Sodium in PDB 6e6p: Hras G13D Bound to Gppnhp (Ha,B,C13GNP)

All present enzymatic activity of Hras G13D Bound to Gppnhp (Ha,B,C13GNP):
3.6.5.2;

The structure of Hras G13D Bound to Gppnhp (Ha,B,C13GNP), PDB code: 6e6p 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)	40.10 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.649, 75.567, 94.722, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.7

The structure of Hras G13D Bound to Gppnhp (Ha,B,C13GNP) also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Hras G13D Bound to Gppnhp (Ha,B,C13GNP) (pdb code 6e6p). 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 Hras G13D Bound to Gppnhp (Ha,B,C13GNP), PDB code: 6e6p:

Sodium binding site 1 out of 1 in the Hras G13D Bound to Gppnhp (Ha,B,C13GNP)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hras G13D Bound to Gppnhp (Ha,B,C13GNP) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:38.0 occ:1.00 O C:HOH373 2.3 43.7 1.0 OD1 C:ASP13 2.3 37.9 1.0 O C:HOH375 2.4 50.1 1.0 O C:HOH322 2.5 39.5 1.0 O C:HOH348 2.5 38.7 1.0 OD2 C:ASP13 2.6 43.1 1.0 CG C:ASP13 2.8 42.2 1.0 O C:HOH386 3.4 55.6 1.0 O C:HOH355 4.1 51.3 1.0 CG C:PRO34 4.2 44.3 1.0 CB C:ASP13 4.3 33.9 1.0 O C:TYR32 4.5 41.6 1.0 CD C:PRO34 4.7 46.5 1.0 O2G C:GNP201 4.7 35.5 1.0 C5' C:GNP201 4.9 28.2 1.0 N C:PRO34 4.9 38.5 1.0 CB C:PRO34 4.9 40.2 1.0 CA C:ASP13 5.0 29.1 1.0 CA C:PRO34 5.0 40.5 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