Magnesium in PDB 4dsu: 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: 4dsu 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)	26.02 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	79.553, 79.553, 78.055, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 20.3

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 4dsu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Small-Molecule Ligands Bind to A Distinct Pocket in Ras and Inhibit Sos-Mediated Nucleotide Exchange Activity, PDB code: 4dsu:

Magnesium binding site 1 out of 1 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:38.1 occ:1.00 O3B A:GDP201 2.1 25.9 1.0 OG A:SER17 2.2 31.6 1.0 O A:HOH304 2.3 31.4 1.0 O A:HOH309 2.3 37.5 1.0 O A:HOH305 2.3 39.9 1.0 O A:HOH346 2.3 33.7 1.0 CB A:SER17 3.2 30.2 1.0 PB A:GDP201 3.3 27.9 1.0 O1B A:GDP201 3.4 29.5 1.0 N A:SER17 3.9 27.2 1.0 OD2 A:ASP57 4.1 39.4 1.0 O1A A:GDP201 4.1 31.9 1.0 CA A:SER17 4.1 28.3 1.0 O A:ASP33 4.2 88.0 1.0 OD1 A:ASP57 4.2 38.0 1.0 O2B A:GDP201 4.3 27.4 1.0 CA A:PRO34 4.3 87.8 1.0 O3A A:GDP201 4.4 29.2 1.0 O A:THR58 4.5 37.5 1.0 O A:HOH356 4.5 47.9 1.0 PA A:GDP201 4.5 29.1 1.0 CG A:ASP57 4.6 38.0 1.0 O2A A:GDP201 4.6 30.5 1.0 C A:ASP33 4.8 88.8 1.0 CB A:LYS16 4.9 23.7 1.0 NZ A:LYS16 4.9 30.6 1.0 N A:PRO34 4.9 88.6 1.0 C A:PRO34 4.9 86.8 1.0 C A:LYS16 5.0 25.6 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