Phosphorus in PDB 1a4r: G12V Mutant of Human Placental CDC42 Gtpase in the Gdp Form

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

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 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 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 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 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

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