Sodium in PDB 5wdo: H-Ras Bound to Gmp-Pnp at 277K

All present enzymatic activity of H-Ras Bound to Gmp-Pnp at 277K:
3.6.5.2;

The structure of H-Ras Bound to Gmp-Pnp at 277K, PDB code: 5wdo was solved by J.C.Cofsky, 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)	45.59 / 1.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.959, 89.959, 136.766, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 16.8

The structure of H-Ras Bound to Gmp-Pnp at 277K also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the H-Ras Bound to Gmp-Pnp at 277K (pdb code 5wdo). 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 Bound to Gmp-Pnp at 277K, PDB code: 5wdo:

Sodium binding site 1 out of 1 in the H-Ras Bound to Gmp-Pnp at 277K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H-Ras Bound to Gmp-Pnp at 277K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:59.5 occ:1.00 HH11 A:ARG68 2.2 72.3 1.0 OE1 A:GLN99 2.3 47.4 1.0 HG2 A:GLN95 2.8 52.0 0.5 NH1 A:ARG68 2.9 60.2 1.0 HB2 A:GLN99 3.0 34.7 1.0 HB3 A:GLN99 3.1 34.7 1.0 HD2 A:ARG68 3.1 52.4 1.0 HA A:TYR96 3.2 29.3 1.0 HD3 A:ARG68 3.2 52.4 1.0 HH12 A:ARG68 3.2 72.3 1.0 O A:GLN95 3.3 25.1 0.5 HE1 A:MET72 3.3 39.7 1.0 HG3 A:GLN95 3.3 52.0 0.5 CD A:GLN99 3.4 64.4 1.0 CB A:GLN99 3.4 28.9 1.0 CG A:GLN95 3.5 43.3 0.5 CD A:ARG68 3.6 43.6 1.0 O A:GLN95 3.7 24.9 0.5 C A:GLN95 4.0 25.8 0.5 CG A:GLN99 4.0 56.1 1.0 CZ A:ARG68 4.0 62.5 1.0 CA A:TYR96 4.1 24.4 1.0 C A:GLN95 4.1 25.9 0.5 HB3 A:GLN95 4.1 34.4 0.5 CD A:GLN95 4.1 50.9 0.5 NE A:ARG68 4.2 41.2 1.0 CE A:MET72 4.3 33.1 1.0 N A:TYR96 4.3 23.2 1.0 HD1 A:TYR96 4.4 37.8 1.0 CD1 A:TYR96 4.4 31.5 1.0 HE3 A:MET72 4.4 39.7 1.0 HG2 A:GLN99 4.5 67.3 1.0 OE1 A:GLN95 4.5 47.0 0.5 NE2 A:GLN99 4.5 58.3 1.0 H A:GLN99 4.5 29.7 1.0 HB3 A:ARG68 4.6 38.8 1.0 HE22 A:GLN99 4.7 70.0 1.0 O A:HOH393 4.7 64.2 1.0 HG3 A:GLN99 4.7 67.3 1.0 CG A:TYR96 4.7 20.9 1.0 NE2 A:GLN95 4.7 44.8 0.5 CE1 A:TYR96 4.7 26.2 1.0 HE21 A:GLN95 4.8 53.7 0.5 CB A:GLN95 4.8 29.3 0.5 HE2 A:MET72 4.8 39.7 1.0 CB A:GLN95 4.8 28.6 0.5 CA A:GLN99 4.8 27.2 1.0 H A:TYR96 4.8 27.8 0.5 HB2 A:GLN95 4.9 34.4 0.5 HE1 A:TYR96 4.9 31.4 1.0 H A:TYR96 4.9 27.8 0.5 CG A:ARG68 4.9 40.6 1.0 O A:TYR96 4.9 25.4 1.0 HB2 A:ARG68 5.0 38.8 1.0 C A:TYR96 5.0 22.5 1.0 CB A:TYR96 5.0 19.8 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