Magnesium in PDB 5wlb: Kras G12V, Bound to Gppnhp and Miniprotein 225-15A/B

The structure of Kras G12V, Bound to Gppnhp and Miniprotein 225-15A/B, PDB code: 5wlb 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)	69.10 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.145, 86.843, 71.038, 90.00, 103.57, 90.00
R / Rfree (%)	19.2 / 23.3

The binding sites of Magnesium atom in the Kras G12V, Bound to Gppnhp and Miniprotein 225-15A/B (pdb code 5wlb). 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 225-15A/B, PDB code: 5wlb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kras G12V, Bound to Gppnhp and Miniprotein 225-15A/B


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 225-15A/B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.7 occ:1.00 O B:HOH109 2.0 20.4 1.0 OG A:SER17 2.1 18.9 1.0 O2G A:GNP201 2.1 25.4 1.0 O2B A:GNP201 2.1 18.4 1.0 O A:HOH427 2.1 22.9 1.0 O A:HOH404 2.1 22.4 1.0 CB A:SER17 3.1 14.8 1.0 PG A:GNP201 3.3 24.5 1.0 PB A:GNP201 3.3 19.6 1.0 N3B A:GNP201 3.4 31.3 1.0 O A:HOH411 3.9 33.9 1.0 N A:SER17 4.0 19.6 1.0 NH2 B:ARG30 4.0 48.9 1.0 CA A:SER17 4.1 20.3 1.0 OD2 A:ASP57 4.1 27.1 1.0 O1A A:GNP201 4.2 21.6 1.0 OD1 A:ASP57 4.2 29.2 1.0 O3G A:GNP201 4.3 28.6 1.0 O1G A:GNP201 4.3 24.3 1.0 O3A A:GNP201 4.3 25.9 1.0 O1B A:GNP201 4.4 21.6 1.0 O A:THR58 4.5 23.6 1.0 CG A:ASP57 4.6 25.2 1.0 PA A:GNP201 4.6 22.3 1.0 O2A A:GNP201 4.8 23.4 1.0 CE A:LYS16 4.8 22.8 1.0 CB A:LYS16 4.9 19.1 1.0 CZ B:ARG30 5.0 56.4 1.0

Magnesium binding site 2 out of 2 in the Kras G12V, Bound to Gppnhp and Miniprotein 225-15A/B


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 225-15A/B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:23.1 occ:1.00 O D:HOH325 2.1 21.5 1.0 O1B D:GNP201 2.1 22.6 1.0 O1G D:GNP201 2.1 19.8 1.0 O D:HOH309 2.1 20.1 1.0 OG D:SER17 2.1 19.9 1.0 O E:HOH112 2.2 25.3 1.0 CB D:SER17 3.2 19.8 1.0 PB D:GNP201 3.2 24.3 1.0 PG D:GNP201 3.3 27.8 1.0 N3B D:GNP201 3.5 27.5 1.0 N D:SER17 3.9 18.9 1.0 O D:HOH340 4.1 44.2 1.0 CA D:SER17 4.1 24.4 1.0 NH2 E:ARG30 4.1 51.5 1.0 OD2 D:ASP57 4.1 25.2 1.0 O D:HOH330 4.2 44.2 1.0 O2A D:GNP201 4.2 22.7 1.0 O3G D:GNP201 4.2 25.8 1.0 OD1 D:ASP57 4.2 31.0 1.0 O2G D:GNP201 4.3 35.4 1.0 O3A D:GNP201 4.3 24.1 1.0 O2B D:GNP201 4.3 20.5 1.0 O D:HOH341 4.4 47.0 1.0 O D:THR58 4.5 24.1 1.0 PA D:GNP201 4.6 25.2 1.0 CG D:ASP57 4.6 24.8 1.0 O1A D:GNP201 4.6 24.9 1.0 CE D:LYS16 4.8 21.1 1.0 CB D:LYS16 4.9 19.3 1.0 C D:LYS16 5.0 17.7 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