Magnesium in PDB 4dsn: Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity

The structure of Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity, PDB code: 4dsn was solved by A.Oh, T.Maurer, L.S.Garrenton, K.Pitts, D.J.Anderson, N.J.Skelton, B.P.Fauber, B.Pan, S.Malek, D.Stokoe, M.Ludlam, K.K.Bowman, J.Wu, A.M.Giannetti, M.A.Starovasnik, I.Mellman, P.K.Jackson, J.Ruldolph, G.Fang, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.56 / 2.03
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	78.638, 78.638, 77.353, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.6

The binding sites of Magnesium atom in the Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity (pdb code 4dsn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity, PDB code: 4dsn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.6 occ:1.00 O1G A:GCP201 2.1 34.6 1.0 O2B A:GCP201 2.2 29.6 1.0 OG1 A:THR35 2.2 38.7 1.0 O A:HOH301 2.3 33.1 1.0 OG A:SER17 2.3 33.8 1.0 O A:HOH302 2.3 34.9 1.0 CB A:SER17 3.1 33.5 1.0 PB A:GCP201 3.2 29.8 1.0 CB A:THR35 3.2 39.3 1.0 PG A:GCP201 3.3 34.5 1.0 C3B A:GCP201 3.3 28.8 1.0 N A:SER17 3.8 27.0 1.0 N A:THR35 3.9 43.1 1.0 CA A:SER17 4.0 32.3 1.0 OD2 A:ASP57 4.0 39.8 1.0 O2A A:GCP201 4.1 33.8 1.0 CA A:THR35 4.2 42.0 1.0 O1B A:GCP201 4.2 31.0 1.0 O3G A:GCP201 4.2 35.5 1.0 OD1 A:ASP57 4.2 36.1 1.0 O2G A:GCP201 4.3 37.6 1.0 CG2 A:THR35 4.3 38.1 1.0 O3A A:GCP201 4.3 25.6 1.0 O A:ASP33 4.4 42.3 1.0 O A:THR58 4.4 31.1 1.0 CG A:ASP57 4.5 38.3 1.0 PA A:GCP201 4.6 31.4 1.0 CB A:LYS16 4.7 27.5 1.0 CE A:LYS16 4.7 25.5 1.0 C A:PRO34 4.8 43.7 1.0 O1A A:GCP201 4.9 33.1 1.0 C A:LYS16 4.9 26.1 1.0 NZ A:LYS16 4.9 26.1 1.0

Magnesium binding site 2 out of 2 in the Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:53.6 occ:1.00 OH A:TYR96 2.4 43.2 1.0 O A:HOH305 2.5 31.9 1.0 O A:ALA59 2.5 31.4 1.0 O A:GLY10 2.5 30.1 1.0 O A:GLY60 2.5 39.0 1.0 O A:HOH365 2.6 58.6 1.0 C A:GLY60 3.0 41.2 1.0 CA A:GLY60 3.3 34.0 1.0 CZ A:TYR96 3.5 40.3 1.0 C A:ALA59 3.5 34.0 1.0 C A:GLY10 3.5 29.5 1.0 O A:HOH329 3.6 43.4 1.0 N A:GLY60 3.9 32.9 1.0 CE1 A:TYR96 3.9 37.1 1.0 N A:GLY10 4.0 27.9 1.0 N A:GLN61 4.1 51.1 1.0 CA A:GLY10 4.3 28.7 1.0 N A:ALA11 4.4 28.3 1.0 O A:HOH321 4.4 58.2 1.0 CA A:ALA11 4.4 28.6 1.0 O A:HOH366 4.6 50.8 1.0 CE2 A:TYR96 4.6 35.6 1.0 CA A:GLN61 4.6 63.9 1.0 OH A:TYR71 4.6 45.2 1.0 CE A:LYS16 4.7 25.5 1.0 OG1 A:THR58 4.7 31.6 1.0 C A:ALA11 4.8 30.1 1.0 NZ A:LYS16 4.8 26.1 1.0 CA A:ALA59 4.9 33.0 1.0

T.Maurer, L.S.Garrenton, A.Oh, K.Pitts, D.J.Anderson, N.J.Skelton, B.P.Fauber, B.Pan, S.Malek, D.Stokoe, M.J.Ludlam, K.K.Bowman, J.Wu, A.M.Giannetti, M.A.Starovasnik, I.Mellman, P.K.Jackson, J.Rudolph, W.Wang, G.Fang. Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity. Proc.Natl.Acad.Sci.Usa V. 109 5299 2012.
ISSN: ISSN 0027-8424
PubMed: 22431598
DOI: 10.1073/PNAS.1116510109