Magnesium in PDB 8cx5: Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)

All present enzymatic activity of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R):
3.6.5.2;

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5 was solved by Z.Zhang, J.Morstein, A.Ecker, K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.83 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.21, 65.661, 61.13, 90, 101.85, 90
R / Rfree (%)	18.9 / 22.1

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) (pdb code 8cx5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:13.2 occ:1.00 O A:HOH344 2.0 13.0 1.0 OG A:SER17 2.1 12.2 1.0 O3B A:GDP203 2.1 13.9 1.0 O A:HOH311 2.2 13.6 1.0 O A:HOH314 2.2 15.2 1.0 CB A:SER17 3.2 13.0 1.0 PB A:GDP203 3.4 13.1 1.0 O1B A:GDP203 3.5 14.0 1.0 OD2 A:ASP57 4.0 22.3 1.0 N A:SER17 4.0 12.2 1.0 O1A A:GDP203 4.1 14.7 1.0 CA A:SER17 4.2 12.4 1.0 OD1 A:ASP57 4.2 21.6 1.0 O A:ASP33 4.2 16.2 1.0 CA A:PRO34 4.3 22.8 1.0 O A:PRO34 4.3 23.7 1.0 O3A A:GDP203 4.4 14.1 1.0 O2B A:GDP203 4.4 13.3 1.0 O A:THR58 4.5 15.7 1.0 CG A:ASP57 4.5 20.6 1.0 O A:ILE36 4.5 16.9 1.0 C A:PRO34 4.6 23.6 1.0 PA A:GDP203 4.6 15.2 1.0 O A:TYR32 4.7 22.2 1.0 CD2 A:TYR32 4.7 19.8 1.0 O2A A:GDP203 4.8 17.3 1.0 O A:HOH345 4.9 29.3 1.0 O A:HOH320 4.9 19.8 1.0 CB A:ALA59 5.0 19.3 1.0 C A:ASP33 5.0 19.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:18.0 occ:1.00 O3B B:GDP205 2.0 14.1 1.0 O B:HOH354 2.1 17.0 1.0 OG B:SER17 2.1 14.6 1.0 O B:HOH317 2.2 18.2 1.0 O B:HOH349 2.2 19.1 1.0 O B:HOH318 2.2 16.8 1.0 CB B:SER17 3.1 13.9 1.0 PB B:GDP205 3.2 14.6 1.0 O1B B:GDP205 3.5 21.3 1.0 N B:SER17 3.8 12.0 1.0 OD2 B:ASP57 4.0 20.6 1.0 CA B:SER17 4.0 14.8 1.0 OD1 B:ASP57 4.1 16.2 1.0 O1A B:GDP205 4.1 18.2 1.0 O3A B:GDP205 4.3 14.6 1.0 O B:TYR32 4.3 38.3 1.0 O2B B:GDP205 4.3 15.3 1.0 O B:PRO34 4.4 21.0 1.0 CG B:ASP57 4.4 22.6 1.0 O B:ASP33 4.4 29.0 1.0 CA B:PRO34 4.4 20.8 1.0 PA B:GDP205 4.5 16.0 1.0 O2A B:GDP205 4.6 15.7 1.0 O B:THR58 4.6 15.8 1.0 C B:PRO34 4.7 23.1 1.0 O B:HOH355 4.7 32.3 1.0 CB B:LYS16 4.9 12.2 1.0 O B:ILE36 4.9 22.0 1.0 C B:LYS16 4.9 11.5 1.0

Z.Zhang, J.Morstein, A.K.Ecker, K.Z.Guiley, K.M.Shokat. Chemoselective Covalent Modification of K-Ras(G12R) with A Small Molecule Electrophile. J.Am.Chem.Soc. V. 144 15916 2022.
ISSN: ESSN 1520-5126
PubMed: 36001446
DOI: 10.1021/JACS.2C05377