Sodium in PDB 6e6g: Kras G13D Bound to Gdp (K13GDP)

The structure of Kras G13D Bound to Gdp (K13GDP), PDB code: 6e6g was solved by C.W.Johnson, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.00 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.096, 37.829, 100.171, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 22.5

The structure of Kras G13D Bound to Gdp (K13GDP) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Kras G13D Bound to Gdp (K13GDP) (pdb code 6e6g). 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 Kras G13D Bound to Gdp (K13GDP), PDB code: 6e6g:

Sodium binding site 1 out of 1 in the Kras G13D Bound to Gdp (K13GDP)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kras G13D Bound to Gdp (K13GDP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:40.4 occ:1.00 OD1 A:ASP13 2.4 28.3 1.0 O A:HOH373 2.5 38.5 1.0 O A:HOH424 2.9 35.9 1.0 O3B A:GDP201 2.9 19.7 1.0 O A:HOH345 3.6 21.1 1.0 CG A:ASP13 3.6 34.7 1.0 N A:ASP13 3.9 17.3 1.0 O2A A:GDP201 3.9 16.1 1.0 O A:HOH362 4.1 17.0 1.0 CA A:ASP13 4.1 16.1 1.0 PB A:GDP201 4.2 15.2 1.0 CB A:ASP13 4.3 22.5 1.0 O3A A:GDP201 4.4 15.9 1.0 OD2 A:ASP13 4.5 46.6 1.0 C5' A:GDP201 4.6 17.3 1.0 PA A:GDP201 4.7 14.9 1.0 O A:HOH411 4.9 20.2 1.0 C A:GLY12 4.9 17.1 1.0

C.W.Johnson, Y.J.Lin, D.Reid, J.Parker, S.Pavlopoulos, P.Dischinger, C.Graveel, A.J.Aguirre, M.Steensma, K.M.Haigis, C.Mattos. Isoform-Specific Destabilization of the Active Site Reveals A Molecular Mechanism of Intrinsic Activation of Kras G13D. Cell Rep V. 28 1538 2019.
ISSN: ESSN 2211-1247
PubMed: 31390567
DOI: 10.1016/J.CELREP.2019.07.026