Magnesium in PDB 4m22: Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C, PDB code: 4m22 was solved by J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.67 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.906, 83.457, 86.924, 90.00, 109.29, 90.00
R / Rfree (%)	17.9 / 21.6

The structure of Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C (pdb code 4m22). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C, PDB code: 4m22:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C


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 Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:32.2 occ:1.00 O A:HOH343 2.0 25.6 1.0 O1B A:GDP202 2.1 28.6 1.0 O A:HOH306 2.2 32.4 1.0 O A:HOH345 2.3 23.7 1.0 O A:HOH342 2.3 35.0 1.0 OG A:SER17 2.3 33.0 1.0 HB2 A:SER17 3.1 39.5 1.0 CB A:SER17 3.2 33.0 1.0 PB A:GDP202 3.3 27.9 1.0 H A:SER17 3.4 34.3 1.0 HB2 A:ALA59 3.4 57.4 1.0 O2B A:GDP202 3.5 27.3 1.0 HB2 A:LYS16 3.8 28.4 1.0 HA A:PRO34 3.8 67.2 1.0 HD2 A:TYR32 3.9 73.5 1.0 HE2 A:LYS16 3.9 27.5 1.0 N A:SER17 4.0 28.6 1.0 HB3 A:SER17 4.0 39.5 1.0 OD1 A:ASP57 4.0 34.5 1.0 OD2 A:ASP57 4.0 30.1 1.0 O A:THR58 4.1 40.4 1.0 O2A A:GDP202 4.1 34.0 1.0 CA A:SER17 4.1 31.2 1.0 HB1 A:ALA59 4.1 57.4 1.0 CB A:ALA59 4.2 47.8 1.0 O3B A:GDP202 4.2 28.8 1.0 O A:PRO34 4.2 53.4 1.0 HA A:SER17 4.4 37.5 1.0 CG A:ASP57 4.4 32.2 1.0 O A:ILE36 4.4 49.3 1.0 O3A A:GDP202 4.5 29.2 1.0 O A:ASP33 4.5 55.8 1.0 CA A:PRO34 4.6 56.0 1.0 HE2 A:TYR32 4.6 74.3 1.0 HZ1 A:LYS16 4.6 27.6 1.0 C A:PRO34 4.7 55.6 1.0 CB A:LYS16 4.7 23.6 1.0 PA A:GDP202 4.7 32.7 1.0 HZ3 A:LYS16 4.7 27.6 1.0 CD2 A:TYR32 4.7 61.3 1.0 HA A:ALA59 4.7 54.5 1.0 HB3 A:LYS16 4.8 28.4 1.0 CE A:LYS16 4.8 22.9 1.0 O1A A:GDP202 4.8 32.1 1.0 HB3 A:ALA59 4.9 57.4 1.0 NZ A:LYS16 4.9 23.0 1.0 O A:HOH331 5.0 27.9 1.0 C A:LYS16 5.0 25.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C


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 Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:21.2 occ:1.00 O B:HOH361 1.9 16.3 1.0 O3B B:GDP203 2.0 19.7 1.0 O B:HOH363 2.1 16.1 1.0 O B:HOH302 2.2 17.0 1.0 OG B:SER17 2.2 23.7 1.0 O B:HOH305 2.3 15.6 1.0 HB2 B:SER17 3.1 28.4 1.0 CB B:SER17 3.2 23.6 1.0 PB B:GDP203 3.3 19.8 1.0 H B:SER17 3.5 25.4 1.0 O2B B:GDP203 3.5 20.7 1.0 HA B:PRO34 3.6 28.4 1.0 HD1 B:TYR32 3.8 38.6 1.0 HB2 B:LYS16 3.9 22.3 1.0 HB3 B:SER17 3.9 28.4 1.0 HE2 B:LYS16 4.0 22.1 1.0 N B:SER17 4.0 21.1 1.0 O2A B:GDP203 4.1 22.5 1.0 OD2 B:ASP57 4.2 27.6 1.0 CA B:SER17 4.2 22.1 1.0 O B:PRO34 4.2 21.4 1.0 OD1 B:ASP57 4.3 25.6 1.0 O B:ASP33 4.3 25.8 1.0 O3A B:GDP203 4.4 16.0 1.0 O1B B:GDP203 4.4 20.0 1.0 CA B:PRO34 4.4 23.7 1.0 HB2 B:ALA59 4.5 27.8 1.0 HA B:SER17 4.5 26.5 1.0 O B:ILE36 4.5 24.2 1.0 O B:THR58 4.5 20.3 1.0 C B:PRO34 4.6 22.8 1.0 PA B:GDP203 4.6 21.8 1.0 CG B:ASP57 4.6 26.6 1.0 O1A B:GDP203 4.7 22.9 1.0 CD1 B:TYR32 4.7 32.1 1.0 HA B:ALA59 4.8 26.9 1.0 O B:HOH315 4.8 20.5 1.0 HZ1 B:LYS16 4.8 24.0 1.0 HB3 B:TYR32 4.8 36.9 1.0 CB B:LYS16 4.8 18.6 1.0 CE B:LYS16 4.9 18.4 1.0 HZ3 B:LYS16 4.9 24.0 1.0 O B:TYR32 5.0 27.1 1.0 HE1 B:TYR32 5.0 40.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:29.1 occ:1.00 O C:HOH339 1.8 30.1 1.0 OG C:SER17 2.0 34.6 1.0 O3B C:GDP203 2.0 24.6 1.0 O C:HOH338 2.0 31.6 1.0 O C:HOH335 2.1 36.6 1.0 O C:HOH309 2.5 33.1 1.0 HB2 C:SER17 2.9 39.4 1.0 CB C:SER17 3.0 32.8 1.0 H C:SER17 3.1 31.1 1.0 PB C:GDP203 3.3 25.3 1.0 HA C:PRO34 3.6 71.3 1.0 O2B C:GDP203 3.6 25.5 1.0 HB3 C:SER17 3.7 39.4 1.0 N C:SER17 3.7 25.9 1.0 HB2 C:LYS16 3.8 27.5 1.0 CA C:SER17 3.9 29.3 1.0 OD1 C:ASP57 3.9 39.0 1.0 O2A C:GDP203 4.1 28.8 1.0 HE2 C:LYS16 4.1 29.8 1.0 OD2 C:ASP57 4.2 41.1 1.0 HA C:SER17 4.2 35.1 1.0 O C:PRO34 4.3 59.0 1.0 HB2 C:ALA59 4.3 63.3 1.0 O1B C:GDP203 4.3 24.4 1.0 O3A C:GDP203 4.3 27.7 1.0 O C:ASP33 4.4 61.6 1.0 CA C:PRO34 4.4 59.5 1.0 CG C:ASP57 4.5 39.9 1.0 PA C:GDP203 4.5 27.2 1.0 O C:THR58 4.6 44.4 1.0 O C:ILE36 4.6 61.6 1.0 O1A C:GDP203 4.6 25.5 1.0 HZ1 C:LYS16 4.7 28.5 1.0 C C:PRO34 4.7 60.8 1.0 CB C:LYS16 4.7 22.9 1.0 HZ3 C:LYS16 4.7 28.5 1.0 C C:LYS16 4.8 24.0 1.0 O C:HOH313 4.8 37.3 1.0 CE C:LYS16 5.0 24.9 1.0 NZ C:LYS16 5.0 23.7 1.0

J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat. K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity and Effector Interactions. Nature V. 503 548 2013.
ISSN: ISSN 0028-0836
PubMed: 24256730
DOI: 10.1038/NATURE12796