Magnesium in PDB 8g9p: Tricomplex of Rmc-4998, Kras G12C, and Cypa

All present enzymatic activity of Tricomplex of Rmc-4998, Kras G12C, and Cypa:
5.2.1.8;

The structure of Tricomplex of Rmc-4998, Kras G12C, and Cypa, PDB code: 8g9p was solved by A.C.A.Tomlinson, M.Saldajeno-Concar, J.E.Knox, J.K.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.43 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.03, 101.76, 66.36, 90, 91.04, 90
R / Rfree (%)	15.6 / 18.8

The structure of Tricomplex of Rmc-4998, Kras G12C, and Cypa also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Tricomplex of Rmc-4998, Kras G12C, and Cypa (pdb code 8g9p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tricomplex of Rmc-4998, Kras G12C, and Cypa, PDB code: 8g9p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tricomplex of Rmc-4998, Kras G12C, and Cypa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tricomplex of Rmc-4998, Kras G12C, and Cypa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:12.8 occ:1.00 O1G A:GNP201 2.0 14.8 1.0 O2B A:GNP201 2.0 12.5 1.0 OG1 A:THR35 2.0 14.9 1.0 O A:HOH343 2.1 14.6 1.0 OG A:SER17 2.1 15.1 1.0 O A:HOH316 2.1 14.6 1.0 CB A:THR35 3.1 12.2 1.0 CB A:SER17 3.1 13.3 1.0 PB A:GNP201 3.2 13.3 1.0 PG A:GNP201 3.2 13.9 1.0 N3B A:GNP201 3.4 12.9 1.0 N A:SER17 3.8 12.1 1.0 N A:THR35 3.9 12.9 1.0 CA A:SER17 4.1 12.5 1.0 CG2 A:THR35 4.1 14.8 1.0 CA A:THR35 4.1 13.9 1.0 OD2 A:ASP57 4.1 15.4 1.0 O2A A:GNP201 4.1 14.6 1.0 O3G A:GNP201 4.2 14.7 1.0 OD1 A:ASP57 4.2 14.8 1.0 O2G A:GNP201 4.2 16.0 1.0 O A:HOH310 4.3 23.1 0.4 O3A A:GNP201 4.3 13.9 1.0 O1B A:GNP201 4.3 12.9 1.0 O A:HOH310 4.5 23.1 0.2 O A:THR58 4.5 13.4 1.0 O A:ASP33 4.5 15.7 1.0 CG A:ASP57 4.5 13.4 1.0 PA A:GNP201 4.6 14.0 1.0 CB A:LYS16 4.7 13.0 1.0 O1A A:GNP201 4.7 13.9 1.0 CE A:LYS16 4.8 12.1 1.0 C A:LYS16 4.9 13.4 1.0 C A:PRO34 4.9 16.5 1.0

Magnesium binding site 2 out of 2 in the Tricomplex of Rmc-4998, Kras G12C, and Cypa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tricomplex of Rmc-4998, Kras G12C, and Cypa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:12.5 occ:1.00 O1G B:GNP201 2.0 14.2 1.0 OG1 B:THR35 2.1 13.6 1.0 OG B:SER17 2.1 13.2 1.0 O B:HOH343 2.1 14.1 1.0 O2B B:GNP201 2.1 12.1 1.0 O B:HOH318 2.1 13.3 1.0 CB B:THR35 3.0 11.8 1.0 CB B:SER17 3.2 12.7 1.0 PG B:GNP201 3.2 12.0 1.0 PB B:GNP201 3.2 11.8 1.0 N3B B:GNP201 3.4 11.5 1.0 N B:SER17 3.9 12.1 1.0 N B:THR35 3.9 13.0 1.0 CG2 B:THR35 4.0 15.4 1.0 CA B:THR35 4.1 13.2 1.0 CA B:SER17 4.1 12.6 1.0 OD2 B:ASP57 4.1 16.4 1.0 O B:HOH305 4.1 25.5 0.4 O2A B:GNP201 4.2 14.2 1.0 O3G B:GNP201 4.2 13.4 1.0 O2G B:GNP201 4.2 15.3 1.0 O B:HOH305 4.3 25.5 0.6 OD1 B:ASP57 4.3 15.5 1.0 O1B B:GNP201 4.3 12.1 1.0 O3A B:GNP201 4.3 12.5 1.0 O B:ASP33 4.5 15.5 1.0 O B:THR58 4.5 13.4 1.0 CG B:ASP57 4.6 12.7 1.0 PA B:GNP201 4.6 12.9 1.0 O1A B:GNP201 4.7 14.6 1.0 CB B:LYS16 4.7 10.5 1.0 CE B:LYS16 4.7 12.2 1.0 C B:PRO34 4.9 14.5 1.0 C B:LYS16 4.9 12.7 1.0

A.C.A.Tomlinson, M.Saldajeno-Concar, J.E.Knox, J.K.Yano. Chemical Remodeling of A Cellular Chaperone to Target the Active State of Mutant Kras Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADG9652