Magnesium in PDB 5wpm: Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R)

The structure of Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R), PDB code: 5wpm was solved by S.-J.Lee, S.Y.Shim, J.H.Mcgee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.28 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.934, 37.810, 70.179, 90.00, 103.38, 90.00
R / Rfree (%)	23.5 / 28.5

The binding sites of Magnesium atom in the Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R) (pdb code 5wpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R), PDB code: 5wpm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R)


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 Gppnhp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:25.2 occ:1.00 O A:HOH314 2.0 29.0 1.0 O2G A:GNP201 2.0 25.5 1.0 O A:HOH316 2.0 22.5 1.0 O2B A:GNP201 2.1 26.9 1.0 O A:HOH309 2.1 25.6 1.0 OG A:SER17 2.2 23.6 1.0 CB A:SER17 3.2 23.9 1.0 PG A:GNP201 3.2 24.9 1.0 PB A:GNP201 3.3 25.3 1.0 N3B A:GNP201 3.4 25.0 1.0 N A:SER17 4.0 24.2 1.0 O2A A:GNP201 4.0 26.4 1.0 O A:HOH306 4.1 32.2 1.0 O1G A:GNP201 4.1 22.0 1.0 CA A:SER17 4.1 24.1 1.0 O A:HOH331 4.2 37.5 1.0 OD2 A:ASP57 4.2 21.6 1.0 O1B A:GNP201 4.3 21.5 1.0 NH2 B:ARG30 4.3 32.9 1.0 O A:HOH330 4.3 31.0 1.0 O3G A:GNP201 4.3 25.7 1.0 O3A A:GNP201 4.4 24.1 1.0 OD1 A:ASP57 4.4 21.0 1.0 PA A:GNP201 4.5 26.7 1.0 CG A:ASP57 4.7 22.5 1.0 O1A A:GNP201 4.7 28.9 1.0 O A:THR58 4.7 22.5 1.0 CB A:LYS16 5.0 25.7 1.0

Magnesium binding site 2 out of 2 in the Kras G12V, Bound to Gppnhp and Miniprotein 225-11(A30R)


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 Gppnhp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:50.9 occ:1.00 O A:SER89 2.5 36.4 1.0 O A:VAL81 2.8 28.1 1.0 CD1 A:ILE93 3.4 34.4 1.0 C A:SER89 3.5 37.5 1.0 N A:ALA11 3.5 28.5 1.0 CA A:PHE82 3.8 37.6 1.0 C A:VAL81 3.8 33.1 1.0 CB A:PHE82 3.8 38.0 1.0 CA A:GLY10 3.9 27.3 1.0 CG1 A:ILE93 4.0 34.9 1.0 CE2 A:TYR96 4.0 32.0 1.0 CA A:SER89 4.0 34.3 1.0 CB A:SER89 4.1 36.0 1.0 N A:PHE82 4.1 37.8 1.0 CB A:ALA11 4.1 29.5 1.0 CD2 A:TYR96 4.1 30.8 1.0 CB A:ASP92 4.2 29.2 1.0 C A:GLY10 4.3 27.8 1.0 CG1 A:VAL14 4.4 27.9 1.0 CA A:ALA11 4.5 29.8 1.0 OG A:SER89 4.6 36.6 1.0 N A:ILE93 4.6 33.4 1.0 N A:PHE90 4.6 39.3 1.0 C A:ASP92 4.8 32.1 1.0 CA A:ILE93 4.8 34.3 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