Magnesium in PDB 4obe: Crystal Structure of Gdp-Bound Human Kras

All present enzymatic activity of Crystal Structure of Gdp-Bound Human Kras:
3.6.5.2;

The structure of Crystal Structure of Gdp-Bound Human Kras, PDB code: 4obe was solved by J.C.Hunter, D.Gurbani, Z.Chen, K.D.Westover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.07 / 1.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.147, 42.096, 114.393, 90.00, 105.32, 90.00
R / Rfree (%)	15.7 / 16.9

The binding sites of Magnesium atom in the Crystal Structure of Gdp-Bound Human Kras (pdb code 4obe). 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 Gdp-Bound Human Kras, PDB code: 4obe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Gdp-Bound Human Kras


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 Gdp-Bound Human Kras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:9.3 occ:1.00 O1B A:GDP201 2.1 10.1 1.0 O A:HOH453 2.1 10.2 1.0 OG A:SER17 2.1 10.5 1.0 O A:HOH302 2.1 10.3 1.0 O A:HOH303 2.1 10.0 1.0 O A:HOH301 2.1 11.3 1.0 HB2 A:SER17 3.2 12.5 1.0 CB A:SER17 3.2 10.4 1.0 PB A:GDP201 3.3 10.3 1.0 H A:SER17 3.3 11.1 1.0 HA A:PRO34 3.3 13.4 1.0 HD2 A:TYR32 3.5 16.8 1.0 O3B A:GDP201 3.5 10.5 1.0 HB3 A:SER17 3.8 12.5 1.0 N A:SER17 3.9 9.3 1.0 HB2 A:LYS16 4.0 12.1 1.0 HE2 A:TYR32 4.0 16.5 1.0 OD2 A:ASP57 4.1 11.8 1.0 CA A:SER17 4.1 9.7 1.0 HE2 A:LYS16 4.1 14.3 1.0 O2A A:GDP201 4.1 13.3 1.0 OD1 A:ASP57 4.2 10.3 1.0 O A:PRO34 4.2 10.9 1.0 CA A:PRO34 4.3 11.2 1.0 CD2 A:TYR32 4.3 14.0 1.0 O A:ASP33 4.3 12.5 1.0 O3A A:GDP201 4.3 10.6 1.0 O2B A:GDP201 4.3 10.4 1.0 HA A:SER17 4.4 11.7 1.0 O A:ILE36 4.5 11.3 1.0 CE2 A:TYR32 4.5 13.7 1.0 PA A:GDP201 4.5 11.7 1.0 CG A:ASP57 4.5 11.9 1.0 O A:THR58 4.6 10.2 1.0 C A:PRO34 4.6 11.4 1.0 O1A A:GDP201 4.7 12.0 1.0 HB2 A:ALA59 4.7 17.2 1.0 HZ1 A:LYS16 4.8 14.5 1.0 HA A:ALA59 4.8 13.3 1.0 HZ3 A:LYS16 4.9 14.5 1.0 CB A:LYS16 4.9 10.1 1.0 O A:TYR32 4.9 14.7 1.0 HB3 A:PRO34 5.0 17.6 1.0 C A:LYS16 5.0 9.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Gdp-Bound Human Kras


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 Gdp-Bound Human Kras within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:8.8 occ:1.00 O B:HOH479 2.0 20.0 1.0 O1B B:GDP201 2.1 8.6 1.0 O B:HOH305 2.1 10.0 1.0 O B:HOH469 2.1 9.6 1.0 OG B:SER17 2.1 9.1 1.0 O B:HOH302 2.1 9.5 1.0 HB2 B:SER17 3.2 11.9 1.0 CB B:SER17 3.2 9.9 1.0 PB B:GDP201 3.3 9.2 1.0 H B:SER17 3.4 10.3 1.0 HA B:PRO34 3.4 12.5 1.0 HD2 B:TYR32 3.5 16.3 1.0 O2B B:GDP201 3.5 9.6 1.0 HB3 B:SER17 3.9 11.9 1.0 N B:SER17 3.9 8.6 1.0 HB2 B:LYS16 4.0 10.6 1.0 HE2 B:TYR32 4.1 18.6 1.0 OD2 B:ASP57 4.1 9.8 1.0 CA B:SER17 4.1 8.4 1.0 O2A B:GDP201 4.1 11.4 1.0 OD1 B:ASP57 4.2 9.3 1.0 HE2 B:LYS16 4.2 12.7 1.0 O B:PRO34 4.3 10.2 1.0 CD2 B:TYR32 4.3 13.6 1.0 CA B:PRO34 4.3 10.4 1.0 O3A B:GDP201 4.3 9.3 1.0 O B:ASP33 4.3 10.6 1.0 O3B B:GDP201 4.4 9.1 1.0 HA B:SER17 4.4 10.0 1.0 O B:ILE36 4.5 10.3 1.0 CE2 B:TYR32 4.5 15.5 1.0 CG B:ASP57 4.6 9.3 1.0 PA B:GDP201 4.6 11.1 1.0 O B:THR58 4.6 9.7 1.0 C B:PRO34 4.6 11.1 1.0 HB2 B:ALA59 4.6 14.9 1.0 O1A B:GDP201 4.7 11.0 1.0 HZ1 B:LYS16 4.7 11.4 1.0 O B:TYR32 4.8 11.7 1.0 HA B:ALA59 4.8 12.4 1.0 HZ3 B:LYS16 4.8 11.4 1.0 HB3 B:TYR32 4.9 15.8 1.0 CB B:LYS16 5.0 8.8 1.0

J.C.Hunter, D.Gurbani, S.B.Ficarro, M.A.Carrasco, S.M.Lim, H.G.Choi, T.Xie, J.A.Marto, Z.Chen, N.S.Gray, K.D.Westover. In Situ Selectivity Profiling and Crystal Structure of Sml-8-73-1, An Active Site Inhibitor of Oncogenic K-Ras G12C. Proc.Natl.Acad.Sci.Usa V. 111 8895 2014.
ISSN: ISSN 0027-8424
PubMed: 24889603
DOI: 10.1073/PNAS.1404639111