Sodium in PDB 4lpk: Crystal Structure of K-Ras Wt, Gdp-Bound

The structure of Crystal Structure of K-Ras Wt, Gdp-Bound, PDB code: 4lpk 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)	20.96 / 1.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.282, 84.282, 41.267, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 19.2

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

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of K-Ras Wt, Gdp-Bound (pdb code 4lpk). 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 K-Ras Wt, Gdp-Bound, PDB code: 4lpk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of K-Ras Wt, 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 K-Ras Wt, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:27.1 occ:1.00 OE1 A:GLU37 2.4 14.8 1.0 O A:HOH321 2.4 41.9 1.0 O A:ALA59 2.5 20.6 1.0 O A:HOH363 2.5 34.4 1.0 O A:HOH328 2.5 31.4 1.0 H A:ALA59 3.2 18.4 1.0 CD A:GLU37 3.4 13.3 1.0 C A:ALA59 3.6 20.7 1.0 OE2 A:GLU37 3.7 15.8 1.0 HB A:THR58 3.8 16.1 1.0 O A:HOH454 3.8 50.3 1.0 N A:ALA59 3.9 15.3 1.0 HA2 A:GLY60 4.2 19.1 1.0 CA A:ALA59 4.3 15.1 1.0 HB3 A:ALA59 4.5 24.3 1.0 O A:GLY60 4.5 24.2 1.0 HB2 A:GLU37 4.6 20.1 1.0 N A:GLY60 4.6 18.1 1.0 HA A:THR58 4.6 17.4 1.0 CB A:THR58 4.7 13.4 1.0 CA A:GLY60 4.8 15.9 1.0 CG A:GLU37 4.8 19.8 1.0 O A:HOH388 4.8 40.3 1.0 C A:THR58 4.9 14.3 1.0 CB A:ALA59 5.0 20.3 1.0 C A:GLY60 5.0 21.1 1.0 CA A:THR58 5.0 14.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of K-Ras Wt, 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 K-Ras Wt, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:34.6 occ:0.33 O B:HOH337 2.3 32.6 1.0 O B:HOH370 2.5 31.0 1.0 O B:HOH400 4.2 42.9 1.0 O B:THR124 4.3 15.5 1.0 HE21 B:GLN129 4.4 19.7 1.0 OE1 B:GLN129 4.7 21.4 1.0 O B:HOH443 5.0 38.6 0.3 NE2 B:GLN129 5.0 16.4 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