Magnesium in PDB 8r7w: Kras G12D in Complex with Compound 3

All present enzymatic activity of Kras G12D in Complex with Compound 3:
3.6.5.2;

The structure of Kras G12D in Complex with Compound 3, PDB code: 8r7w was solved by K.M.Zak, D.Kessler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.02 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.72, 72.343, 54.514, 90, 103.45, 90
R / Rfree (%)	17.9 / 20.2

The binding sites of Magnesium atom in the Kras G12D in Complex with Compound 3 (pdb code 8r7w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kras G12D in Complex with Compound 3, PDB code: 8r7w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kras G12D in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12D in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:12.1 occ:1.00 OG A:SER17 2.1 12.4 1.0 OG1 A:THR35 2.1 14.8 1.0 O A:HOH336 2.1 14.3 1.0 O2B A:GCP201 2.1 12.5 1.0 O1G A:GCP201 2.1 14.1 1.0 O A:HOH309 2.1 11.3 1.0 HB A:THR35 3.0 14.9 1.0 CB A:THR35 3.1 14.9 1.0 HB2 A:SER17 3.2 11.6 1.0 CB A:SER17 3.2 11.6 1.0 PG A:GCP201 3.3 13.9 1.0 H A:SER17 3.3 10.8 1.0 PB A:GCP201 3.3 12.3 1.0 H A:THR35 3.3 17.1 1.0 C3B A:GCP201 3.4 13.3 1.0 H3B2 A:GCP201 3.5 13.3 1.0 N A:THR35 3.8 17.1 1.0 HB3 A:SER17 3.8 11.6 1.0 HB2 A:LYS16 3.8 10.1 1.0 N A:SER17 3.9 10.8 1.0 HG21 A:THR35 3.9 15.3 1.0 HE2 A:LYS16 4.1 11.3 1.0 OD2 A:ASP57 4.1 14.4 1.0 CA A:SER17 4.1 11.0 1.0 O A:HOH319 4.1 28.1 1.0 CG2 A:THR35 4.1 15.3 1.0 CA A:THR35 4.1 15.8 1.0 OD1 A:ASP57 4.1 13.5 1.0 O2A A:GCP201 4.2 13.8 1.0 O2G A:GCP201 4.2 13.7 1.0 HA A:PRO34 4.3 20.5 1.0 O A:ASP33 4.4 22.3 1.0 O3G A:GCP201 4.4 14.6 1.0 O3A A:GCP201 4.4 12.5 1.0 O1B A:GCP201 4.4 12.2 1.0 HA A:SER17 4.4 11.0 1.0 O A:THR58 4.5 13.2 1.0 CG A:ASP57 4.5 12.8 1.0 H3B1 A:GCP201 4.5 13.3 1.0 HA A:THR35 4.5 15.8 1.0 HG23 A:THR35 4.6 15.3 1.0 PA A:GCP201 4.6 13.3 1.0 HZ3 A:LYS16 4.8 11.9 1.0 C A:PRO34 4.8 19.5 1.0 O1A A:GCP201 4.8 13.3 1.0 CB A:LYS16 4.8 10.1 1.0 HOA2 A:GCP201 4.9 13.8 1.0 HG22 A:THR35 4.9 15.3 1.0 CE A:LYS16 4.9 11.3 1.0 C A:LYS16 5.0 10.0 1.0

Magnesium binding site 2 out of 2 in the Kras G12D in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12D in Complex with Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:15.0 occ:1.00 O3G B:GCP201 2.0 16.0 1.0 OG B:SER17 2.0 15.1 1.0 O B:HOH305 2.1 13.5 1.0 O2B B:GCP201 2.1 15.4 1.0 O B:HOH319 2.1 16.8 1.0 OG1 B:THR35 2.1 15.7 1.0 HB B:THR35 3.0 16.2 1.0 HB2 B:SER17 3.1 14.2 1.0 CB B:THR35 3.1 16.2 1.0 CB B:SER17 3.1 14.2 1.0 H B:SER17 3.2 12.7 1.0 PG B:GCP201 3.3 16.8 1.0 PB B:GCP201 3.3 15.2 1.0 H B:THR35 3.3 18.4 1.0 C3B B:GCP201 3.4 16.5 1.0 H3B2 B:GCP201 3.5 16.5 1.0 HB3 B:SER17 3.8 14.2 1.0 HB2 B:LYS16 3.8 11.6 1.0 N B:THR35 3.9 18.5 1.0 N B:SER17 3.9 12.7 1.0 HG21 B:THR35 3.9 16.5 1.0 HE2 B:LYS16 4.0 12.4 1.0 CA B:SER17 4.1 13.7 1.0 O B:HOH304 4.1 25.8 1.0 OD2 B:ASP57 4.1 15.4 1.0 CG2 B:THR35 4.1 16.5 1.0 OD1 B:ASP57 4.1 14.7 1.0 CA B:THR35 4.1 16.6 1.0 O2A B:GCP201 4.1 18.0 1.0 O1G B:GCP201 4.1 15.9 1.0 HA B:PRO34 4.3 19.9 1.0 O3A B:GCP201 4.3 16.1 1.0 O1B B:GCP201 4.4 14.9 1.0 HA B:SER17 4.4 13.7 1.0 O2G B:GCP201 4.4 17.4 1.0 O B:THR58 4.4 14.6 1.0 O B:ASP33 4.4 22.1 1.0 CG B:ASP57 4.5 14.4 1.0 H3B1 B:GCP201 4.5 16.5 1.0 HG23 B:THR35 4.6 16.5 1.0 PA B:GCP201 4.6 17.6 1.0 HA B:THR35 4.6 16.6 1.0 HZ3 B:LYS16 4.7 13.1 1.0 O1A B:GCP201 4.7 17.3 1.0 CB B:LYS16 4.8 11.6 1.0 C B:PRO34 4.8 19.4 1.0 HOA2 B:GCP201 4.8 18.1 1.0 HG22 B:THR35 4.9 16.5 1.0 CE B:LYS16 4.9 12.4 1.0 C B:LYS16 4.9 12.2 1.0 HZ1 B:LYS16 5.0 13.1 1.0

K.M.Zak, D.Kessler. Kras G12D in Complex with Compound 3 To Be Published.