Magnesium in PDB 7tlg: Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)

All present enzymatic activity of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S):
3.6.5.2;

The structure of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S), PDB code: 7tlg was solved by Z.Ziyang, 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)	44.35 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.55, 66.53, 60.8, 90, 101.89, 90
R / Rfree (%)	17.9 / 23.3

The structure of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S) (pdb code 7tlg). 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 Beta-Lactone 5 Covalently Bound to K-Ras(G12S), PDB code: 7tlg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)


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 Beta-Lactone 5 Covalently Bound to K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:9.1 occ:1.00 O A:HOH327 2.1 8.2 1.0 O A:HOH334 2.1 9.6 1.0 OG A:SER17 2.1 9.0 1.0 O A:HOH328 2.1 7.1 1.0 O A:HOH333 2.1 8.9 1.0 O2B A:GDP201 2.2 8.9 1.0 CB A:SER17 3.2 9.8 1.0 PB A:GDP201 3.4 8.9 1.0 O3B A:GDP201 3.5 10.8 1.0 N A:SER17 3.9 7.5 1.0 OD2 A:ASP57 4.0 12.5 1.0 CA A:SER17 4.1 8.8 1.0 OD1 A:ASP57 4.2 11.6 1.0 O1A A:GDP201 4.2 11.7 1.0 O A:ASP33 4.2 11.2 1.0 O A:PRO34 4.3 13.9 1.0 O1B A:GDP201 4.3 9.8 1.0 CA A:PRO34 4.4 15.1 1.0 O3A A:GDP201 4.4 9.3 1.0 CB A:ALA59 4.5 11.4 1.0 O A:ILE36 4.5 9.0 1.0 CG A:ASP57 4.5 10.0 1.0 O A:THR58 4.5 9.6 1.0 CD1 A:TYR32 4.6 15.1 1.0 PA A:GDP201 4.6 10.7 1.0 C A:PRO34 4.6 12.4 1.0 O2A A:GDP201 4.7 9.1 1.0 CB A:LYS16 4.9 7.8 1.0 O A:TYR32 4.9 13.6 1.0 C A:LYS16 5.0 9.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)


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 Beta-Lactone 5 Covalently Bound to K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:21.1 occ:1.00 O3B B:GDP201 2.0 19.9 1.0 O B:HOH325 2.1 26.9 1.0 O B:HOH331 2.1 19.3 1.0 OG B:SER17 2.1 15.5 1.0 O B:HOH335 2.1 16.4 1.0 O B:HOH312 2.2 23.1 1.0 CB B:SER17 3.1 16.6 1.0 PB B:GDP201 3.3 20.0 1.0 O1B B:GDP201 3.6 25.5 1.0 N B:SER17 3.9 16.7 1.0 OD2 B:ASP57 4.0 27.0 1.0 O1A B:GDP201 4.0 26.2 1.0 CA B:SER17 4.1 18.7 1.0 O B:PRO34 4.1 29.0 1.0 OD1 B:ASP57 4.1 20.7 1.0 O2B B:GDP201 4.3 21.8 1.0 O B:ASP33 4.3 37.0 1.0 CB B:ALA59 4.3 19.6 1.0 O B:THR58 4.4 20.2 1.0 CA B:PRO34 4.4 32.5 1.0 CG B:ASP57 4.4 22.8 1.0 O B:ILE36 4.5 23.3 1.0 O3A B:GDP201 4.5 19.6 1.0 C B:PRO34 4.6 28.1 1.0 PA B:GDP201 4.7 22.3 1.0 O2A B:GDP201 4.7 23.5 1.0 CB B:LYS16 4.9 17.6 1.0 C B:LYS16 5.0 18.2 1.0

Z.Zhang, K.Z.Guiley, K.M.Shokat. Chemical Acylation of An Acquired Serine Suppresses Oncogenic Signaling of K-Ras(G12S). Nat.Chem.Biol. V. 18 1177 2022.
ISSN: ESSN 1552-4469
PubMed: 35864332
DOI: 10.1038/S41589-022-01065-9