
1.0
|
|
O1B
|
E:GDP220
|
3.7
|
31.7
|
1.0
|
|
OG1
|
E:THR25
|
3.8
|
26.3
|
1.0
|
|
CA
|
E:GLY22
|
3.9
|
33.2
|
1.0
|
|
O2B
|
E:GDP220
|
4.0
|
33.5
|
1.0
|
|
O4'
|
E:GDP220
|
4.2
|
36.2
|
1.0
|
|
C3'
|
E:GDP220
|
4.2
|
38.8
|
1.0
|
|
N
|
E:GLY22
|
4.2
|
29.6
|
1.0
|
|
N
|
E:THR25
|
4.3
|
29.0
|
1.0
|
|
C
|
E:GLY22
|
4.4
|
30.2
|
1.0
|
|
CB
|
E:THR24
|
4.4
|
28.3
|
1.0
|
|
N
|
E:THR24
|
4.4
|
26.9
|
1.0
|
|
N
|
E:LYS23
|
4.5
|
29.9
|
1.0
|
|
MG
|
E:MG221
|
4.6
|
25.3
|
1.0
|
|
C2'
|
E:GDP220
|
4.6
|
35.4
|
1.0
|
|
CB
|
E:THR25
|
4.8
|
27.2
|
1.0
|
|
CA
|
E:THR24
|
4.8
|
28.9
|
1.0
|
|
C8
|
E:GDP220
|
4.8
|
28.2
|
1.0
|
|
OG1
|
E:THR24
|
5.0
|
24.5
|
1.0
|
|
Reference:
M.Stewart,
H.M.Kent,
A.J.Mccoy.
Structural Basis For Molecular Recognition Between Nuclear Transport Factor 2 (NTF2) and the Gdp-Bound Form of the Ras-Family Gtpase Ran. J.Mol.Biol. V. 277 635 1998.
ISSN: ISSN 0022-2836
PubMed: 9533885
DOI: 10.1006/JMBI.1997.1602
Page generated: Fri Sep 25 12:03:46 2020
|
