Magnesium in PDB 7yce: Kras G12C in Complex with Compound 7B

All present enzymatic activity of Kras G12C in Complex with Compound 7B:
3.6.5.2;

The structure of Kras G12C in Complex with Compound 7B, PDB code: 7yce was solved by Y.Amano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.94 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	94.809, 94.809, 119.41, 90, 90, 120
R / Rfree (%)	27.4 / 29.1

The structure of Kras G12C in Complex with Compound 7B also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Kras G12C in Complex with Compound 7B (pdb code 7yce). 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 Compound 7B, PDB code: 7yce:

Magnesium binding site 1 out of 1 in the Kras G12C in Complex with Compound 7B


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 Compound 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.6 occ:1.00 O A:HOH345 2.0 17.4 1.0 O A:HOH325 2.1 17.0 1.0 O A:HOH324 2.1 17.7 1.0 OG A:SER17 2.1 14.1 1.0 O2B A:GDP201 2.1 14.0 1.0 O A:HOH346 2.2 18.2 1.0 CB A:SER17 3.1 12.4 1.0 PB A:GDP201 3.3 12.9 1.0 O3B A:GDP201 3.6 13.1 1.0 N A:SER17 4.0 13.4 1.0 OD2 A:ASP57 4.1 18.4 1.0 CA A:SER17 4.1 13.1 1.0 O2A A:GDP201 4.2 15.8 1.0 OD1 A:ASP57 4.2 17.2 1.0 O3A A:GDP201 4.3 13.0 1.0 O A:ASP33 4.3 24.8 1.0 CD2 A:TYR32 4.4 25.1 1.0 O32 A:IQN204 4.4 19.7 1.0 O1B A:GDP201 4.4 13.8 1.0 CA A:PRO34 4.5 25.4 1.0 CG A:ASP57 4.6 18.9 1.0 PA A:GDP201 4.6 14.9 1.0 O A:THR58 4.7 21.0 1.0 O A:ILE36 4.7 23.5 1.0 O A:TYR32 4.8 25.3 1.0 O1A A:GDP201 4.9 16.4 1.0 O A:PRO34 4.9 23.5 1.0 NZ A:LYS16 4.9 11.4 1.0 CE2 A:TYR32 5.0 24.5 1.0 C A:PRO34 5.0 25.9 1.0

T.Imaizumi, M.Akaiwa, T.Abe, T.Nigawara, T.Koike, Y.Satake, K.Watanabe, O.Kaneko, Y.Amano, K.Mori, Y.Yamanaka, T.Nagashima, M.Shimazaki, K.Kuramoto. Discovery and Biological Evaluation of 1-{2,7-Diazaspiro[3.5]Nonan-2-Yl}Prop-2-En-1-One Derivatives As Covalent Inhibitors of Kras G12C with Favorable Metabolic Stability and Anti-Tumor Activity. Bioorg.Med.Chem. V. 71 16949 2022.
ISSN: ESSN 1464-3391
PubMed: 35926326
DOI: 10.1016/J.BMC.2022.116949