Sodium in PDB 6d5j: 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: 6d5j 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)	48.72 / 1.75
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.627, 183.627, 179.056, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.5

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

Fluorine	(F)	1 atom
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 6d5j). 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: 6d5j:

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:34.8 occ:1.00 O C:HOH475 2.2 48.6 1.0 O C:HOH461 2.6 42.4 1.0 N C:THR87 2.9 14.1 0.7 N C:THR87 2.9 14.8 0.3 OG1 C:THR87 3.1 18.7 0.3 OG1 C:THR124 3.1 19.0 1.0 OG1 C:THR87 3.3 21.7 0.7 O C:HOH442 3.3 20.5 1.0 O C:ASN85 3.4 18.6 1.0 CA C:ASN86 3.6 15.6 1.0 CB C:THR87 3.7 19.3 0.7 CG2 C:THR87 3.7 21.0 0.3 CG2 C:THR124 3.7 23.5 1.0 C C:ASN86 3.7 14.2 1.0 CB C:THR87 3.7 19.5 0.3 CB C:THR124 3.7 18.1 1.0 CA C:THR87 3.9 16.9 0.7 CA C:THR87 3.9 16.6 0.3 C C:ASN85 4.0 19.7 1.0 N C:ASN86 4.0 16.6 1.0 O C:HOH398 4.5 54.7 1.0 O C:HOH441 4.5 37.6 1.0 CB C:ASN86 4.8 16.9 1.0 N C:LYS88 4.9 16.2 1.0 O C:ASN86 4.9 14.2 1.0 C C:THR87 5.0 14.2 0.7 C C:THR87 5.0 15.2 0.3 CG C:ASN86 5.0 19.8 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