Magnesium in PDB 5wha: Kras G12V, Bound to Gdp and Miniprotein 225-11

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11, PDB code: 5wha was solved by S.Y.Shim, J.H.Mcgee, S.-J.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.45 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.003, 40.328, 230.939, 90.00, 90.99, 90.00
R / Rfree (%)	23.8 / 27.7

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11 also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Magnesium atom in the Kras G12V, Bound to Gdp and Miniprotein 225-11 (pdb code 5wha). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Kras G12V, Bound to Gdp and Miniprotein 225-11, PDB code: 5wha:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:18.7 occ:1.00 O1B A:GDP202 2.1 19.0 1.0 OG A:SER17 2.1 25.5 1.0 O A:HOH313 2.1 18.4 1.0 O A:HOH310 2.4 23.9 1.0 CB A:SER17 3.3 23.6 1.0 PB A:GDP202 3.4 22.8 1.0 O2B A:GDP202 3.6 35.2 1.0 OD2 A:ASP57 3.9 33.0 1.0 N A:SER17 4.0 23.2 1.0 O A:HOH307 4.1 31.5 1.0 CA A:SER17 4.2 26.5 1.0 O1A A:GDP202 4.2 20.8 1.0 OD1 A:ASP57 4.3 43.0 1.0 O3B A:GDP202 4.3 19.3 1.0 O A:THR58 4.4 18.8 1.0 O3A A:GDP202 4.4 69.5 1.0 CG A:ASP57 4.5 37.4 1.0 CA A:ALA59 4.6 25.8 1.0 PA A:GDP202 4.6 22.0 1.0 O2A A:GDP202 4.6 24.1 1.0 NZ A:LYS16 4.8 21.7 1.0 CE A:LYS16 4.9 19.2 1.0

Magnesium binding site 2 out of 4 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:27.2 occ:1.00 OG D:SER17 2.0 21.5 1.0 O D:HOH305 2.2 17.3 1.0 O3B D:GDP202 2.4 22.2 1.0 O D:HOH329 2.9 40.0 1.0 CB D:SER17 3.2 27.6 1.0 PB D:GDP202 3.8 16.7 1.0 OD2 D:ASP57 3.8 45.1 1.0 N D:SER17 4.0 24.9 1.0 CA D:SER17 4.2 27.6 1.0 O2B D:GDP202 4.2 21.8 1.0 O2A D:GDP202 4.3 53.0 1.0 O D:THR58 4.3 26.7 1.0 OD1 D:ASP57 4.3 40.4 1.0 CG D:ASP57 4.5 39.8 1.0 O1B D:GDP202 4.5 20.5 1.0 CA D:ALA59 4.8 27.1 1.0 O D:HOH315 4.9 18.2 1.0 O3A D:GDP202 4.9 34.4 1.0 O1A D:GDP202 4.9 36.0 1.0 PA D:GDP202 4.9 44.0 1.0

Magnesium binding site 3 out of 4 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg201 b:17.9 occ:1.00 O G:HOH317 2.0 17.0 1.0 O1B G:GDP202 2.0 16.9 1.0 O G:HOH312 2.2 31.8 1.0 O G:HOH303 2.4 20.5 1.0 OG G:SER17 2.5 37.6 1.0 PB G:GDP202 3.2 16.7 1.0 O2B G:GDP202 3.2 22.8 1.0 CB G:SER17 3.7 17.7 1.0 O1A G:GDP202 4.0 25.8 1.0 O G:HOH326 4.1 15.9 1.0 O3B G:GDP202 4.1 27.4 1.0 OD2 G:ASP57 4.2 44.6 1.0 O3A G:GDP202 4.3 26.6 1.0 N G:SER17 4.5 25.6 1.0 O G:THR58 4.5 35.5 1.0 CA G:ALA59 4.5 30.4 1.0 PA G:GDP202 4.6 30.4 1.0 CA G:SER17 4.7 17.8 1.0 OD1 G:ASP57 4.7 37.9 1.0 CB G:ALA59 4.8 35.1 1.0 O2A G:GDP202 4.9 33.8 1.0 CG G:ASP57 4.9 39.0 1.0 N G:GLY60 5.0 34.8 1.0

Magnesium binding site 4 out of 4 in the Kras G12V, Bound to Gdp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras G12V, Bound to Gdp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg201 b:17.1 occ:1.00 O J:HOH310 2.1 25.2 1.0 O J:HOH316 2.1 22.9 1.0 O3B J:GDP202 2.1 32.1 1.0 OG J:SER17 2.3 18.8 1.0 CB J:SER17 3.5 24.8 1.0 PB J:GDP202 3.5 24.9 1.0 O2B J:GDP202 3.9 40.7 1.0 OD2 J:ASP57 4.0 29.4 1.0 O J:HOH304 4.1 28.8 1.0 O2A J:GDP202 4.1 19.4 1.0 N J:SER17 4.3 25.3 1.0 O1B J:GDP202 4.3 26.1 1.0 OD1 J:ASP57 4.4 39.0 1.0 CA J:SER17 4.4 28.3 1.0 CA J:ALA59 4.5 31.5 1.0 O J:THR58 4.5 23.6 1.0 CG J:ASP57 4.6 31.0 1.0 O3A J:GDP202 4.6 91.2 1.0 CB J:ALA59 4.7 27.0 1.0 PA J:GDP202 4.7 25.2 1.0 O1A J:GDP202 4.8 17.6 1.0

J.H.Mcgee, S.Y.Shim, S.J.Lee, P.K.Swanson, S.Y.Jiang, M.A.Durney, G.L.Verdine. Exceptionally High-Affinity Ras Binders That Remodel Its Effector Domain. J. Biol. Chem. V. 293 3265 2018.
ISSN: ESSN 1083-351X
PubMed: 29282294
DOI: 10.1074/JBC.M117.816348