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

Enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8, PDB code: 8txg 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) 19.28 / 1.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 74.327, 74.327, 202.985, 90, 90, 120
R / Rfree (%) 19.8 / 22.3

Other elements in 8txg:

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8 (pdb code 8txg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8, PDB code: 8txg:

Magnesium binding site 1 out of 1 in 8txg

Go back to Magnesium Binding Sites List in 8txg
Magnesium binding site 1 out of 1 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:15.9
occ:1.00
 O3B A:GDP201 2.0 15.1 1.0
O A:HOH318 2.1 17.3 1.0
O A:HOH361 2.1 17.3 1.0
OG A:SER17 2.1 17.4 1.0
O A:HOH308 2.1 16.1 1.0
O A:HOH313 2.1 16.1 1.0
CB A:SER17 3.2 16.3 1.0
PB A:GDP201 3.3 16.0 1.0
O2B A:GDP201 3.5 16.4 1.0
N A:SER17 3.9 14.6 1.0
OD2 A:ASP57 4.1 18.9 1.0
O2A A:GDP201 4.1 16.9 1.0
CA A:SER17 4.1 14.8 1.0
O A:ASP33 4.2 18.3 1.0
O A:PRO34 4.2 17.8 1.0
OD1 A:ASP57 4.2 18.4 1.0
O3A A:GDP201 4.3 15.7 1.0
O1B A:GDP201 4.3 15.6 1.0
CA A:PRO34 4.5 17.7 1.0
O A:ILE36 4.5 17.2 1.0
O A:THR58 4.5 15.7 1.0
O A:HOH332 4.5 16.9 1.0
CG A:ASP57 4.5 17.9 1.0
C A:PRO34 4.6 17.3 1.0
PA A:GDP201 4.6 16.5 1.0
CB A:ALA59 4.7 16.5 1.0
CD2 A:TYR32 4.7 19.3 1.0
O1A A:GDP201 4.8 16.8 1.0
O A:TYR32 4.9 18.2 1.0
CB A:LYS16 5.0 15.0 1.0

Reference:

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
Page generated: Fri Aug 15 16:44:10 2025

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