Magnesium in PDB 5whe: Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11

The structure of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11, PDB code: 5whe 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)	19.54 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.549, 232.525, 48.213, 90.00, 90.16, 90.00
R / Rfree (%)	18.4 / 22.7

The structure of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Magnesium atom in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 (pdb code 5whe). 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/D38P, Bound to Gppnhp and Miniprotein 225-11, PDB code: 5whe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Kras G12V/D38P, Bound to Gppnhp 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/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg806 b:12.4 occ:1.00 O A:HOH966 2.0 35.6 1.0 O A:HOH938 2.1 28.9 1.0 O1G A:GNP801 2.2 21.3 1.0 O2B A:GNP801 2.2 15.5 1.0 OG A:SER17 2.2 18.0 1.0 O A:HOH924 2.3 20.3 1.0 CB A:SER17 3.3 17.9 1.0 PB A:GNP801 3.4 19.5 1.0 PG A:GNP801 3.4 23.1 1.0 N3B A:GNP801 3.5 20.5 1.0 N A:SER17 4.1 19.3 1.0 OD2 A:ASP57 4.2 27.0 1.0 CA A:SER17 4.2 18.1 1.0 O2A A:GNP801 4.4 14.3 1.0 OD1 A:ASP57 4.4 23.2 1.0 O1B A:GNP801 4.4 13.3 1.0 O3G A:GNP801 4.4 29.2 1.0 O3A A:GNP801 4.5 20.7 1.0 O2G A:GNP801 4.5 27.4 1.0 CG A:ASP57 4.7 21.1 1.0 O A:THR58 4.7 20.4 1.0 PA A:GNP801 4.7 20.7 1.0 O1A A:GNP801 4.8 16.6 1.0 CB A:LYS16 4.9 11.8 1.0

Magnesium binding site 2 out of 4 in the Kras G12V/D38P, Bound to Gppnhp 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/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg804 b:15.3 occ:1.00 O2G D:GNP801 2.0 23.1 1.0 O D:HOH918 2.2 26.4 1.0 O D:HOH946 2.3 24.2 1.0 O2B D:GNP801 2.3 24.9 1.0 O D:HOH908 2.3 26.7 1.0 OG D:SER17 2.4 21.6 1.0 PG D:GNP801 3.2 31.9 1.0 PB D:GNP801 3.4 22.1 1.0 N3B D:GNP801 3.4 28.2 1.0 CB D:SER17 3.6 14.5 1.0 N D:SER17 4.2 17.6 1.0 O1G D:GNP801 4.3 21.3 1.0 O3G D:GNP801 4.3 24.8 1.0 O1A D:GNP801 4.3 22.5 1.0 OD2 D:ASP57 4.3 27.4 1.0 O1B D:GNP801 4.4 20.4 1.0 OD1 D:ASP57 4.4 21.1 1.0 CA D:SER17 4.5 23.8 1.0 O3A D:GNP801 4.5 20.8 1.0 O D:THR58 4.7 26.5 1.0 PA D:GNP801 4.8 21.2 1.0 CG D:ASP57 4.8 25.0 1.0 CB D:LYS16 4.9 22.0 1.0 CE D:LYS16 4.9 22.9 1.0 O2A D:GNP801 4.9 16.8 1.0

Magnesium binding site 3 out of 4 in the Kras G12V/D38P, Bound to Gppnhp 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/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg804 b:16.0 occ:1.00 O G:HOH920 2.1 27.0 1.0 O2G G:GNP801 2.2 28.7 1.0 O G:HOH922 2.2 21.4 1.0 O2B G:GNP801 2.2 19.8 1.0 O G:HOH940 2.3 27.1 1.0 OG G:SER17 2.3 22.6 1.0 PG G:GNP801 3.4 28.4 1.0 PB G:GNP801 3.4 19.8 1.0 CB G:SER17 3.5 20.5 1.0 N3B G:GNP801 3.5 17.8 1.0 N G:SER17 4.1 18.0 1.0 OD2 G:ASP57 4.2 26.9 1.0 O1A G:GNP801 4.3 21.9 1.0 CA G:SER17 4.4 20.1 1.0 OD1 G:ASP57 4.4 28.6 1.0 O1B G:GNP801 4.5 15.7 1.0 O3A G:GNP801 4.5 21.7 1.0 O1G G:GNP801 4.5 31.9 1.0 O3G G:GNP801 4.5 25.4 1.0 PA G:GNP801 4.7 21.3 1.0 CG G:ASP57 4.8 24.1 1.0 CE G:LYS16 4.8 21.7 1.0 CB G:ALA59 4.8 36.4 1.0 CA G:ALA59 4.9 39.6 1.0 CB G:LYS16 4.9 20.2 1.0 O2A G:GNP801 4.9 19.3 1.0 O G:THR58 4.9 21.4 1.0

Magnesium binding site 4 out of 4 in the Kras G12V/D38P, Bound to Gppnhp 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/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg802 b:18.5 occ:1.00 O J:HOH922 2.1 27.6 1.0 OG J:SER17 2.2 22.9 1.0 O2B J:GNP801 2.2 20.1 1.0 O J:HOH954 2.3 29.0 1.0 O J:HOH915 2.3 22.0 1.0 O2G J:GNP801 2.4 19.9 1.0 CB J:SER17 3.3 21.4 1.0 PB J:GNP801 3.4 25.8 1.0 PG J:GNP801 3.5 26.8 1.0 N3B J:GNP801 3.6 29.1 1.0 O J:HOH924 4.0 26.9 1.0 N J:SER17 4.0 23.7 1.0 O2A J:GNP801 4.2 25.8 1.0 CA J:SER17 4.2 23.0 1.0 OD2 J:ASP57 4.3 32.0 1.0 O3G J:GNP801 4.4 30.8 1.0 O1B J:GNP801 4.4 22.9 1.0 OD1 J:ASP57 4.4 27.0 1.0 O3A J:GNP801 4.5 25.5 1.0 O1G J:GNP801 4.6 28.9 1.0 PA J:GNP801 4.7 26.4 1.0 CG J:ASP57 4.7 31.7 1.0 O1A J:GNP801 4.8 20.4 1.0 O J:THR58 4.9 24.3 1.0 CE J:LYS16 4.9 21.6 1.0 CB J:LYS16 4.9 17.1 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