Magnesium in PDB 6qux: Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15

The structure of Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15, PDB code: 6qux was solved by G.Fischer, D.Kessler, B.Muellauer, B.Wolkerstorfer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.33 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.761, 72.728, 54.858, 90.00, 103.69, 90.00
R / Rfree (%)	20.4 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15 (pdb code 6qux). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15, PDB code: 6qux:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15


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 Natural Product-Like Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:15.5 occ:1.00 OG A:SER17 2.0 15.6 1.0 O1G A:GCP201 2.0 16.6 1.0 O1B A:GCP201 2.1 11.5 1.0 OG1 A:THR35 2.1 14.3 1.0 O A:HOH303 2.1 12.9 1.0 O A:HOH306 2.2 17.1 1.0 HB A:THR35 3.1 13.1 0.0 H A:SER17 3.1 10.6 0.0 CB A:THR35 3.1 13.1 1.0 HOA2 A:GCP201 3.1 14.7 0.0 CB A:SER17 3.2 11.6 1.0 HB2 A:SER17 3.2 11.6 0.0 H A:THR35 3.3 18.0 0.0 PG A:GCP201 3.3 17.6 1.0 PB A:GCP201 3.3 15.9 1.0 C3B A:GCP201 3.6 16.8 1.0 H3B1 A:GCP201 3.6 16.9 0.0 HB2 A:LYS16 3.7 12.4 0.0 N A:SER17 3.8 10.6 1.0 N A:THR35 3.9 18.0 1.0 HE2 A:LYS16 3.9 11.7 0.0 HB3 A:SER17 3.9 11.6 0.0 HG21 A:THR35 4.0 15.7 0.0 CA A:SER17 4.0 10.8 1.0 O2A A:GCP201 4.1 14.7 1.0 CA A:THR35 4.1 15.5 1.0 OD1 A:ASP57 4.1 15.0 1.0 OD2 A:ASP57 4.1 20.4 1.0 CG2 A:THR35 4.1 15.6 1.0 O3G A:GCP201 4.2 16.6 1.0 HA A:PRO34 4.3 22.7 0.0 O A:HOH333 4.3 35.3 1.0 O2B A:GCP201 4.3 13.4 1.0 O A:ASP33 4.4 26.1 1.0 O2G A:GCP201 4.4 13.6 1.0 O3A A:GCP201 4.4 12.4 1.0 HA A:SER17 4.4 10.8 0.0 O A:THR58 4.5 15.4 1.0 CG A:ASP57 4.5 16.1 1.0 HG23 A:THR35 4.6 15.7 0.0 H3B2 A:GCP201 4.6 16.9 0.0 PA A:GCP201 4.6 15.9 1.0 HA A:THR35 4.6 15.5 0.0 O1A A:GCP201 4.8 14.2 1.0 CB A:LYS16 4.8 12.4 1.0 C A:PRO34 4.8 24.3 1.0 HZ3 A:LYS16 4.8 13.5 0.0 C A:LYS16 4.9 11.4 1.0 HZ1 A:LYS16 4.9 13.5 0.0 CE A:LYS16 4.9 11.7 1.0 H A:LYS16 4.9 10.3 0.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:15.3 occ:1.00 OG B:SER17 1.9 13.6 1.0 O1G B:GCP203 2.0 13.3 1.0 OG1 B:THR35 2.1 12.2 1.0 O B:HOH306 2.1 11.2 1.0 O B:HOH313 2.2 15.0 1.0 O1B B:GCP203 2.2 11.7 1.0 HB B:THR35 3.1 14.6 0.0 CB B:SER17 3.1 14.2 1.0 CB B:THR35 3.1 14.6 1.0 H B:SER17 3.1 14.2 0.0 HB2 B:SER17 3.2 14.2 0.0 H B:THR35 3.3 15.1 0.0 PG B:GCP203 3.3 16.3 1.0 HOA2 B:GCP203 3.3 13.3 0.0 PB B:GCP203 3.3 14.5 1.0 H3B1 B:GCP203 3.4 12.3 0.0 C3B B:GCP203 3.5 12.3 1.0 HB2 B:LYS16 3.7 13.5 0.0 N B:SER17 3.8 14.2 1.0 HB3 B:SER17 3.8 14.2 0.0 HE2 B:LYS16 3.9 12.5 0.0 N B:THR35 3.9 15.1 1.0 HG21 B:THR35 3.9 15.6 0.0 CA B:SER17 4.0 13.5 1.0 OD2 B:ASP57 4.0 18.2 1.0 OD1 B:ASP57 4.1 15.9 1.0 CA B:THR35 4.1 13.1 1.0 CG2 B:THR35 4.1 15.8 1.0 O2A B:GCP203 4.1 13.3 1.0 O3G B:GCP203 4.2 16.0 1.0 O B:HOH353 4.2 25.3 1.0 HA B:PRO34 4.3 16.2 0.0 O B:ASP33 4.4 19.7 1.0 HA B:SER17 4.4 13.5 0.0 O2B B:GCP203 4.4 16.3 1.0 O B:THR58 4.4 14.6 1.0 O2G B:GCP203 4.4 13.7 1.0 CG B:ASP57 4.4 17.9 1.0 O3A B:GCP203 4.5 14.4 1.0 HG23 B:THR35 4.6 15.6 0.0 PA B:GCP203 4.6 14.8 1.0 H3B2 B:GCP203 4.6 12.3 0.0 O1A B:GCP203 4.6 13.6 1.0 HA B:THR35 4.6 13.1 0.0 CB B:LYS16 4.8 13.5 1.0 HZ3 B:LYS16 4.8 9.8 0.0 C B:PRO34 4.8 20.0 1.0 HZ1 B:LYS16 4.9 9.8 0.0 CE B:LYS16 4.9 12.5 1.0 C B:LYS16 4.9 14.7 1.0 HA B:ALA59 5.0 14.0 0.0 HG22 B:THR35 5.0 15.6 0.0 H B:LYS16 5.0 11.4 0.0

A.Bergner, X.Cockcroft, G.Fischer, A.Gollner, W.Hela, R.Kousek, A.Mantoulidis, L.J.Martin, M.Mayer, B.Mullauer, G.Siszler, B.Wolkerstorfer, D.Kessler, D.B.Mcconnell. Kras Binders Hidden in Nature. Chemistry V. 25 12037 2019.
ISSN: ISSN 0947-6539
PubMed: 31231840
DOI: 10.1002/CHEM.201902810