Magnesium in PDB 6gj5: Crystal Structure of Kras G12D (Gppcp) in Complex with 15

The structure of Crystal Structure of Kras G12D (Gppcp) in Complex with 15, PDB code: 6gj5 was solved by D.Kessler, D.M.Mcconnell, A.Mantoulidis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.75 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.074, 40.043, 94.284, 90.00, 101.14, 90.00
R / Rfree (%)	18.4 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D (Gppcp) in Complex with 15 (pdb code 6gj5). 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 Kras G12D (Gppcp) in Complex with 15, PDB code: 6gj5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras G12D (Gppcp) in Complex with 15


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 Kras G12D (Gppcp) in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:19.7 occ:1.00 O2G A:GCP201 2.0 21.8 1.0 O A:HOH327 2.0 20.4 1.0 OG1 A:THR35 2.0 24.5 1.0 OG A:SER17 2.0 21.9 1.0 O2B A:GCP201 2.1 20.3 1.0 O A:HOH337 2.1 21.4 1.0 CB A:THR35 3.0 26.0 1.0 CB A:SER17 3.2 19.2 1.0 PG A:GCP201 3.3 21.7 1.0 PB A:GCP201 3.3 20.5 1.0 C3B A:GCP201 3.6 21.0 1.0 N A:SER17 3.9 16.7 1.0 N A:THR35 3.9 28.3 1.0 OD2 A:ASP57 4.0 22.7 1.0 CA A:THR35 4.1 27.8 1.0 CA A:SER17 4.1 16.7 1.0 CG2 A:THR35 4.1 25.0 1.0 OD1 A:ASP57 4.2 23.0 1.0 O1A A:GCP201 4.2 20.6 1.0 O1G A:GCP201 4.2 21.9 1.0 O A:HOH382 4.3 37.4 1.0 O3G A:GCP201 4.4 21.8 1.0 O A:THR58 4.4 22.9 1.0 O3A A:GCP201 4.4 20.4 1.0 O1B A:GCP201 4.4 20.6 1.0 O A:ASP33 4.4 29.0 1.0 CG A:ASP57 4.5 22.9 1.0 PA A:GCP201 4.6 20.5 1.0 O2A A:GCP201 4.6 20.6 1.0 CB A:LYS16 4.8 16.7 1.0 C A:PRO34 4.8 30.4 1.0 CE A:LYS16 4.8 18.9 1.0 C A:LYS16 4.9 14.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras G12D (Gppcp) in Complex with 15


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 Kras G12D (Gppcp) in Complex with 15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:20.1 occ:1.00 O2G B:GCP201 1.9 22.2 1.0 O1B B:GCP201 2.1 20.8 1.0 O B:HOH337 2.1 18.5 1.0 OG1 B:THR35 2.1 26.8 1.0 OG B:SER17 2.1 21.8 1.0 O B:HOH340 2.2 21.0 1.0 CB B:THR35 3.1 29.4 1.0 CB B:SER17 3.1 19.1 1.0 PG B:GCP201 3.3 22.1 1.0 PB B:GCP201 3.3 21.0 1.0 C3B B:GCP201 3.5 21.4 1.0 N B:SER17 3.8 17.4 1.0 N B:THR35 3.9 29.4 1.0 CA B:SER17 4.0 20.5 1.0 OD2 B:ASP57 4.1 24.6 1.0 CA B:THR35 4.1 29.2 1.0 O1A B:GCP201 4.1 21.3 1.0 CG2 B:THR35 4.2 27.8 1.0 O3G B:GCP201 4.2 22.1 1.0 O B:HOH308 4.2 27.4 1.0 OD1 B:ASP57 4.2 22.2 1.0 O2B B:GCP201 4.3 20.9 1.0 O1G B:GCP201 4.3 22.1 1.0 O B:THR58 4.3 22.6 1.0 O3A B:GCP201 4.4 20.9 1.0 O B:ASP33 4.5 32.8 0.5 O B:ASP33 4.5 32.9 0.5 CG B:ASP57 4.5 22.6 1.0 PA B:GCP201 4.6 21.3 1.0 CE B:LYS16 4.7 20.2 1.0 CB B:LYS16 4.7 17.3 1.0 C B:PRO34 4.8 31.6 1.0 C B:LYS16 4.9 16.8 1.0 O2A B:GCP201 4.9 21.3 1.0 NZ B:LYS16 5.0 19.6 1.0

D.Kessler, M.Gmachl, A.Mantoulidis, L.J.Martin, A.Zoephel, M.Mayer, A.Gollner, D.Covini, S.Fischer, T.Gerstberger, T.Gmaschitz, C.Goodwin, P.Greb, D.Haring, W.Hela, J.Hoffmann, J.Karolyi-Oezguer, P.Knesl, S.Kornigg, M.Koegl, R.Kousek, L.Lamarre, F.Moser, S.Munico-Martinez, C.Peinsipp, J.Phan, J.Rinnenthal, J.Sai, C.Salamon, Y.Scherbantin, K.Schipany, R.Schnitzer, A.Schrenk, B.Sharps, G.Siszler, Q.Sun, A.Waterson, B.Wolkerstorfer, M.Zeeb, M.Pearson, S.W.Fesik, D.B.Mcconnell. Drugging An Undruggable Pocket on Kras. Proc.Natl.Acad.Sci.Usa V. 116 15823 2019.
ISSN: ESSN 1091-6490
PubMed: 31332011
DOI: 10.1073/PNAS.1904529116