Magnesium in PDB 6v9f: Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods

The structure of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods, PDB code: 6v9f was solved by J.Phan, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.11 / 1.85
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.851, 183.851, 178.740, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.1

The structure of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods (pdb code 6v9f). 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 Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods, PDB code: 6v9f:

Magnesium binding site 1 out of 1 in the Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:5.6 occ:1.00 O2G A:GNP201 2.0 21.5 1.0 O2B A:GNP201 2.0 19.7 1.0 O A:HOH322 2.1 17.8 1.0 OG1 A:THR35 2.1 22.9 1.0 O A:HOH341 2.2 20.3 1.0 OG A:SER17 2.2 18.9 1.0 CB A:THR35 3.1 21.8 1.0 CB A:SER17 3.2 20.5 1.0 PG A:GNP201 3.2 20.3 1.0 PB A:GNP201 3.2 19.3 1.0 N3B A:GNP201 3.4 20.1 1.0 N A:THR35 3.8 21.1 1.0 N A:SER17 3.9 18.9 1.0 OD2 A:ASP57 4.0 24.4 1.0 O3G A:GNP201 4.1 20.0 1.0 CA A:THR35 4.1 21.3 1.0 CA A:SER17 4.1 18.5 1.0 O2A A:GNP201 4.2 22.4 1.0 CG2 A:THR35 4.2 19.5 1.0 O B:HOH2384 4.2 37.5 1.0 OD1 A:ASP57 4.3 22.5 1.0 O1B A:GNP201 4.3 18.7 1.0 O3A A:GNP201 4.3 21.1 1.0 O1G A:GNP201 4.3 24.3 1.0 O A:THR58 4.4 23.5 1.0 O A:ASP33 4.4 21.0 1.0 CG A:ASP57 4.5 20.8 1.0 PA A:GNP201 4.6 21.4 1.0 O1A A:GNP201 4.6 18.9 1.0 C A:PRO34 4.8 21.1 1.0 CB A:LYS16 4.9 15.1 1.0 C A:LYS16 4.9 19.8 1.0 CE A:LYS16 5.0 19.1 1.0 CA A:PRO34 5.0 18.9 1.0

D.Sarkar, E.T.Olejniczak, J.Phan, J.A.Coker, J.Sai, A.Arnold, Y.Beesetty, A.G.Waterson, S.W.Fesik. Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on Ras Using Fragment-Based Methods. J.Med.Chem. V. 63 8325 2020.
ISSN: ISSN 0022-2623
PubMed: 32673492
DOI: 10.1021/ACS.JMEDCHEM.0C00511