Magnesium in PDB 5us4: Crystal Structure of Human Kras G12D Mutant in Complex with Gdp

The structure of Crystal Structure of Human Kras G12D Mutant in Complex with Gdp, PDB code: 5us4 was solved by T.Tran, A.Kaplan, B.R.Stockwell, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.53 / 1.83
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	93.822, 93.822, 121.352, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 20.1

The binding sites of Magnesium atom in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdp (pdb code 5us4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdp, PDB code: 5us4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Kras G12D Mutant in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.3 occ:1.00 OG A:SER17 2.1 15.2 1.0 O2B A:GDP201 2.1 16.4 1.0 O A:HOH338 2.1 18.8 1.0 O A:HOH327 2.2 16.0 1.0 O A:HOH312 2.2 16.0 1.0 O A:HOH310 2.2 18.1 1.0 CB A:SER17 3.1 16.2 1.0 PB A:GDP201 3.2 16.5 1.0 O3B A:GDP201 3.4 16.4 1.0 N A:SER17 4.0 15.2 1.0 O2A A:GDP201 4.1 18.0 1.0 CA A:SER17 4.1 16.8 1.0 OD2 A:ASP57 4.1 17.4 1.0 OD1 A:ASP57 4.2 16.2 1.0 O A:ASP33 4.3 30.2 1.0 O3A A:GDP201 4.3 15.0 1.0 O1B A:GDP201 4.3 14.0 1.0 O A:PRO34 4.4 26.5 1.0 CA A:PRO34 4.4 29.6 1.0 CD2 A:TYR32 4.4 23.1 1.0 O A:ILE36 4.5 26.9 1.0 CG A:ASP57 4.5 15.9 1.0 PA A:GDP201 4.6 16.5 1.0 O A:THR58 4.6 18.0 1.0 O1A A:GDP201 4.6 19.4 1.0 C A:PRO34 4.7 30.4 1.0 O A:HOH301 4.9 32.3 1.0 CB A:ALA59 4.9 17.0 1.0 CE2 A:TYR32 5.0 22.2 1.0 CB A:LYS16 5.0 13.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Kras G12D Mutant in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:18.0 occ:1.00 O2B B:GDP201 2.1 14.3 1.0 OG B:SER17 2.1 14.9 1.0 O B:HOH333 2.1 15.4 1.0 O B:HOH324 2.2 18.9 1.0 O B:HOH344 2.2 16.0 1.0 O B:HOH314 2.2 18.7 1.0 CB B:SER17 3.1 14.7 1.0 PB B:GDP201 3.2 15.9 1.0 O1B B:GDP201 3.5 15.5 1.0 N B:SER17 3.9 13.5 1.0 CA B:SER17 4.1 13.9 1.0 OD2 B:ASP57 4.1 18.8 1.0 O1A B:GDP201 4.2 19.0 1.0 OD1 B:ASP57 4.2 15.8 1.0 O B:ASP33 4.3 25.7 1.0 O3B B:GDP201 4.3 13.5 1.0 O3A B:GDP201 4.3 13.9 1.0 O B:PRO34 4.3 24.5 1.0 CA B:PRO34 4.4 29.1 1.0 CD2 B:TYR32 4.5 22.1 1.0 O B:ILE36 4.5 26.2 1.0 CG B:ASP57 4.5 16.1 1.0 O B:THR58 4.6 16.9 1.0 PA B:GDP201 4.6 16.5 1.0 O2A B:GDP201 4.7 18.6 1.0 C B:PRO34 4.7 30.6 1.0 CB B:ALA59 4.9 16.8 1.0 O B:HOH301 5.0 28.5 1.0 CB B:LYS16 5.0 13.9 1.0

M.E.Welsch, A.Kaplan, J.M.Chambers, M.E.Stokes, P.H.Bos, A.Zask, Y.Zhang, M.Sanchez-Martin, M.A.Badgley, C.S.Huang, T.H.Tran, H.Akkiraju, L.M.Brown, R.Nandakumar, S.Cremers, W.S.Yang, L.Tong, K.P.Olive, A.Ferrando, B.R.Stockwell. Multivalent Small-Molecule Pan-Ras Inhibitors. Cell V. 168 878 2017.
ISSN: ISSN 1097-4172
PubMed: 28235199
DOI: 10.1016/J.CELL.2017.02.006