Magnesium 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:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the H-Ras Bound to Gmp-Pnp at 277K, PDB code: 5wdo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the H-Ras Bound to Gmp-Pnp at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg202 b:16.3 occ:1.00 O3G A:GNP205 2.0 18.0 1.0 O2B A:GNP205 2.0 16.1 1.0 OG A:SER17 2.1 16.4 1.0 O A:HOH323 2.1 18.3 1.0 OG1 A:THR35 2.1 18.3 1.0 O A:HOH322 2.2 18.7 1.0 HB A:THR35 2.9 24.0 1.0 CB A:THR35 3.1 20.0 1.0 CB A:SER17 3.2 19.5 1.0 HB2 A:SER17 3.2 23.4 1.0 PB A:GNP205 3.2 17.1 1.0 PG A:GNP205 3.3 18.0 1.0 H A:THR35 3.3 22.8 1.0 H A:SER17 3.3 19.1 1.0 N3B A:GNP205 3.5 15.8 1.0 N A:THR35 3.8 19.0 1.0 N A:SER17 3.9 15.9 1.0 HB3 A:SER17 3.9 23.4 1.0 HB2 A:LYS16 3.9 21.0 1.0 HG21 A:THR35 3.9 24.9 1.0 O1G A:GNP205 4.0 20.1 1.0 OD2 A:ASP57 4.1 19.6 1.0 CA A:THR35 4.1 17.7 1.0 CG2 A:THR35 4.1 20.8 1.0 CA A:SER17 4.1 15.6 1.0 HE2 A:LYS16 4.1 20.2 1.0 O2A A:GNP205 4.1 19.7 1.0 OD1 A:ASP57 4.2 20.0 1.0 O A:HOH331 4.2 24.2 1.0 O1B A:GNP205 4.3 16.9 1.0 HA A:PRO34 4.3 20.6 1.0 HNB3 A:GNP205 4.3 18.9 1.0 O3A A:GNP205 4.3 15.8 1.0 HA A:SER17 4.4 18.8 1.0 O A:ASP33 4.4 18.5 0.4 O2G A:GNP205 4.4 18.5 1.0 O A:THR58 4.5 20.9 1.0 O A:ASP33 4.5 18.4 0.6 CG A:ASP57 4.5 18.2 1.0 HG23 A:THR35 4.5 24.9 1.0 PA A:GNP205 4.6 17.7 1.0 HA A:THR35 4.6 21.2 1.0 O1A A:GNP205 4.6 15.6 1.0 HE1 A:TYR32 4.7 27.9 1.0 HZ1 A:LYS16 4.7 19.8 1.0 C A:PRO34 4.8 23.1 1.0 HZ3 A:LYS16 4.8 19.8 1.0 CB A:LYS16 4.8 17.5 1.0 HG22 A:THR35 4.8 24.9 1.0 C A:LYS16 4.9 15.5 1.0 CE A:LYS16 5.0 16.9 1.0 CA A:PRO34 5.0 17.1 1.0

Magnesium binding site 2 out of 2 in the H-Ras Bound to Gmp-Pnp at 277K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H-Ras Bound to Gmp-Pnp at 277K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:26.3 occ:0.16 O A:HOH314 2.1 29.2 1.0 O A:HOH347 2.3 23.4 1.0 HE22 A:GLN129 3.4 32.5 0.6 OE1 A:GLU126 4.0 47.5 0.5 NE2 A:GLN129 4.1 27.1 0.6 OE1 A:GLN129 4.3 21.6 0.4 O A:THR124 4.3 19.8 1.0 HE22 A:GLN129 4.4 23.7 0.4 O A:HOH350 4.4 28.4 1.0 OE1 A:GLN129 4.6 22.1 0.6 HE21 A:GLN129 4.6 32.5 0.6 HG3 A:GLU126 4.7 33.0 0.5 CD A:GLN129 4.8 29.1 0.6 HG2 A:GLU126 4.8 32.7 0.5 CD A:GLN129 4.8 28.1 0.4 NE2 A:GLN129 4.9 19.7 0.4

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