Chlorine 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:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl201 b:52.3 occ:1.00 CL1 A:9LI201 0.0 52.3 1.0 C11 A:9LI201 1.7 55.5 1.0 C10 A:9LI201 2.7 47.2 1.0 C4 A:9LI201 2.8 61.1 1.0 C14 A:9LI201 3.4 66.8 1.0 C3 A:9LI201 3.4 65.8 1.0 O A:ILE55 3.8 32.0 1.0 C A:ILE55 3.8 30.1 1.0 C A:ASP54 3.9 32.3 1.0 CB A:ASP54 3.9 45.5 1.0 N A:ILE55 3.9 27.5 1.0 C9 A:9LI201 4.0 46.3 1.0 C15 A:9LI201 4.0 67.0 1.0 CB A:SER39 4.1 41.5 1.0 C5 A:9LI201 4.1 58.9 1.0 N A:LEU56 4.1 27.9 1.0 O A:ASP54 4.1 32.2 1.0 OG A:SER39 4.2 46.0 1.0 CA A:ASP54 4.2 36.1 1.0 CB A:LEU56 4.4 25.5 1.0 CA A:LEU56 4.4 25.9 1.0 O A:TYR40 4.4 35.1 1.0 CA A:ILE55 4.4 28.0 1.0 CA A:SER39 4.5 38.9 1.0 C8 A:9LI201 4.5 52.1 1.0 N16 A:9LI201 4.6 64.3 1.0 N A:TYR40 4.6 32.6 1.0 CD1 A:LEU56 4.7 25.8 1.0 C2 A:9LI201 4.7 66.2 1.0 CG A:ASP54 4.7 56.8 1.0 OD2 A:ASP54 4.8 62.8 1.0 C A:SER39 5.0 38.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl201 b:49.6 occ:1.00 CL2 A:9LI201 0.0 49.6 1.0 C9 A:9LI201 1.7 46.3 1.0 C8 A:9LI201 2.7 52.1 1.0 C10 A:9LI201 2.7 47.2 1.0 CA A:GLY75 3.4 25.5 1.0 CG2 A:VAL7 3.4 13.7 1.0 CB A:LYS5 3.5 35.1 1.0 N A:GLY75 3.5 26.6 1.0 OG1 A:THR74 3.6 31.3 1.0 C A:THR74 3.8 29.3 1.0 C5 A:9LI201 4.0 58.9 1.0 C11 A:9LI201 4.0 55.5 1.0 O A:THR74 4.0 28.3 1.0 CB A:THR74 4.2 30.2 1.0 CD A:LYS5 4.2 47.8 1.0 CG A:LYS5 4.3 40.2 1.0 C A:LYS5 4.3 32.2 1.0 CA A:LYS5 4.3 32.8 1.0 O A:LYS5 4.5 32.3 1.0 C4 A:9LI201 4.5 61.1 1.0 O A:LEU6 4.6 28.2 1.0 C A:GLY75 4.6 24.1 1.0 CA A:THR74 4.6 29.0 1.0 N A:LEU6 4.7 30.5 1.0 CB A:LEU56 4.8 25.5 1.0 O A:TYR71 4.8 31.5 1.0 C A:LEU6 4.8 25.6 1.0 N A:GLU76 4.8 25.2 1.0 O A:ASP54 4.9 32.2 1.0 CB A:VAL7 4.9 18.8 1.0 CD2 A:LEU56 5.0 28.0 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