Magnesium in PDB 7tlk: Crystal Structure of K-Ras(G12S)

All present enzymatic activity of Crystal Structure of K-Ras(G12S):
3.6.5.2;

The structure of Crystal Structure of K-Ras(G12S), PDB code: 7tlk 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)	41.80 / 1.71
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	83.609, 83.609, 41.27, 90, 90, 120
R / Rfree (%)	16.9 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of K-Ras(G12S) (pdb code 7tlk). 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 K-Ras(G12S), PDB code: 7tlk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 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 K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.8 occ:1.00 O2B A:GDP201 2.3 4.5 1.0 O A:HOH414 2.3 9.0 1.0 O A:HOH332 2.3 8.6 1.0 O A:HOH322 2.4 9.2 1.0 OG A:SER17 2.4 6.8 1.0 O A:HOH366 2.4 7.8 1.0 CB A:SER17 3.4 8.7 1.0 PB A:GDP201 3.5 14.9 1.0 O1B A:GDP201 3.7 9.5 1.0 N A:SER17 4.1 6.4 1.0 O1A A:GDP201 4.2 8.4 1.0 OD2 A:ASP57 4.3 12.0 1.0 CA A:SER17 4.3 6.9 1.0 OD1 A:ASP57 4.4 11.3 1.0 O3B A:GDP201 4.5 5.0 1.0 O3A A:GDP201 4.5 6.1 1.0 O A:THR58 4.5 11.0 1.0 O A:ASP33 4.6 11.2 1.0 CD2 A:TYR32 4.6 14.6 1.0 CA A:PRO34 4.6 14.5 1.0 O A:ILE36 4.7 13.0 1.0 O A:TYR32 4.7 13.4 1.0 PA A:GDP201 4.7 7.5 1.0 CG A:ASP57 4.7 13.2 1.0 O2A A:GDP201 4.8 10.2 1.0 CE A:LYS16 4.8 8.6 1.0 O A:HOH356 4.9 16.2 1.0 CB A:LYS16 4.9 6.8 1.0 CB A:ALA59 4.9 14.0 1.0 O A:PRO34 5.0 20.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 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 K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:14.8 occ:1.00 O3B B:GDP201 2.2 5.1 1.0 O B:HOH439 2.3 10.8 1.0 O B:HOH335 2.3 7.8 1.0 O B:HOH358 2.3 8.1 1.0 O B:HOH345 2.3 7.1 1.0 OG B:SER17 2.4 5.5 1.0 CB B:SER17 3.4 9.6 1.0 PB B:GDP201 3.5 8.6 1.0 O1B B:GDP201 3.7 9.6 1.0 N B:SER17 4.0 5.0 1.0 O1A B:GDP201 4.2 10.0 1.0 CD1 B:TYR32 4.2 10.7 1.0 OD2 B:ASP57 4.2 12.1 1.0 OD1 B:ASP57 4.3 9.5 1.0 CA B:SER17 4.3 7.0 1.0 CA B:PRO34 4.3 12.5 1.0 O B:PRO34 4.4 14.4 1.0 O B:ASP33 4.5 10.2 1.0 O2B B:GDP201 4.5 7.3 1.0 O3A B:GDP201 4.5 7.9 1.0 O B:ILE36 4.5 13.5 1.0 CE1 B:TYR32 4.6 12.2 1.0 O B:THR58 4.6 12.0 1.0 CG B:ASP57 4.7 10.7 1.0 C B:PRO34 4.7 13.3 1.0 PA B:GDP201 4.7 10.1 1.0 CE B:LYS16 4.8 9.5 1.0 O2A B:GDP201 4.8 9.5 1.0 CB B:LYS16 4.9 5.6 1.0 O B:TYR32 4.9 12.4 1.0 CB B:ALA59 5.0 13.6 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