Magnesium in PDB 6d5m: Ras:Sos:Ras in Complex with A Small Molecule Activator

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5m was solved by J.Phan, T.Hodges, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.01 / 2.08
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.134, 183.134, 178.329, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.4

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Ras:Sos:Ras in Complex with A Small Molecule Activator (pdb code 6d5m). 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 Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5m:

Magnesium binding site 1 out of 1 in the Ras:Sos:Ras in Complex with A Small Molecule Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg201 b:11.7 occ:1.00 O1G Q:GNP202 1.9 18.2 1.0 O1B Q:GNP202 2.0 13.1 1.0 O Q:HOH330 2.0 15.0 1.0 OG1 Q:THR35 2.0 15.1 1.0 OG Q:SER17 2.1 14.4 1.0 O Q:HOH313 2.4 15.8 1.0 CB Q:THR35 3.1 16.4 1.0 PG Q:GNP202 3.1 16.0 1.0 CB Q:SER17 3.2 13.9 1.0 PB Q:GNP202 3.2 13.0 1.0 N3B Q:GNP202 3.3 13.5 1.0 N Q:THR35 3.8 16.0 1.0 N Q:SER17 3.8 16.6 1.0 OD2 Q:ASP57 4.0 20.9 1.0 O Q:HOH358 4.0 26.5 1.0 CA Q:THR35 4.0 15.6 1.0 O3G Q:GNP202 4.0 16.1 1.0 CA Q:SER17 4.1 14.2 1.0 O2A Q:GNP202 4.1 16.0 1.0 CG2 Q:THR35 4.2 14.2 1.0 O3A Q:GNP202 4.2 14.0 1.0 O2B Q:GNP202 4.2 14.1 1.0 OD1 Q:ASP57 4.2 18.0 1.0 O2G Q:GNP202 4.3 17.7 1.0 O Q:THR58 4.3 15.4 1.0 O Q:ASP33 4.4 16.6 1.0 PA Q:GNP202 4.5 16.4 1.0 CG Q:ASP57 4.5 16.7 1.0 O1A Q:GNP202 4.6 14.7 1.0 C Q:PRO34 4.8 18.6 1.0 CB Q:LYS16 4.8 12.9 1.0 C Q:LYS16 4.9 17.1 1.0 CE Q:LYS16 4.9 13.1 1.0

T.R.Hodges, J.R.Abbott, A.J.Little, D.Sarkar, J.M.Salovich, J.E.Howes, D.T.Akan, J.Sai, A.L.Arnold, C.Browning, M.C.Burns, T.Sobolik, Q.Sun, Y.Beesetty, J.A.Coker, D.Scharn, H.Stadtmueller, O.W.Rossanese, J.Phan, A.G.Waterson, D.B.Mcconnell, S.W.Fesik. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on Ras. J. Med. Chem. V. 61 8875 2018.
ISSN: ISSN 1520-4804
PubMed: 30205005
DOI: 10.1021/ACS.JMEDCHEM.8B01108