Magnesium in PDB 6t5u: KRASG12C Ligand Complex

The structure of KRASG12C Ligand Complex, PDB code: 6t5u was solved by C.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.94 / 1.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.597, 41.084, 65.192, 78.47, 85.59, 68.14
R / Rfree (%)	23.7 / 29.1

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

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the KRASG12C Ligand Complex (pdb code 6t5u). 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: 6t5u:
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:21.0 occ:1.00 O3B A:GDP202 1.9 19.2 1.0 O A:HOH303 2.1 16.4 1.0 O A:HOH310 2.1 19.4 1.0 O A:HOH346 2.1 19.6 1.0 OG A:SER17 2.2 16.8 1.0 O A:HOH322 2.3 21.5 1.0 CB A:SER17 3.1 14.0 1.0 PB A:GDP202 3.2 19.8 1.0 O1B A:GDP202 3.5 22.1 1.0 N A:SER17 3.9 12.1 1.0 CA A:SER17 4.0 13.0 1.0 O1A A:GDP202 4.0 24.7 1.0 OD2 A:ASP57 4.1 26.5 1.0 OD1 A:ASP57 4.1 24.6 1.0 O3A A:GDP202 4.3 20.8 1.0 CB A:ALA59 4.4 19.1 1.0 O A:ASP33 4.4 27.7 1.0 O2B A:GDP202 4.4 18.4 1.0 O A:PRO34 4.4 25.0 1.0 PA A:GDP202 4.5 19.6 1.0 O A:THR58 4.5 18.1 1.0 CG A:ASP57 4.5 21.9 1.0 CA A:PRO34 4.6 27.6 1.0 CD2 A:TYR32 4.7 40.9 1.0 O2A A:GDP202 4.7 23.9 1.0 O A:ILE36 4.7 21.8 1.0 C A:PRO34 4.7 26.3 1.0 O A:TYR32 5.0 33.8 1.0 O A:HOH323 5.0 26.7 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 B:Mg201 b:37.9 occ:1.00 O B:HOH318 2.0 34.7 1.0 O B:HOH307 2.0 31.8 1.0 O1B B:GDP202 2.2 31.4 1.0 O B:HOH314 2.2 35.9 1.0 OG B:SER17 2.2 27.7 1.0 O B:HOH301 2.4 34.2 1.0 CB B:SER17 3.1 25.2 1.0 PB B:GDP202 3.5 31.7 1.0 O2B B:GDP202 3.5 39.4 1.0 OD2 B:ASP57 3.8 46.9 1.0 N B:SER17 4.1 24.1 1.0 CA B:SER17 4.2 26.1 1.0 CA B:PRO34 4.3 41.7 1.0 O B:ASP33 4.3 48.6 1.0 O2A B:GDP202 4.3 37.2 1.0 O B:THR58 4.3 27.1 1.0 CB B:ALA59 4.4 31.3 1.0 OD1 B:ASP57 4.4 51.6 1.0 CG B:ASP57 4.5 41.4 1.0 O3B B:GDP202 4.5 30.1 1.0 O B:ILE36 4.6 38.6 1.0 O3A B:GDP202 4.6 31.0 1.0 O B:MKW203 4.7 37.4 1.0 CD1 B:TYR32 4.7 46.4 1.0 O B:PRO34 4.9 39.6 1.0 C B:PRO34 4.9 42.6 1.0 O B:TYR32 4.9 50.5 1.0 C B:ASP33 5.0 54.4 1.0 CE B:LYS16 5.0 29.0 1.0

J.G.Kettle, S.Bagal, S.Bickerton, M.S.Bodnarchuk, J.Breed, R.J.Carbajo, D.Cassar, A.Chakraborty, S.Cosulich, I.Cumming, M.Davies, A.Eatherton, L.Evans, L.J.Feron, S.M.Fillery, E.S.Gleave, F.W.Goldberg, S.Harlfinger, L.Hanson, M.Howard, R.Howells, A.Jackson, P.D.Kemmitt, J.Kingston, S.Lamont, H.Lewis, S.Li, L.Liu, D.Ogg, C.Phillips, R.Polanski, G.R.Robb, D.Robinson, S.Ross, J.Smith, M.Tonge, R.Whiteley, J.Yang, L.Zhang, X.Zhao. Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant Gtpase KRASG12C. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32023060
DOI: 10.1021/ACS.JMEDCHEM.9B01720