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

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R), PDB code: 5whb 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)	116.00 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.002, 232.043, 47.924, 90.00, 90.10, 90.00
R / Rfree (%)	20.5 / 25.2

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Magnesium atom in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) (pdb code 5whb). 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(A30R), PDB code: 5whb:
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(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 Gdp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.8 occ:1.00 O3B A:GDP201 2.1 31.0 1.0 OG A:SER17 2.2 36.5 1.0 CB A:SER17 3.3 35.4 1.0 PB A:GDP201 3.3 36.7 1.0 O1B A:GDP201 3.5 38.6 1.0 OD2 A:ASP57 3.9 46.8 1.0 O1A A:GDP201 4.0 46.9 1.0 N A:SER17 4.2 27.5 1.0 O2B A:GDP201 4.3 27.9 1.0 CA A:SER17 4.3 27.6 1.0 CB A:ALA59 4.3 33.9 1.0 O3A A:GDP201 4.4 49.6 1.0 PA A:GDP201 4.5 44.8 1.0 O2A A:GDP201 4.5 37.8 1.0 OD1 A:ASP57 4.7 58.1 1.0 CG A:ASP57 4.7 48.9 1.0

Magnesium binding site 2 out of 4 in the Kras G12V, Bound to Gdp 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 Gdp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:25.7 occ:1.00 OG D:SER17 2.1 43.2 1.0 O1B D:GDP201 2.2 35.0 1.0 O D:HOH310 2.3 26.1 1.0 O D:HOH301 2.6 25.4 1.0 CB D:SER17 3.3 37.5 1.0 PB D:GDP201 3.5 36.7 1.0 O2B D:GDP201 3.7 30.3 1.0 CB D:ALA59 4.0 60.8 1.0 OD2 D:ASP57 4.1 41.7 1.0 N D:SER17 4.1 25.8 1.0 O2A D:GDP201 4.1 47.8 1.0 CA D:SER17 4.2 34.6 1.0 O3B D:GDP201 4.4 25.9 1.0 OD1 D:ASP57 4.6 52.3 1.0 O3A D:GDP201 4.6 36.2 1.0 O D:THR58 4.6 32.8 1.0 O D:HOH325 4.7 27.3 1.0 PA D:GDP201 4.7 42.8 1.0 CG D:ASP57 4.7 46.4 1.0 O1A D:GDP201 4.7 38.4 1.0 CA D:ALA59 4.9 59.7 1.0

Magnesium binding site 3 out of 4 in the Kras G12V, Bound to Gdp 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 3 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg202 b:35.6 occ:1.00 OG G:SER17 2.1 39.5 1.0 O3B G:GDP201 2.2 38.0 1.0 O G:HOH315 2.7 35.0 1.0 OD2 G:ASP57 3.4 81.0 1.0 CB G:SER17 3.4 35.4 1.0 PB G:GDP201 3.4 40.4 1.0 O G:THR58 3.7 48.5 1.0 O1B G:GDP201 3.8 47.8 1.0 OD1 G:ASP57 3.8 69.8 1.0 N G:SER17 3.9 34.0 1.0 CG G:ASP57 3.9 70.7 1.0 O2B G:GDP201 4.0 39.8 1.0 CA G:SER17 4.1 34.4 1.0 CB G:ALA59 4.5 49.5 1.0 CA G:ALA59 4.5 52.1 1.0 CE G:LYS16 4.5 34.4 1.0 O G:HOH327 4.6 30.7 1.0 O1A G:GDP201 4.6 44.4 1.0 O G:HOH320 4.6 38.9 1.0 NZ G:LYS16 4.6 35.0 1.0 C G:THR58 4.6 49.1 1.0 CB G:LYS16 4.7 31.1 1.0 O3A G:GDP201 4.7 53.2 1.0 C G:LYS16 4.8 35.7 1.0 O2A G:GDP201 5.0 35.8 1.0 PA G:GDP201 5.0 40.7 1.0

Magnesium binding site 4 out of 4 in the Kras G12V, Bound to Gdp 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 4 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg202 b:34.1 occ:1.00 O3B J:GDP201 2.0 50.6 1.0 OG J:SER17 2.1 49.3 1.0 O J:HOH319 2.3 36.9 1.0 O J:HOH328 2.8 34.9 1.0 CB J:SER17 3.3 44.9 1.0 PB J:GDP201 3.4 49.6 1.0 O2B J:GDP201 3.8 35.7 1.0 OD2 J:ASP57 4.0 46.4 1.0 N J:SER17 4.1 49.6 1.0 O2A J:GDP201 4.2 51.0 1.0 CB J:ALA59 4.2 34.2 1.0 O1B J:GDP201 4.2 57.0 1.0 CA J:SER17 4.3 41.2 1.0 O J:THR58 4.5 36.5 1.0 O3A J:GDP201 4.5 79.8 1.0 OD1 J:ASP57 4.5 46.1 1.0 CG J:ASP57 4.7 45.8 1.0 PA J:GDP201 4.7 44.4 1.0 O1A J:GDP201 4.7 41.7 1.0 CA J:ALA59 4.8 39.9 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