Magnesium in PDB 8jgd: Gdp-Bound Kras G12C in Complex with Yk-8S

All present enzymatic activity of Gdp-Bound Kras G12C in Complex with Yk-8S:
3.6.5.2;

The structure of Gdp-Bound Kras G12C in Complex with Yk-8S, PDB code: 8jgd was solved by Z.M.Zhang, R.L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 1.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.284, 82.284, 97.479, 90, 90, 120
R / Rfree (%)	16.8 / 20.1

The structure of Gdp-Bound Kras G12C in Complex with Yk-8S also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Gdp-Bound Kras G12C in Complex with Yk-8S (pdb code 8jgd). 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 Gdp-Bound Kras G12C in Complex with Yk-8S, PDB code: 8jgd:

Magnesium binding site 1 out of 1 in the Gdp-Bound Kras G12C in Complex with Yk-8S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdp-Bound Kras G12C in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:9.3 occ:1.00 O3B A:GDP201 2.3 14.9 1.0 OG A:SER17 2.3 18.1 1.0 O A:HOH324 2.3 13.8 1.0 O A:HOH346 2.3 18.1 1.0 O A:HOH330 2.3 16.3 1.0 O A:HOH334 2.4 16.8 1.0 CB A:SER17 3.3 17.7 1.0 PB A:GDP201 3.5 14.3 1.0 O1B A:GDP201 3.6 14.9 1.0 N A:SER17 4.0 13.2 1.0 OD2 A:ASP57 4.1 17.7 1.0 CA A:SER17 4.2 13.2 1.0 O1A A:GDP201 4.2 18.9 1.0 CA A:PRO34 4.3 21.7 1.0 CB A:ALA59 4.3 21.6 1.0 OD1 A:ASP57 4.3 17.4 1.0 O A:ASP33 4.4 22.2 1.0 O2B A:GDP201 4.5 13.5 1.0 CD2 A:TYR32 4.5 21.9 1.0 O3A A:GDP201 4.5 13.5 1.0 O A:PRO34 4.6 20.2 1.0 O A:THR58 4.6 16.1 1.0 CG A:ASP57 4.6 16.9 1.0 PA A:GDP201 4.7 17.4 1.0 O A:ILE36 4.7 18.7 1.0 OBF A:DWI203 4.7 17.8 1.0 C A:PRO34 4.8 20.6 1.0 O2A A:GDP201 4.8 15.9 1.0 CB A:LYS16 4.9 13.5 1.0 CE A:LYS16 4.9 15.2 1.0 O A:TYR32 5.0 24.6 1.0

Z.Yu, X.He, R.Wang, X.Xu, Z.Zhang, K.Ding, Z.M.Zhang, Y.Tan, Z.Li. Simultaneous Covalent Modification of K-Ras(G12D) and K-Ras(G12C) with Tunable Oxirane Electrophiles. J.Am.Chem.Soc. V. 145 20403 2023.
ISSN: ESSN 1520-5126
PubMed: 37534597
DOI: 10.1021/JACS.3C05899