Sodium in PDB 6bvk: 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: 6bvk was solved by J.Phan, J.Abbott, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.53 / 1.80
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.421, 184.421, 179.008, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.9

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

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Ras:Sos:Ras in Complex with A Small Molecule Activator (pdb code 6bvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6bvk:

Sodium 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 Sodium with other atoms in the Na 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 C:Na202 b:33.3 occ:1.00 O C:HOH483 2.3 47.3 1.0 O C:HOH481 2.8 38.8 1.0 N C:THR87 2.9 13.3 0.7 N C:THR87 2.9 13.5 0.3 OG1 C:THR124 3.2 17.0 1.0 OG1 C:THR87 3.2 15.7 0.3 OG1 C:THR87 3.3 20.5 0.7 O C:HOH444 3.3 18.8 1.0 O C:ASN85 3.4 16.2 1.0 CA C:ASN86 3.5 12.6 1.0 CG2 C:THR87 3.7 18.4 0.3 C C:ASN86 3.7 15.1 1.0 CB C:THR87 3.7 17.6 0.7 CG2 C:THR124 3.8 22.8 1.0 CB C:THR87 3.8 17.1 0.3 CB C:THR124 3.8 18.2 1.0 CA C:THR87 3.9 13.6 0.7 CA C:THR87 3.9 14.4 0.3 C C:ASN85 3.9 17.7 1.0 N C:ASN86 4.0 13.7 1.0 O C:HOH346 4.0 56.6 1.0 O C:HOH427 4.6 39.0 1.0 CB C:ASN86 4.7 15.5 1.0 O C:HOH413 4.8 52.9 1.0 N C:LYS88 4.9 14.2 1.0 O C:ASN86 4.9 13.1 1.0 CG C:ASN86 4.9 20.8 1.0 C C:THR87 5.0 9.6 0.7 C C:THR87 5.0 15.2 0.3

J.R.Abbott, T.R.Hodges, R.N.Daniels, P.A.Patel, J.P.Kennedy, J.E.Howes, D.T.Akan, M.C.Burns, J.Sai, T.Sobolik, Y.Beesetty, T.Lee, O.W.Rossanese, J.Phan, A.G.Waterson, S.W.Fesik. Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate Ras Signaling. J. Med. Chem. V. 61 6002 2018.
ISSN: ISSN 1520-4804
PubMed: 29856609
DOI: 10.1021/ACS.JMEDCHEM.8B00360