Magnesium in PDB 7ycc: Kras G12C in Complex with Compound 5C

All present enzymatic activity of Kras G12C in Complex with Compound 5C:
3.6.5.2;

The structure of Kras G12C in Complex with Compound 5C, PDB code: 7ycc was solved by Y.Amano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.72 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.268, 94.407, 67.423, 90, 91.49, 90
R / Rfree (%)	21.2 / 25.5

The structure of Kras G12C in Complex with Compound 5C also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Kras G12C in Complex with Compound 5C (pdb code 7ycc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Kras G12C in Complex with Compound 5C, PDB code: 7ycc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Kras G12C in Complex with Compound 5C


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 5C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:31.1 occ:1.00 O A:HOH330 1.9 31.5 1.0 OG A:SER17 2.0 30.9 1.0 O A:HOH339 2.1 33.3 1.0 O A:HOH311 2.1 35.0 1.0 O A:HOH326 2.1 30.8 1.0 O1B A:GDP201 2.2 28.4 1.0 CB A:SER17 3.1 24.6 1.0 PB A:GDP201 3.4 30.0 1.0 O3B A:GDP201 3.7 35.9 1.0 N A:SER17 4.0 29.3 1.0 CA A:SER17 4.1 28.9 1.0 O1A A:GDP201 4.1 35.3 1.0 OD2 A:ASP57 4.1 38.6 1.0 OD1 A:ASP57 4.2 30.4 1.0 O34 A:IQC203 4.2 34.5 1.0 CD2 A:TYR32 4.4 40.5 1.0 O3A A:GDP201 4.4 26.9 1.0 O2B A:GDP201 4.4 30.6 1.0 O A:ASP33 4.5 42.1 1.0 CB A:ALA59 4.5 39.5 1.0 CG A:ASP57 4.5 38.0 1.0 CA A:PRO34 4.5 46.2 1.0 O A:THR58 4.6 32.8 1.0 PA A:GDP201 4.7 31.2 1.0 O A:ILE36 4.7 41.3 1.0 CE2 A:TYR32 4.8 44.4 1.0 O A:PRO34 4.9 46.0 1.0 C A:PRO34 5.0 45.5 1.0 NZ A:LYS16 5.0 25.1 1.0 O A:TYR32 5.0 47.6 1.0

Magnesium binding site 2 out of 3 in the Kras G12C in Complex with Compound 5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12C in Complex with Compound 5C within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:31.5 occ:1.00 O B:HOH309 1.9 32.0 1.0 O B:HOH311 2.0 34.1 1.0 OG B:SER17 2.1 32.1 1.0 O2B B:GDP201 2.1 28.8 1.0 O B:HOH351 2.2 34.1 1.0 O B:HOH327 2.2 38.2 1.0 CB B:SER17 3.0 24.3 1.0 PB B:GDP201 3.3 29.2 1.0 O3B B:GDP201 3.6 33.0 1.0 N B:SER17 3.9 29.7 1.0 CA B:SER17 4.0 27.8 1.0 OD1 B:ASP57 4.1 28.5 1.0 O2A B:GDP201 4.1 29.8 1.0 OD2 B:ASP57 4.1 34.6 1.0 O34 B:IQC203 4.2 34.8 1.0 O3A B:GDP201 4.3 25.0 1.0 O1B B:GDP201 4.3 29.3 1.0 O B:ASP33 4.4 44.3 1.0 CB B:ALA59 4.5 37.1 1.0 CG B:ASP57 4.5 36.8 1.0 O B:THR58 4.5 30.5 1.0 CA B:PRO34 4.5 42.4 1.0 CD1 B:TYR32 4.6 45.8 1.0 PA B:GDP201 4.6 30.4 1.0 O B:ILE36 4.8 41.7 1.0 NZ B:LYS16 4.9 27.1 1.0 O B:PRO34 4.9 39.3 1.0 CB B:LYS16 4.9 23.1 1.0

Magnesium binding site 3 out of 3 in the Kras G12C in Complex with Compound 5C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12C in Complex with Compound 5C within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:31.8 occ:1.00 O C:HOH311 1.9 29.9 1.0 O C:HOH316 2.0 34.0 1.0 OG C:SER17 2.1 32.1 1.0 O2B C:GDP201 2.1 27.1 1.0 O C:HOH340 2.2 31.4 1.0 O C:HOH318 2.2 31.8 1.0 CB C:SER17 3.1 25.8 1.0 PB C:GDP201 3.3 28.7 1.0 O1B C:GDP201 3.6 31.3 1.0 N C:SER17 3.9 29.2 1.0 CA C:SER17 4.0 30.5 1.0 O1A C:GDP201 4.0 32.9 1.0 OD1 C:ASP57 4.1 27.6 1.0 OD2 C:ASP57 4.1 35.8 1.0 O34 C:IQC203 4.3 34.2 1.0 O3A C:GDP201 4.3 25.2 1.0 O3B C:GDP201 4.3 30.0 1.0 CD2 C:TYR32 4.4 43.3 1.0 O C:ASP33 4.4 41.0 1.0 CA C:PRO34 4.5 41.7 1.0 CB C:ALA59 4.5 34.4 1.0 CG C:ASP57 4.5 35.4 1.0 O C:THR58 4.6 29.4 1.0 PA C:GDP201 4.6 30.7 1.0 O C:ILE36 4.7 44.5 1.0 CE2 C:TYR32 4.9 47.3 1.0 O C:PRO34 5.0 38.2 1.0 NZ C:LYS16 5.0 24.9 1.0 O2A C:GDP201 5.0 32.5 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