Magnesium in PDB 8jhl: Gdp-Bound Kras G12D in Complex with Yk-8S

The structure of Gdp-Bound Kras G12D in Complex with Yk-8S, PDB code: 8jhl 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)	41.18 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.353, 82.353, 97.912, 90, 90, 120
R / Rfree (%)	16.5 / 20.8

The structure of Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S (pdb code 8jhl). 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 G12D in Complex with Yk-8S, PDB code: 8jhl:

Magnesium binding site 1 out of 1 in the Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.0 occ:1.00 OG A:SER17 2.2 25.0 1.0 O3B A:GDP201 2.2 27.5 1.0 O A:HOH345 2.3 25.8 1.0 O A:HOH320 2.4 18.8 1.0 O A:HOH308 2.4 31.9 1.0 CB A:SER17 3.3 25.4 1.0 PB A:GDP201 3.4 26.3 1.0 O1B A:GDP201 3.6 23.5 1.0 N A:SER17 4.1 18.9 1.0 O1A A:GDP201 4.1 23.9 1.0 CA A:SER17 4.2 25.9 1.0 O A:PRO34 4.3 29.7 1.0 CA A:PRO34 4.3 32.8 1.0 OD2 A:ASP57 4.3 24.7 1.0 OD1 A:ASP57 4.3 24.0 1.0 O A:ASP33 4.3 32.9 1.0 CD2 A:TYR32 4.4 34.3 1.0 O2B A:GDP201 4.4 23.0 1.0 O3A A:GDP201 4.5 23.7 1.0 C A:PRO34 4.6 32.9 1.0 PA A:GDP201 4.7 22.4 1.0 CG A:ASP57 4.7 24.4 1.0 CB A:ALA59 4.7 30.8 1.0 O A:ILE36 4.7 29.6 1.0 O A:THR58 4.8 20.3 1.0 CE2 A:TYR32 4.8 35.9 1.0 O2A A:GDP201 4.8 27.3 1.0 CB A:LYS16 4.9 22.1 1.0 O A:HOH337 5.0 37.7 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