Magnesium in PDB 6quw: Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 9B

The structure of Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 9B, PDB code: 6quw 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)	35.90 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.539, 72.097, 54.616, 90.00, 103.31, 90.00
R / Rfree (%)	19.3 / 21

The binding sites of Magnesium atom in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 9B (pdb code 6quw). 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 9B, PDB code: 6quw:
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 9B


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 9B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:11.6 occ:1.00 O A:HOH346 2.0 14.4 1.0 O1G A:GCP201 2.1 14.0 1.0 OG1 A:THR35 2.1 13.3 1.0 OG A:SER17 2.1 11.4 1.0 O A:HOH311 2.1 11.5 1.0 O1B A:GCP201 2.1 10.9 1.0 CB A:THR35 3.1 12.9 1.0 CB A:SER17 3.2 10.7 1.0 PG A:GCP201 3.2 13.9 1.0 H3B1 A:GCP201 3.3 14.3 0.0 PB A:GCP201 3.3 11.7 1.0 C3B A:GCP201 3.5 12.7 1.0 HOA2 A:GCP201 3.7 14.1 0.0 N A:THR35 3.8 14.1 1.0 N A:SER17 3.9 9.7 1.0 CA A:SER17 4.1 9.8 1.0 CA A:THR35 4.1 13.6 1.0 OD2 A:ASP57 4.1 14.3 1.0 O2A A:GCP201 4.1 13.5 1.0 OD1 A:ASP57 4.1 12.6 1.0 CG2 A:THR35 4.1 13.7 1.0 O2G A:GCP201 4.2 14.3 1.0 O3A A:GCP201 4.4 12.1 1.0 O3G A:GCP201 4.4 14.3 1.0 O2B A:GCP201 4.4 10.4 1.0 O A:ASP33 4.4 21.1 1.0 O A:THR58 4.5 14.2 1.0 CG A:ASP57 4.5 13.3 1.0 H3B2 A:GCP201 4.5 14.3 0.0 PA A:GCP201 4.6 13.9 1.0 O1A A:GCP201 4.7 13.7 1.0 C A:PRO34 4.8 18.6 1.0 CB A:LYS16 4.8 10.1 1.0 CE A:LYS16 4.9 12.0 1.0 C A:LYS16 5.0 10.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras-G12D in Complex with Natural Product-Like Compound 9B


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 9B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:12.3 occ:1.00 O1G B:GCP201 2.0 13.8 1.0 O B:HOH304 2.0 10.7 1.0 OG1 B:THR35 2.0 12.3 1.0 OG B:SER17 2.0 13.5 1.0 O B:HOH319 2.1 14.1 1.0 O1B B:GCP201 2.1 12.9 1.0 CB B:THR35 3.1 16.1 1.0 CB B:SER17 3.2 12.2 1.0 PG B:GCP201 3.2 14.7 1.0 PB B:GCP201 3.3 13.2 1.0 H3B1 B:GCP201 3.3 15.2 0.0 C3B B:GCP201 3.5 14.9 1.0 N B:THR35 3.9 15.7 1.0 N B:SER17 3.9 11.5 1.0 OD2 B:ASP57 4.1 15.4 1.0 CA B:SER17 4.1 10.1 1.0 OD1 B:ASP57 4.1 12.5 1.0 CG2 B:THR35 4.1 15.1 1.0 O B:HOH308 4.1 22.1 1.0 CA B:THR35 4.1 12.8 1.0 O2A B:GCP201 4.1 15.8 1.0 O2G B:GCP201 4.2 13.3 1.0 O3G B:GCP201 4.4 12.2 1.0 O3A B:GCP201 4.4 14.2 1.0 O2B B:GCP201 4.4 13.2 1.0 O B:THR58 4.4 14.3 1.0 O B:ASP33 4.4 18.9 1.0 HOA2 B:GCP201 4.4 15.8 0.0 CG B:ASP57 4.5 15.6 1.0 H3B2 B:GCP201 4.6 15.2 0.0 PA B:GCP201 4.6 15.0 1.0 O1A B:GCP201 4.7 14.6 1.0 CB B:LYS16 4.8 10.6 1.0 C B:PRO34 4.8 19.0 1.0 CE B:LYS16 4.9 12.2 1.0 C B:LYS16 4.9 12.3 1.0

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