Magnesium in PDB 8txh: Crystal Structure of Kras G12D in Complex with Gdp and Compound 14

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 14:
3.6.5.2;

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 14, PDB code: 8txh was solved by P.Chen, A.Irimia, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.475, 62.392, 72.132, 90, 91.86, 90
R / Rfree (%)	19 / 20.3

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 14 also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 14 (pdb code 8txh). 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 Kras G12D in Complex with Gdp and Compound 14, PDB code: 8txh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 14


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 Kras G12D in Complex with Gdp and Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:8.0 occ:1.00 O1B A:GDP201 2.0 7.5 1.0 O A:HOH306 2.1 8.9 1.0 O A:HOH316 2.1 8.2 1.0 O A:HOH312 2.1 8.6 1.0 OG A:SER17 2.1 7.5 1.0 O A:HOH348 2.1 8.8 1.0 CB A:SER17 3.2 8.1 1.0 PB A:GDP201 3.3 7.8 1.0 O3B A:GDP201 3.5 8.2 1.0 N A:SER17 3.9 7.2 1.0 OD2 A:ASP57 4.1 10.5 1.0 CA A:SER17 4.1 7.2 1.0 O1A A:GDP201 4.1 9.9 1.0 OD1 A:ASP57 4.1 9.8 1.0 O A:ASP33 4.2 11.3 1.0 O A:PRO34 4.2 9.8 1.0 O3A A:GDP201 4.3 8.1 1.0 O2B A:GDP201 4.3 7.4 1.0 CA A:PRO34 4.4 10.0 1.0 O A:ILE36 4.5 9.0 1.0 CG A:ASP57 4.5 11.1 1.0 PA A:GDP201 4.5 8.9 1.0 O A:THR58 4.5 8.2 1.0 C A:PRO34 4.6 9.8 1.0 O A:HOH371 4.6 9.8 1.0 CD2 A:TYR32 4.6 15.6 1.0 O2A A:GDP201 4.6 10.1 1.0 CB A:ALA59 4.8 9.5 1.0 O A:TYR32 4.9 13.0 1.0 CB A:LYS16 4.9 7.2 1.0 C A:LYS16 5.0 7.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 14


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 Kras G12D in Complex with Gdp and Compound 14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:7.5 occ:1.00 O3B B:GDP201 2.0 7.4 1.0 OG B:SER17 2.1 7.5 1.0 O B:HOH311 2.1 8.0 1.0 O B:HOH366 2.1 7.8 1.0 O B:HOH319 2.1 7.8 1.0 O B:HOH313 2.1 8.6 1.0 CB B:SER17 3.2 7.6 1.0 PB B:GDP201 3.3 7.1 1.0 O2B B:GDP201 3.5 7.3 1.0 N B:SER17 3.9 6.8 1.0 OD2 B:ASP57 4.1 10.7 1.0 CA B:SER17 4.1 6.7 1.0 OD1 B:ASP57 4.1 9.6 1.0 O2A B:GDP201 4.2 9.0 1.0 O B:ASP33 4.2 11.1 1.0 O B:PRO34 4.2 9.8 1.0 O3A B:GDP201 4.3 7.5 1.0 O1B B:GDP201 4.4 7.5 1.0 CA B:PRO34 4.4 9.9 1.0 O B:ILE36 4.4 9.1 1.0 CG B:ASP57 4.5 9.6 1.0 O B:THR58 4.5 8.3 1.0 PA B:GDP201 4.5 8.3 1.0 C B:PRO34 4.6 10.1 1.0 O B:HOH379 4.6 9.2 1.0 CD2 B:TYR32 4.7 15.9 1.0 O1A B:GDP201 4.7 9.4 1.0 CB B:ALA59 4.8 9.1 1.0 O B:TYR32 4.9 12.4 1.0 CB B:LYS16 4.9 6.5 1.0 C B:LYS16 5.0 7.0 1.0

H.Cheng, P.Li, P.Chen, A.Irimia, J.H.Bae, A.Brooun, P.Fagan, R.Lam, B.Lin, J.Zhang, X.Zhan, X.Wu, N.Xie, G.Chiang, R.Shoemaker, J.M.Vernier. Structure-Based Design and Synthesis of Potent and Selective Kras G12D Inhibitors. Acs Med.Chem.Lett. V. 14 1351 2023.
ISSN: ISSN 1948-5875
PubMed: 37849557
DOI: 10.1021/ACSMEDCHEMLETT.3C00245