Magnesium in PDB 8t4v: Crystal Structure of Compound 1 Bound to K-Ras(G12D)

All present enzymatic activity of Crystal Structure of Compound 1 Bound to K-Ras(G12D):
3.6.5.2;

The structure of Crystal Structure of Compound 1 Bound to K-Ras(G12D), PDB code: 8t4v was solved by Z.Zhang, Q.Zheng, 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)	59.57 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.32, 65.84, 60.85, 90, 101.75, 90
R / Rfree (%)	19 / 21.1

The structure of Crystal Structure of Compound 1 Bound to K-Ras(G12D) also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Compound 1 Bound to K-Ras(G12D) (pdb code 8t4v). 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 Compound 1 Bound to K-Ras(G12D), PDB code: 8t4v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Compound 1 Bound to K-Ras(G12D)


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 Compound 1 Bound to K-Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.0 occ:1.00 O1B A:GDP201 2.0 16.9 1.0 O A:HOH319 2.1 16.5 1.0 OG A:SER17 2.1 16.0 1.0 O A:HOH362 2.1 15.6 1.0 O A:HOH336 2.1 17.6 1.0 O A:HOH325 2.2 24.1 1.0 CB A:SER17 3.1 15.7 1.0 PB A:GDP201 3.3 16.1 1.0 O2B A:GDP201 3.6 18.7 1.0 N A:SER17 3.9 13.8 1.0 OD2 A:ASP57 4.0 20.0 1.0 O2A A:GDP201 4.1 20.0 1.0 CA A:SER17 4.1 15.8 1.0 OD1 A:ASP57 4.1 19.3 1.0 O A:PRO34 4.2 26.8 1.0 O A:ASP33 4.3 29.5 1.0 O3B A:GDP201 4.3 14.9 1.0 O3A A:GDP201 4.4 15.5 1.0 O A:HOH327 4.4 23.7 1.0 CG A:ASP57 4.4 18.7 1.0 CA A:PRO34 4.5 29.6 1.0 PA A:GDP201 4.6 17.1 1.0 O A:THR58 4.6 15.2 1.0 C A:PRO34 4.6 25.6 1.0 O1A A:GDP201 4.7 18.3 1.0 CB A:ALA59 4.7 21.4 1.0 O A:ILE36 4.9 22.4 1.0 CB A:LYS16 4.9 14.5 1.0 O A:TYR32 5.0 35.7 1.0 C A:LYS16 5.0 13.0 1.0 C A:ASP33 5.0 32.3 1.0 O A:HOH353 5.0 25.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Compound 1 Bound to K-Ras(G12D)


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 Compound 1 Bound to K-Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:12.6 occ:1.00 O B:HOH332 2.0 13.2 1.0 OG B:SER17 2.1 11.2 1.0 O B:HOH357 2.1 12.7 1.0 O1B B:GDP201 2.1 12.7 1.0 O B:HOH327 2.1 12.4 1.0 O B:HOH322 2.1 12.3 1.0 CB B:SER17 3.2 10.8 1.0 PB B:GDP201 3.3 11.9 1.0 O2B B:GDP201 3.5 14.1 1.0 N B:SER17 3.9 10.6 1.0 OD2 B:ASP57 4.0 15.8 1.0 CA B:SER17 4.1 10.4 1.0 O2A B:GDP201 4.1 14.3 1.0 OD1 B:ASP57 4.2 17.3 1.0 O B:PRO34 4.2 16.5 1.0 O B:ASP33 4.2 15.0 1.0 CA B:PRO34 4.3 16.8 1.0 O3A B:GDP201 4.4 11.2 1.0 O3B B:GDP201 4.4 12.4 1.0 CG B:ASP57 4.5 14.3 1.0 O B:THR58 4.5 14.3 1.0 O B:ILE36 4.5 14.4 1.0 O B:HOH318 4.5 21.0 1.0 C B:PRO34 4.6 14.8 1.0 CD2 B:TYR32 4.6 17.4 1.0 PA B:GDP201 4.6 13.2 1.0 O1A B:GDP201 4.6 13.9 1.0 CB B:ALA59 4.8 16.6 1.0 O B:TYR32 4.8 16.4 1.0 CB B:LYS16 5.0 11.3 1.0

Q.Zheng, Z.Zhang, K.Z.Guiley, K.M.Shokat. Strain-Release Alkylation of ASP12 Enables Mutant Selective Targeting of K-Ras-G12D. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38443470
DOI: 10.1038/S41589-024-01565-W