Magnesium in PDB 5wdp: H-Ras Mutant L120A Bound to Gmp-Pnp at 277K

All present enzymatic activity of H-Ras Mutant L120A Bound to Gmp-Pnp at 277K:
3.6.5.2;

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 277K, PDB code: 5wdp 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)	45.32 / 1.35
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.988, 89.988, 135.969, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 15.4

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 277K also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the H-Ras Mutant L120A Bound to Gmp-Pnp at 277K (pdb code 5wdp). 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 Mutant L120A Bound to Gmp-Pnp at 277K, PDB code: 5wdp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the H-Ras Mutant L120A 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 Mutant L120A Bound to Gmp-Pnp at 277K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:15.0 occ:0.29 CA A:CA203 0.0 15.1 0.7 O3G A:GNP202 2.0 16.7 1.0 O2B A:GNP202 2.0 14.2 1.0 O A:HOH318 2.1 15.6 1.0 OG A:SER17 2.1 14.6 1.0 O A:HOH326 2.1 16.4 1.0 OG1 A:THR35 2.1 16.9 1.0 HB A:THR35 3.0 20.3 1.0 CB A:THR35 3.1 16.9 1.0 HB2 A:SER17 3.1 18.5 1.0 CB A:SER17 3.2 15.4 1.0 PG A:GNP202 3.2 15.5 1.0 PB A:GNP202 3.2 14.1 1.0 H A:THR35 3.3 20.4 1.0 H A:SER17 3.3 16.3 1.0 N3B A:GNP202 3.4 14.2 1.0 N A:THR35 3.8 17.0 1.0 HB3 A:SER17 3.8 18.5 1.0 N A:SER17 3.9 13.6 1.0 HB2 A:LYS16 3.9 17.1 1.0 HG21 A:THR35 4.0 22.5 1.0 O1G A:GNP202 4.0 17.2 1.0 OD2 A:ASP57 4.1 17.3 1.0 CA A:THR35 4.1 17.0 1.0 CA A:SER17 4.1 13.3 1.0 O2A A:GNP202 4.1 16.1 1.0 O A:HOH331 4.1 21.3 1.0 CG2 A:THR35 4.1 18.8 1.0 HE2 A:LYS16 4.2 20.1 1.0 OD1 A:ASP57 4.2 17.0 1.0 O3A A:GNP202 4.2 14.1 1.0 HNB3 A:GNP202 4.3 17.0 1.0 O1B A:GNP202 4.3 13.9 1.0 O2G A:GNP202 4.4 17.1 1.0 HA A:PRO34 4.4 20.5 1.0 HA A:SER17 4.4 16.0 1.0 O A:ASP33 4.5 17.0 0.4 O A:ASP33 4.5 17.1 0.6 PA A:GNP202 4.5 14.6 1.0 CG A:ASP57 4.5 15.6 1.0 O A:THR58 4.5 18.6 1.0 HA A:THR35 4.6 20.4 1.0 HG23 A:THR35 4.6 22.5 1.0 HE1 A:TYR32 4.6 24.7 1.0 O1A A:GNP202 4.7 15.1 1.0 HZ1 A:LYS16 4.7 18.4 1.0 C A:PRO34 4.8 17.3 1.0 CB A:LYS16 4.8 14.2 1.0 HZ3 A:LYS16 4.8 18.4 1.0 HG22 A:THR35 4.9 22.5 1.0 C A:LYS16 5.0 13.6 1.0

Magnesium binding site 2 out of 2 in the H-Ras Mutant L120A 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 Mutant L120A Bound to Gmp-Pnp at 277K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:20.4 occ:0.14 O A:HOH325 2.1 24.7 1.0 O A:HOH344 2.3 21.2 1.0 HE22 A:GLN129 3.4 27.6 0.6 NE2 A:GLN129 4.1 23.0 0.6 O A:THR124 4.2 17.9 1.0 O A:HOH338 4.4 26.0 1.0 OE1 A:GLN129 4.4 17.4 0.4 HE22 A:GLN129 4.5 22.2 0.4 HE21 A:GLN129 4.6 27.6 0.6 OE1 A:GLU126 4.6 41.5 0.5 OE1 A:GLN129 4.6 22.4 0.6 CD A:GLN129 4.8 23.3 0.6 HG3 A:GLU126 4.8 27.0 0.5 HG2 A:GLU126 4.9 26.9 0.6 NE2 A:GLN129 4.9 18.5 0.4 CD A:GLN129 4.9 24.1 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