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

The structure of Kras G12V, Bound to Gppnhp and Miniprotein 225-11, PDB code: 5wpl 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)	48.14 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.861, 234.507, 48.143, 90.00, 90.13, 90.00
R / Rfree (%)	20.5 / 25.8

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

Magnesium binding site 1 out of 5 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:6.5 occ:1.00 O A:HOH341 1.7 30.5 1.0 O A:HOH304 2.1 18.5 1.0 O A:HOH324 2.2 21.3 1.0 O2B A:GNP201 2.2 16.5 1.0 OG A:SER17 2.3 15.6 1.0 O2G A:GNP201 2.4 20.3 1.0 CB A:SER17 3.4 16.8 1.0 PG A:GNP201 3.5 19.6 1.0 PB A:GNP201 3.5 18.8 1.0 N3B A:GNP201 3.6 19.2 1.0 O2A A:GNP201 4.1 19.3 1.0 O A:HOH310 4.1 32.5 1.0 N A:SER17 4.2 17.3 1.0 OD2 A:ASP57 4.3 18.2 1.0 CA A:SER17 4.3 17.3 1.0 OD1 A:ASP57 4.4 21.8 1.0 O1B A:GNP201 4.5 16.9 1.0 O3G A:GNP201 4.5 21.0 1.0 O1G A:GNP201 4.6 20.4 1.0 O3A A:GNP201 4.7 19.4 1.0 O A:THR58 4.7 25.9 1.0 CG A:ASP57 4.7 19.6 1.0 PA A:GNP201 4.8 18.1 1.0 CE A:LYS16 5.0 17.4 1.0 O1A A:GNP201 5.0 19.0 1.0

Magnesium binding site 2 out of 5 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:5.3 occ:1.00 O D:HOH320 1.9 20.8 1.0 O D:HOH326 2.0 23.9 1.0 O2G D:GNP201 2.2 16.7 1.0 O D:HOH316 2.2 11.1 1.0 O2B D:GNP201 2.2 15.0 1.0 OG D:SER17 2.3 15.7 1.0 CB D:SER17 3.3 15.9 1.0 PG D:GNP201 3.5 17.8 1.0 PB D:GNP201 3.5 17.6 1.0 N3B D:GNP201 3.7 18.0 1.0 N D:SER17 4.0 16.0 1.0 O1A D:GNP201 4.2 21.8 1.0 OD1 D:ASP57 4.2 19.2 1.0 OD2 D:ASP57 4.3 16.5 1.0 CA D:SER17 4.3 15.5 1.0 O3G D:GNP201 4.4 18.5 1.0 O1B D:GNP201 4.5 14.2 1.0 O1G D:GNP201 4.6 16.2 1.0 O3A D:GNP201 4.6 18.5 1.0 CG D:ASP57 4.7 17.6 1.0 CB D:LYS16 4.7 16.2 1.0 O D:THR58 4.8 22.8 1.0 PA D:GNP201 4.8 19.9 1.0 CE D:LYS16 4.9 16.1 1.0 O2A D:GNP201 4.9 20.4 1.0 CA D:ALA59 5.0 36.8 1.0 C D:LYS16 5.0 15.5 1.0

Magnesium binding site 3 out of 5 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg202 b:7.0 occ:1.00 O2G G:GNP201 2.1 17.1 1.0 O G:HOH324 2.2 20.9 1.0 O G:HOH305 2.2 13.9 1.0 O2B G:GNP201 2.3 15.7 1.0 OG G:SER17 2.3 15.2 1.0 O G:HOH333 2.3 23.3 1.0 CB G:SER17 3.3 15.8 1.0 PG G:GNP201 3.5 19.0 1.0 PB G:GNP201 3.5 17.5 1.0 N3B G:GNP201 3.6 17.9 1.0 N G:SER17 4.1 15.5 1.0 O1A G:GNP201 4.1 19.5 1.0 OD2 G:ASP57 4.3 17.7 1.0 CA G:SER17 4.3 15.4 1.0 OD1 G:ASP57 4.4 18.3 1.0 O3G G:GNP201 4.4 21.0 1.0 O1B G:GNP201 4.5 15.8 1.0 O1G G:GNP201 4.6 18.1 1.0 O3A G:GNP201 4.7 17.3 1.0 CG G:ASP57 4.7 17.5 1.0 PA G:GNP201 4.8 19.7 1.0 O G:HOH335 4.9 36.8 1.0 CB G:LYS16 5.0 14.5 1.0 CB G:ALA59 5.0 31.8 1.0 O G:THR58 5.0 22.9 1.0 O2A G:GNP201 5.0 20.8 1.0

Magnesium binding site 4 out of 5 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg203 b:9.4 occ:1.00 OE2 G:GLU63 2.2 32.6 1.0 OE1 G:GLU63 2.2 27.1 1.0 O H:ALA32 2.4 21.6 1.0 CD G:GLU63 2.5 32.2 1.0 C H:ALA32 3.0 22.5 1.0 CG G:GLU63 3.8 34.7 1.0 CA G:CA204 3.9 21.3 1.0 CA H:ALA32 4.5 21.9 1.0 CB G:GLU63 5.0 36.4 1.0

Magnesium binding site 5 out of 5 in the Kras G12V, 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 5 of Kras G12V, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg202 b:7.6 occ:1.00 O J:HOH317 2.0 15.9 1.0 O J:HOH330 2.1 22.4 1.0 O2B J:GNP201 2.1 21.7 1.0 O J:HOH302 2.2 11.3 1.0 O1G J:GNP201 2.3 22.0 1.0 OG J:SER17 2.3 19.1 1.0 CB J:SER17 3.3 20.9 1.0 PB J:GNP201 3.4 23.0 1.0 PG J:GNP201 3.6 24.2 1.0 N3B J:GNP201 3.7 23.2 1.0 N J:SER17 4.1 20.8 1.0 O2A J:GNP201 4.1 24.7 1.0 OD2 J:ASP57 4.1 19.7 1.0 CA J:SER17 4.3 20.5 1.0 O1B J:GNP201 4.3 22.8 1.0 O2G J:GNP201 4.4 22.4 1.0 OD1 J:ASP57 4.5 21.9 1.0 O3A J:GNP201 4.6 23.0 1.0 O3G J:GNP201 4.7 23.6 1.0 CG J:ASP57 4.7 19.8 1.0 PA J:GNP201 4.8 24.6 1.0 CE J:LYS16 4.8 23.7 1.0 O J:THR58 4.8 22.1 1.0 CB J:LYS16 4.9 22.5 1.0 O1A J:GNP201 4.9 24.1 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