Magnesium in PDB 4dst: 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: 4dst 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)	25.79 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	78.923, 78.923, 78.631, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 20.9

The structure of Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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 4dst). 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: 4dst:
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:Mg203 b:32.2 occ:1.00 O2B A:GCP202 2.2 23.0 1.0 O1G A:GCP202 2.2 27.3 1.0 OG A:SER17 2.3 24.4 1.0 O A:HOH302 2.3 24.7 1.0 O A:HOH301 2.3 29.3 1.0 OG1 A:THR35 2.4 30.9 1.0 CB A:THR35 3.1 26.8 1.0 CB A:SER17 3.2 26.2 1.0 PB A:GCP202 3.3 23.4 1.0 PG A:GCP202 3.4 25.4 1.0 C3B A:GCP202 3.5 14.3 1.0 N A:SER17 3.8 27.6 1.0 OD2 A:ASP57 3.9 31.8 1.0 N A:THR35 3.9 31.5 1.0 CA A:SER17 4.1 26.2 1.0 CA A:THR35 4.1 26.2 1.0 CG2 A:THR35 4.2 25.2 1.0 O2A A:GCP202 4.2 26.0 1.0 OD1 A:ASP57 4.2 31.7 1.0 O1B A:GCP202 4.3 20.4 1.0 O3G A:GCP202 4.3 30.1 1.0 O2G A:GCP202 4.4 27.5 1.0 O A:THR58 4.4 28.9 1.0 CG A:ASP57 4.4 28.8 1.0 O3A A:GCP202 4.4 23.2 1.0 O A:ASP33 4.5 26.5 1.0 CB A:LYS16 4.6 19.7 1.0 PA A:GCP202 4.7 24.6 1.0 CE A:LYS16 4.8 18.1 1.0 C A:LYS16 4.8 28.7 1.0 C A:PRO34 4.9 31.6 1.0 O1A A:GCP202 4.9 26.5 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:Mg208 b:38.0 occ:1.00 OH A:TYR96 2.4 24.6 1.0 O A:HOH305 2.5 20.4 1.0 O A:HOH308 2.5 39.5 1.0 O A:GLY60 2.6 29.7 1.0 O A:GLY10 2.6 23.8 1.0 O A:ALA59 2.7 21.3 1.0 C A:GLY60 3.1 25.7 1.0 CA A:GLY60 3.4 23.5 1.0 CZ A:TYR96 3.4 25.4 1.0 C A:GLY10 3.5 21.1 1.0 C A:ALA59 3.7 23.2 1.0 O A:HOH335 3.7 32.3 1.0 CE1 A:TYR96 3.7 25.9 1.0 N A:GLY10 4.0 16.3 1.0 N A:GLN61 4.0 29.9 1.0 N A:GLY60 4.0 26.9 1.0 O A:HOH344 4.3 34.8 1.0 CA A:GLY10 4.3 19.0 1.0 N A:ALA11 4.4 23.4 1.0 O A:HOH323 4.4 24.3 1.0 CA A:ALA11 4.5 22.9 1.0 O A:HOH390 4.6 45.7 1.0 CE2 A:TYR96 4.6 26.3 1.0 CA A:GLN61 4.6 41.6 1.0 OH A:TYR71 4.7 28.9 1.0 OG1 A:THR58 4.7 18.8 1.0 NZ A:LYS16 4.8 16.1 1.0 CE A:LYS16 4.8 18.1 1.0 C A:ALA11 4.9 23.3 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