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

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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

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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

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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

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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

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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

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