Magnesium in PDB 6zli: Crystal Structure of Kras-G12D in Complex with Compound 13 and Gcp

The structure of Crystal Structure of Kras-G12D in Complex with Compound 13 and Gcp, PDB code: 6zli was solved by D.Kessler, G.Fischer, J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.80 / 1.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.642, 73.164, 54.194, 90.00, 103.15, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Magnesium atom in the Crystal Structure of Kras-G12D in Complex with Compound 13 and Gcp (pdb code 6zli). 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 Compound 13 and Gcp, PDB code: 6zli:
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 Compound 13 and Gcp


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 Compound 13 and Gcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:11.0 occ:1.00 O1G A:GCP201 2.0 10.0 1.0 O A:HOH318 2.0 5.5 1.0 OG1 A:THR35 2.0 9.8 1.0 O A:HOH326 2.1 8.7 1.0 OG A:SER17 2.2 8.8 1.0 O2B A:GCP201 2.2 8.2 1.0 CB A:THR35 3.0 10.2 1.0 CB A:SER17 3.2 7.2 1.0 PG A:GCP201 3.3 9.8 1.0 PB A:GCP201 3.4 7.7 1.0 C3B A:GCP201 3.6 8.0 1.0 N A:THR35 3.8 11.2 1.0 N A:SER17 3.8 6.1 1.0 CA A:THR35 4.0 10.7 1.0 OD1 A:ASP57 4.1 7.1 1.0 CG2 A:THR35 4.1 10.9 1.0 CA A:SER17 4.1 6.9 1.0 OD2 A:ASP57 4.1 9.8 1.0 O2A A:GCP201 4.2 10.0 1.0 O2G A:GCP201 4.2 9.2 1.0 O A:HOH321 4.2 21.6 1.0 O A:THR58 4.3 7.5 1.0 O1B A:GCP201 4.4 7.8 1.0 O3G A:GCP201 4.4 10.1 1.0 O A:ASP33 4.4 13.9 1.0 CG A:ASP57 4.5 8.6 1.0 O3A A:GCP201 4.5 9.2 1.0 CB A:LYS16 4.7 4.5 1.0 PA A:GCP201 4.7 10.6 1.0 C A:PRO34 4.7 12.2 1.0 O1A A:GCP201 4.8 10.4 1.0 CE A:LYS16 4.8 7.0 1.0 C A:LYS16 4.9 5.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras-G12D in Complex with Compound 13 and Gcp


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 Compound 13 and Gcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:7.8 occ:1.00 O B:HOH310 2.0 7.3 1.0 O1G B:GCP201 2.0 8.4 1.0 OG B:SER17 2.1 9.3 1.0 O2B B:GCP201 2.1 7.2 1.0 OG1 B:THR35 2.1 8.4 1.0 O B:HOH328 2.2 6.5 1.0 CB B:THR35 3.1 7.9 1.0 CB B:SER17 3.2 7.2 1.0 PG B:GCP201 3.2 8.0 1.0 PB B:GCP201 3.3 6.9 1.0 C3B B:GCP201 3.5 7.2 1.0 N B:SER17 3.8 6.4 1.0 N B:THR35 3.9 8.6 1.0 OD1 B:ASP57 4.0 9.4 1.0 CA B:SER17 4.0 6.9 1.0 OD2 B:ASP57 4.1 8.6 1.0 O2G B:GCP201 4.1 7.6 1.0 CA B:THR35 4.1 8.1 1.0 CG2 B:THR35 4.2 7.5 1.0 O2A B:GCP201 4.2 7.9 1.0 O B:HOH346 4.2 19.4 1.0 O1B B:GCP201 4.3 7.2 1.0 O B:THR58 4.4 7.6 1.0 O3A B:GCP201 4.4 6.7 1.0 O B:ASP33 4.4 12.3 1.0 CG B:ASP57 4.5 9.2 1.0 O3G B:GCP201 4.5 7.6 1.0 PA B:GCP201 4.6 8.3 1.0 O1A B:GCP201 4.6 7.7 1.0 CB B:LYS16 4.6 5.6 1.0 CE B:LYS16 4.8 9.8 1.0 C B:LYS16 4.8 6.4 1.0 C B:PRO34 4.9 9.7 1.0

D.Kessler, A.Bergner, J.Bottcher, G.Fischer, S.Dobel, M.Hinkel, B.Mullauer, A.Weiss-Puxbaum, D.B.Mcconnell. Drugging All Ras Isoforms with One Pocket. Future Med Chem V. 12 1911 2020.
ISSN: ISSN 1756-8927
PubMed: 32779487
DOI: 10.4155/FMC-2020-0221