Magnesium in PDB 7yuz: Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784, PDB code: 7yuz was solved by M.Irie, T.A.Fukami, M.Tanada, A.Ohta, T.Torizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.45 / 1.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.012, 66.012, 86.33, 90, 90, 120
R / Rfree (%)	25.9 / 29.9

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 (pdb code 7yuz). 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 Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784, PDB code: 7yuz:

Magnesium binding site 1 out of 1 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:39.3 occ:1.00 O A:HOH314 1.9 34.2 1.0 O A:HOH305 2.0 38.2 1.0 O A:HOH309 2.1 37.3 1.0 OG A:SER17 2.1 40.5 1.0 O A:HOH315 2.2 39.0 1.0 O3B A:GDP201 2.2 40.0 1.0 CB A:SER17 3.2 40.2 1.0 PB A:GDP201 3.4 41.1 1.0 O2B A:GDP201 3.6 40.2 1.0 N A:SER17 4.0 39.9 1.0 O2A A:GDP201 4.0 41.0 1.0 OD2 A:ASP57 4.1 48.2 1.0 CA A:SER17 4.1 40.2 1.0 OD1 A:ASP57 4.2 46.2 1.0 O A:ASP33 4.3 46.0 1.0 O3A A:GDP201 4.3 42.5 1.0 O A:PRO34 4.3 47.7 1.0 O A:ILE36 4.4 49.0 1.0 CD2 A:TYR32 4.4 53.5 1.0 O1B A:GDP201 4.5 41.1 1.0 O A:THR58 4.5 41.8 1.0 CA A:PRO34 4.5 47.2 1.0 CG A:ASP57 4.5 47.0 1.0 PA A:GDP201 4.6 42.3 1.0 C A:PRO34 4.7 47.4 1.0 CB A:ALA59 4.7 45.3 1.0 O1A A:GDP201 4.7 42.7 1.0 CE2 A:TYR32 4.8 54.5 1.0 O A:HOH301 4.9 34.7 1.0 NZ A:LYS16 4.9 53.9 1.0

M.Tanada, A.Ohta. Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 To Be Published.