Sodium in PDB 5wdq: H-Ras Mutant L120A Bound to Gmp-Pnp at 100K

All present enzymatic activity of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K:
3.6.5.2;

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K, PDB code: 5wdq was solved by P.Bandaru, C.L.Gee, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.37 / 1.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	87.960, 87.960, 133.105, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 15

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K (pdb code 5wdq). 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 H-Ras Mutant L120A Bound to Gmp-Pnp at 100K, PDB code: 5wdq:

Sodium binding site 1 out of 1 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:48.4 occ:1.00 OD1 A:ASP92 2.2 21.4 1.0 HA A:ASP92 2.5 20.9 1.0 HE22 A:GLN95 2.7 46.9 0.6 HE21 A:GLN95 2.8 46.9 0.6 HZ3 A:LYS88 2.9 54.7 1.0 NE2 A:GLN95 2.9 39.0 0.6 O A:HOH310 3.1 46.6 1.0 HE2 A:LYS88 3.2 36.4 1.0 CA A:ASP92 3.2 17.4 1.0 CG A:ASP92 3.3 25.2 1.0 HD2 A:LYS88 3.3 31.7 1.0 N A:ASP92 3.4 15.2 1.0 O A:HOH341 3.4 29.1 1.0 O A:GLU91 3.5 23.3 1.0 C A:GLU91 3.5 17.0 1.0 NZ A:LYS88 3.6 45.6 1.0 CE A:LYS88 3.7 30.3 1.0 HB3 A:GLU91 3.7 18.2 1.0 HB2 A:GLU91 3.8 18.2 1.0 CB A:ASP92 3.8 22.0 1.0 H A:ASP92 3.8 18.2 1.0 HZ1 A:LYS88 3.9 54.7 1.0 CD A:GLN95 4.0 35.5 0.6 CD A:LYS88 4.0 26.4 1.0 CB A:GLU91 4.1 15.2 1.0 O A:LYS88 4.2 14.4 1.0 HB3 A:ASP92 4.3 26.4 1.0 HZ2 A:LYS88 4.3 54.7 1.0 HD2 A:HIS94 4.4 26.5 0.5 OD2 A:ASP92 4.4 25.6 1.0 HG3 A:GLN95 4.4 27.7 0.6 CA A:GLU91 4.4 15.2 1.0 OE1 A:GLN95 4.5 34.5 0.4 NE2 A:HIS94 4.5 26.4 0.5 HB2 A:ASP92 4.5 26.4 1.0 C A:ASP92 4.6 16.9 1.0 HG3 A:LYS88 4.6 23.9 1.0 OE1 A:GLN95 4.6 35.5 0.6 HD3 A:LYS88 4.6 31.7 1.0 HE3 A:LYS88 4.6 36.4 1.0 CD2 A:HIS94 4.7 22.1 0.5 CG A:GLN95 4.8 23.1 0.6 HB3 A:GLN95 4.9 27.3 0.4 CG A:LYS88 4.9 19.9 1.0

P.Bandaru, N.H.Shah, M.Bhattacharyya, J.P.Barton, Y.Kondo, J.C.Cofsky, C.L.Gee, A.K.Chakraborty, T.Kortemme, R.Ranganathan, J.Kuriyan. Deconstruction of the Ras Switching Cycle Through Saturation Mutagenesis. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28686159
DOI: 10.7554/ELIFE.27810