Magnesium in PDB 4lrw: Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound

The structure of Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound, PDB code: 4lrw 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)	23.92 / 2.15
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	82.862, 82.862, 38.397, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.4

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

Magnesium binding site 1 out of 4 in the Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound


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 K-Ras G12C (Cysteine-Light), Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:15.7 occ:1.00 O A:HOH307 2.0 18.3 1.0 O A:HOH301 2.1 11.9 1.0 OG A:SER17 2.1 18.8 1.0 O1B A:GDP202 2.1 19.9 1.0 O A:HOH306 2.3 13.4 1.0 O A:HOH302 2.4 19.2 1.0 CB A:SER17 3.2 13.2 1.0 PB A:GDP202 3.4 19.2 1.0 O2B A:GDP202 3.7 19.7 1.0 OD2 A:ASP57 3.9 56.5 1.0 O1A A:GDP202 4.0 13.9 1.0 O A:ASP33 4.0 22.2 1.0 N A:SER17 4.1 17.1 1.0 CD2 A:TYR32 4.2 20.8 1.0 CA A:PRO34 4.2 24.4 1.0 CA A:SER17 4.2 17.0 1.0 O A:PRO34 4.3 21.4 1.0 O A:ILE36 4.3 31.2 1.0 O3B A:GDP202 4.4 15.9 1.0 O3A A:GDP202 4.5 15.7 1.0 OD1 A:ASP57 4.5 58.9 1.0 PA A:GDP202 4.5 14.4 1.0 O2A A:GDP202 4.6 16.0 1.0 C A:PRO34 4.6 22.2 1.0 CG A:ASP57 4.6 53.9 1.0 O A:HOH311 4.6 37.0 1.0 C A:ASP33 4.7 23.6 1.0 O A:THR58 4.7 19.6 1.0 CE2 A:TYR32 4.7 24.5 1.0 N A:PRO34 4.8 25.0 1.0 O A:TYR32 4.8 22.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound


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 K-Ras G12C (Cysteine-Light), Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:30.3 occ:0.33 O A:HOH326 2.2 17.8 1.0 O A:HOH325 2.2 23.1 1.0 OE1 A:GLN129 3.9 44.9 1.0 O A:THR124 4.0 26.8 1.0 CD A:GLN129 4.8 37.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound


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 K-Ras G12C (Cysteine-Light), Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:27.9 occ:0.33 O B:HOH322 2.1 27.6 1.0 O B:HOH323 2.3 16.9 1.0 OE1 B:GLN129 3.8 48.2 1.0 O B:THR124 4.0 26.2 1.0 CD B:GLN129 4.8 41.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of K-Ras G12C (Cysteine-Light), Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.5 occ:1.00 O B:HOH304 1.9 16.1 1.0 O1B B:GDP203 2.1 20.0 1.0 O B:HOH301 2.1 13.7 1.0 OG B:SER17 2.1 18.0 1.0 O B:HOH303 2.2 13.6 1.0 O B:HOH302 2.3 19.9 1.0 CB B:SER17 3.2 12.0 1.0 PB B:GDP203 3.4 15.8 1.0 O2B B:GDP203 3.7 20.6 1.0 O1A B:GDP203 3.8 12.1 1.0 OD2 B:ASP57 3.9 68.9 1.0 O B:ASP33 4.0 18.9 1.0 CA B:PRO34 4.0 21.2 1.0 N B:SER17 4.1 16.5 1.0 CD2 B:TYR32 4.2 17.4 1.0 CA B:SER17 4.2 16.4 1.0 O B:PRO34 4.4 20.6 1.0 O3A B:GDP203 4.4 16.8 1.0 O3B B:GDP203 4.4 14.5 1.0 O B:ILE36 4.4 23.2 1.0 PA B:GDP203 4.4 13.7 1.0 O2A B:GDP203 4.5 16.6 1.0 C B:PRO34 4.5 22.1 1.0 OD1 B:ASP57 4.6 71.8 1.0 C B:ASP33 4.6 16.3 1.0 CG B:ASP57 4.6 64.7 1.0 N B:PRO34 4.7 19.6 1.0 O B:TYR32 4.7 20.2 1.0 O B:HOH312 4.7 21.4 1.0 O B:HOH314 4.8 37.7 1.0 CE2 B:TYR32 4.8 20.7 1.0 O B:THR58 4.9 22.4 1.0 CB B:PRO34 5.0 19.4 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