Sodium in PDB 4l9s: Crystal Structure of H-Ras G12C, Gdp-Bound

All present enzymatic activity of Crystal Structure of H-Ras G12C, Gdp-Bound:
3.6.5.2;

The structure of Crystal Structure of H-Ras G12C, Gdp-Bound, PDB code: 4l9s was solved by J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.50 / 1.61
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	92.725, 92.725, 121.897, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 17.3

The structure of Crystal Structure of H-Ras G12C, Gdp-Bound also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of H-Ras G12C, Gdp-Bound (pdb code 4l9s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of H-Ras G12C, Gdp-Bound, PDB code: 4l9s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of H-Ras G12C, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of H-Ras G12C, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:21.6 occ:0.33 O A:HOH338 2.6 32.2 1.0 O A:HOH306 2.6 34.8 1.0 O A:HOH466 4.1 67.9 0.3 O A:HOH339 4.4 33.1 1.0 O A:THR124 4.4 22.9 1.0 OE2 A:GLU126 4.6 47.4 0.5 O A:HOH450 4.7 43.2 1.0 HE21 A:GLN129 4.8 47.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of H-Ras G12C, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of H-Ras G12C, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:32.6 occ:1.00 O A:HOH423 2.3 44.0 1.0 O A:HOH365 2.3 28.4 1.0 O A:GLY138 2.4 23.7 1.0 O A:HOH383 2.4 34.5 1.0 O A:HOH366 2.5 30.3 1.0 O A:HOH455 2.6 48.8 1.0 C A:GLY138 3.5 22.1 1.0 HA3 A:GLY138 3.5 27.7 1.0 HG22 A:ILE139 3.9 24.5 1.0 CA A:GLY138 4.0 23.1 1.0 O A:HOH405 4.1 48.3 1.0 HA A:ILE139 4.3 22.4 1.0 O A:HOH368 4.3 32.4 1.0 HG23 A:ILE139 4.4 24.5 1.0 O A:TYR137 4.5 27.4 1.0 O A:HOH363 4.5 20.4 1.0 OD2 A:ASP108 4.5 43.1 1.0 HA2 A:GLY138 4.5 27.7 1.0 N A:ILE139 4.6 20.7 1.0 CG2 A:ILE139 4.6 20.4 1.0 O A:HOH364 4.7 25.8 1.0 CA A:ILE139 4.9 18.6 1.0 HA A:ASP108 5.0 38.5 1.0

J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat. K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity and Effector Interactions. Nature V. 503 548 2013.
ISSN: ISSN 0028-0836
PubMed: 24256730
DOI: 10.1038/NATURE12796