Magnesium in PDB 7oo7: KRASG12C Ligand Complex

All present enzymatic activity of KRASG12C Ligand Complex:
3.6.5.2;

The structure of KRASG12C Ligand Complex, PDB code: 7oo7 was solved by C.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.289, 72.012, 65.821, 90, 90.32, 90
R / Rfree (%)	19 / 22.6

The structure of KRASG12C Ligand Complex also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the KRASG12C Ligand Complex (pdb code 7oo7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the KRASG12C Ligand Complex, PDB code: 7oo7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the KRASG12C Ligand Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:14.1 occ:1.00 O A:HOH310 2.1 11.8 1.0 O A:HOH337 2.1 12.9 1.0 O A:HOH315 2.1 17.1 1.0 O1B A:GDP202 2.1 12.8 1.0 OG A:SER17 2.2 12.7 1.0 O A:HOH333 2.2 14.8 1.0 CB A:SER17 3.1 11.2 1.0 PB A:GDP202 3.3 12.7 1.0 O2B A:GDP202 3.5 17.0 1.0 N A:SER17 3.9 10.2 1.0 CA A:SER17 4.1 10.4 1.0 O2A A:GDP202 4.1 15.3 1.0 OD2 A:ASP57 4.1 18.5 1.0 OD1 A:ASP57 4.2 16.6 1.0 O A:ASP33 4.3 22.4 1.0 O3A A:GDP202 4.3 13.7 1.0 O3B A:GDP202 4.4 13.9 1.0 CA A:PRO34 4.4 24.1 1.0 O A:THR58 4.5 14.2 1.0 CG A:ASP57 4.5 16.5 1.0 O A:ILE36 4.6 16.5 1.0 PA A:GDP202 4.6 14.9 1.0 CD2 A:TYR32 4.6 19.2 1.0 O A:PRO34 4.7 23.3 1.0 O1A A:GDP202 4.8 16.4 1.0 CB A:ALA59 4.8 16.3 1.0 C A:PRO34 4.8 23.7 1.0 O A:HOH322 4.9 22.1 1.0 CB A:LYS16 4.9 10.7 1.0 O A:TYR32 4.9 27.2 1.0 CE A:LYS16 5.0 12.7 1.0

Magnesium binding site 2 out of 2 in the KRASG12C Ligand Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:10.4 occ:1.00 OG D:SER17 2.1 9.6 1.0 O D:HOH316 2.1 8.9 1.0 O3B D:GDP202 2.1 8.0 1.0 O D:HOH358 2.1 10.1 1.0 O D:HOH312 2.1 11.0 1.0 O D:HOH331 2.2 11.2 1.0 CB D:SER17 3.1 8.5 1.0 PB D:GDP202 3.3 9.5 1.0 O2B D:GDP202 3.5 10.4 1.0 N D:SER17 3.9 8.4 1.0 CA D:SER17 4.1 8.5 1.0 OD2 D:ASP57 4.1 14.7 1.0 O1A D:GDP202 4.1 12.3 1.0 OD1 D:ASP57 4.3 14.6 1.0 O3A D:GDP202 4.3 9.8 1.0 O D:ASP33 4.3 14.6 1.0 O1B D:GDP202 4.4 7.7 1.0 CA D:PRO34 4.4 15.6 1.0 CB D:ALA59 4.5 11.7 1.0 PA D:GDP202 4.5 11.4 1.0 O D:THR58 4.5 11.2 1.0 CG D:ASP57 4.5 13.8 1.0 O D:ILE36 4.6 12.6 1.0 CD2 D:TYR32 4.6 14.7 1.0 O2A D:GDP202 4.7 12.0 1.0 O D:PRO34 4.8 13.8 1.0 C D:PRO34 4.9 14.0 1.0 CB D:LYS16 4.9 8.9 1.0 O D:TYR32 4.9 15.8 1.0 CE D:LYS16 4.9 8.7 1.0 C D:LYS16 5.0 8.5 1.0

J.G.Kettle, S.K.Bagal, S.Bickerton, M.S.Bodnarchuk, S.Boyd, J.Breed, R.J.Carbajo, D.J.Cassar, A.Chakraborty, S.Cosulich, I.Cumming, M.Davies, N.L.Davies, A.Eatherton, L.Evans, L.Feron, S.Fillery, E.S.Gleave, F.W.Goldberg, L.Hanson, S.Harlfinger, M.Howard, R.Howells, A.Jackson, P.Kemmitt, G.Lamont, S.Lamont, H.J.Lewis, L.Liu, M.J.Niedbala, C.Phillips, R.Polanski, P.Raubo, G.Robb, D.M.Robinson, S.Ross, M.G.Sanders, M.Tonge, R.Whiteley, S.Wilkinson, J.Yang, W.Zhang. Discovery of AZD4625, A Covalent Allosteric Inhibitor of the Mutant Gtpase Kras G12C . J.Med.Chem. V. 65 6940 2022.
ISSN: ISSN 0022-2623
PubMed: 35471939
DOI: 10.1021/ACS.JMEDCHEM.2C00369