Magnesium in PDB 8txe: Crystal Structure of Kras G12D in Complex with Gdp and Compound 5

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5:
3.6.5.2;

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5, PDB code: 8txe 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)	29.77 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.815, 62.166, 71.925, 90, 91.86, 90
R / Rfree (%)	18.8 / 21.5

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	10 atoms

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 (pdb code 8txe). 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 5, PDB code: 8txe:
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 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:8.5 occ:1.00 O1B A:GDP201 2.0 7.5 1.0 O A:HOH325 2.1 9.8 1.0 O A:HOH307 2.1 9.0 1.0 OG A:SER17 2.1 8.7 1.0 O A:HOH320 2.1 9.1 1.0 O A:HOH355 2.1 10.1 1.0 CB A:SER17 3.2 9.0 1.0 PB A:GDP201 3.2 8.4 1.0 O3B A:GDP201 3.5 8.9 1.0 N A:SER17 3.9 7.9 1.0 CA A:SER17 4.1 7.8 1.0 O1A A:GDP201 4.1 10.3 1.0 OD1 A:ASP57 4.2 13.2 1.0 OD2 A:ASP57 4.2 14.8 1.0 O A:ASP33 4.2 10.2 1.0 O3A A:GDP201 4.2 8.5 1.0 O A:PRO34 4.3 10.3 1.0 O2B A:GDP201 4.3 8.5 1.0 CA A:PRO34 4.4 10.4 1.0 O A:ILE36 4.5 9.2 1.0 PA A:GDP201 4.5 9.7 1.0 O A:THR58 4.6 7.6 1.0 CG A:ASP57 4.6 14.0 1.0 C A:PRO34 4.6 10.0 1.0 O A:HOH376 4.6 10.8 1.0 O2A A:GDP201 4.6 11.3 1.0 CD2 A:TYR32 4.6 16.8 1.0 CB A:ALA59 4.8 9.6 1.0 CB A:LYS16 5.0 7.2 1.0 C A:LYS16 5.0 7.6 1.0 O A:TYR32 5.0 12.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:8.2 occ:1.00 O B:HOH314 2.0 7.4 1.0 O3B B:GDP201 2.0 6.8 1.0 O B:HOH329 2.1 7.7 1.0 O B:HOH359 2.1 7.7 1.0 O B:HOH349 2.1 7.8 1.0 OG B:SER17 2.1 7.1 1.0 CB B:SER17 3.2 6.1 1.0 PB B:GDP201 3.3 7.0 1.0 O2B B:GDP201 3.5 7.5 1.0 N B:SER17 3.9 6.0 1.0 O2A B:GDP201 4.1 8.6 1.0 CA B:SER17 4.1 5.8 1.0 OD1 B:ASP57 4.1 10.5 1.0 OD2 B:ASP57 4.1 12.9 1.0 O B:ASP33 4.2 10.2 1.0 O B:PRO34 4.2 10.0 1.0 O3A B:GDP201 4.3 7.3 1.0 O1B B:GDP201 4.4 6.9 1.0 CA B:PRO34 4.4 9.4 1.0 O B:ILE36 4.4 9.4 1.0 C B:PRO34 4.5 9.4 1.0 O B:THR58 4.5 7.3 1.0 PA B:GDP201 4.6 8.2 1.0 CG B:ASP57 4.6 12.1 1.0 O B:HOH402 4.6 10.0 1.0 CD2 B:TYR32 4.6 15.2 1.0 O1A B:GDP201 4.6 8.7 1.0 CB B:ALA59 4.8 9.1 1.0 CB B:LYS16 5.0 6.0 1.0 C B:LYS16 5.0 5.9 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