Magnesium in PDB 8aq5: Kras G12C in Complex with Gdp and Compound 16

The structure of Kras G12C in Complex with Gdp and Compound 16, PDB code: 8aq5 was solved by N.Ostermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.69 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.105, 40.324, 52.292, 90, 100.95, 90
R / Rfree (%)	17.6 / 21.5

The structure of Kras G12C in Complex with Gdp and Compound 16 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Kras G12C in Complex with Gdp and Compound 16 (pdb code 8aq5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Kras G12C in Complex with Gdp and Compound 16, PDB code: 8aq5:

Magnesium binding site 1 out of 1 in the Kras G12C in Complex with Gdp and Compound 16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12C in Complex with Gdp and Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:11.3 occ:1.00 O A:HOH1160 2.1 5.8 1.0 O3B A:GDP1003 2.1 8.1 1.0 O A:HOH1126 2.1 9.6 1.0 O A:HOH1122 2.1 7.1 1.0 O A:HOH1184 2.2 6.9 1.0 OG A:SER17 2.2 9.3 1.0 CB A:SER17 3.2 8.5 1.0 PB A:GDP1003 3.3 8.8 1.0 O1B A:GDP1003 3.6 8.1 1.0 N A:SER17 4.0 7.4 1.0 OD2 A:ASP57 4.1 16.1 1.0 O1A A:GDP1003 4.1 10.4 1.0 CA A:SER17 4.2 8.4 1.0 OD1 A:ASP57 4.2 13.7 1.0 CB A:ALA59 4.3 9.9 1.0 O2B A:GDP1003 4.4 8.7 1.0 O A:ASP33 4.4 11.3 1.0 O3A A:GDP1003 4.4 9.9 1.0 CA A:PRO34 4.4 13.7 1.0 O32 A:NZ61002 4.5 9.8 1.0 PA A:GDP1003 4.6 11.0 1.0 CG A:ASP57 4.6 15.0 1.0 O A:THR58 4.7 7.8 1.0 O2A A:GDP1003 4.7 10.2 1.0 CD2 A:TYR32 4.7 13.5 1.0 O A:TYR32 4.7 11.9 1.0 O A:ILE36 4.7 11.4 1.0 O A:PRO34 4.8 15.3 1.0 C A:PRO34 4.9 14.8 1.0 CB A:LYS16 5.0 7.2 1.0

E.Lorthiois, M.Gerspacher, K.S.Beyer, A.Vaupel, C.Leblanc, R.Stringer, A.Weiss, R.Wilcken, D.A.Guthy, A.Lingel, C.Bomio-Confaglia, R.Machauer, P.Rigollier, J.Ottl, D.Arz, P.Bernet, G.Desjonqueres, S.Dussauge, M.Kazic-Legueux, M.A.Lozac'h, C.Mura, M.Sorge, M.Todorov, N.Warin, F.Zink, H.Voshol, F.J.Zecri, R.C.Sedrani, N.Ostermann, S.M.Brachmann, S.Cotesta. JDQ443, A Structurally Novel, Pyrazole-Based, Covalent Inhibitor of Kras G12C For the Treatment of Solid Tumors. J.Med.Chem. V. 65 16173 2022.
ISSN: ISSN 0022-2623
PubMed: 36399068
DOI: 10.1021/ACS.JMEDCHEM.2C01438