Magnesium in PDB 6gof: Kras Full Length G12D Gppnhp

The structure of Kras Full Length G12D Gppnhp, PDB code: 6gof was solved by A.Cruz-Migoni, C.E.Quevedo, S.B.Carr, M.T.Ehebauer, S.V.E.Phillips, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.31 / 1.98
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	78.630, 78.630, 77.540, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 25.2

The binding sites of Magnesium atom in the Kras Full Length G12D Gppnhp (pdb code 6gof). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kras Full Length G12D Gppnhp, PDB code: 6gof:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kras Full Length G12D Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras Full Length G12D Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:29.9 occ:1.00 O2G A:GNP202 1.9 29.2 1.0 O A:HOH328 2.0 25.6 1.0 O2B A:GNP202 2.0 24.0 1.0 O A:HOH329 2.1 24.5 1.0 OG1 A:THR35 2.1 32.8 1.0 OG A:SER17 2.2 26.1 1.0 PB A:GNP202 3.1 25.9 1.0 CB A:SER17 3.1 24.7 1.0 PG A:GNP202 3.2 29.8 1.0 CB A:THR35 3.3 37.2 1.0 N3B A:GNP202 3.3 26.3 1.0 N A:SER17 3.8 22.9 1.0 N A:THR35 4.0 39.0 1.0 CA A:SER17 4.0 25.1 1.0 O1G A:GNP202 4.0 28.3 1.0 O2A A:GNP202 4.1 31.0 1.0 OD2 A:ASP57 4.1 33.9 1.0 O1B A:GNP202 4.1 21.2 1.0 OD1 A:ASP57 4.2 31.6 1.0 O3A A:GNP202 4.2 24.6 1.0 CG2 A:THR35 4.2 40.0 1.0 CA A:THR35 4.3 39.9 1.0 O3G A:GNP202 4.4 34.2 1.0 PA A:GNP202 4.4 28.6 1.0 O A:THR58 4.5 29.3 1.0 CG A:ASP57 4.5 33.7 1.0 O1A A:GNP202 4.6 25.7 1.0 O A:ASP33 4.6 37.8 1.0 CB A:LYS16 4.6 22.9 1.0 CE A:LYS16 4.8 20.6 1.0 NZ A:LYS16 4.8 20.6 1.0 C A:LYS16 4.8 21.9 1.0 C A:PRO34 4.9 38.8 1.0

Magnesium binding site 2 out of 2 in the Kras Full Length G12D Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras Full Length G12D Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:28.2 occ:0.30 O A:HOH334 2.2 19.9 1.0 OH A:TYR96 2.2 34.3 1.0 O A:GLY10 2.4 28.0 1.0 O A:ALA59 2.6 28.4 1.0 O A:GLY60 2.7 42.5 1.0 NH1 A:ARG68 3.2 77.3 1.0 C A:GLY60 3.2 44.5 1.0 CA A:GLY60 3.4 38.4 1.0 CZ A:TYR96 3.4 31.6 1.0 C A:GLY10 3.4 24.6 1.0 O A:HOH301 3.4 45.4 1.0 C A:ALA59 3.6 32.5 1.0 O A:HOH304 3.7 40.7 1.0 N A:GLY60 3.9 35.1 1.0 CE1 A:TYR96 3.9 28.0 1.0 N A:GLY10 3.9 23.6 1.0 CA A:GLY10 4.2 25.4 1.0 N A:GLN61 4.2 53.0 1.0 N A:ALA11 4.3 24.5 1.0 CZ A:ARG68 4.3 72.0 1.0 CA A:ALA11 4.3 25.0 1.0 OH A:TYR71 4.4 42.9 1.0 CE2 A:TYR96 4.5 29.0 1.0 CE A:LYS16 4.6 20.6 1.0 OG1 A:THR58 4.7 30.0 1.0 CA A:GLN61 4.7 61.9 1.0 C A:ALA11 4.7 27.2 1.0 NZ A:LYS16 4.8 20.6 1.0 NH2 A:ARG68 4.8 60.7 1.0 CA A:ALA59 4.9 30.8 1.0

A.Cruz-Migoni, P.Canning, C.E.Quevedo, C.J.R.Bataille, N.Bery, A.Miller, A.J.Russell, S.E.V.Phillips, S.B.Carr, T.H.Rabbitts. Structure-Based Development of New Ras-Effector Inhibitors From A Combination of Active and Inactive Ras-Binding Compounds. Proc. Natl. Acad. Sci. V. 116 2545 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30683716
DOI: 10.1073/PNAS.1811360116