Magnesium in PDB 7ew9: Gdp-Bound Kras G12D in Complex with Th-Z816

All present enzymatic activity of Gdp-Bound Kras G12D in Complex with Th-Z816:
3.6.5.2;

The structure of Gdp-Bound Kras G12D in Complex with Th-Z816, PDB code: 7ew9 was solved by P.Shen, Y.Yang, Y.Y.Yang, L.Zhang, Y.Zhang, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.014, 103.381, 56.269, 90, 106.4, 90
R / Rfree (%)	20.1 / 25.7

The binding sites of Magnesium atom in the Gdp-Bound Kras G12D in Complex with Th-Z816 (pdb code 7ew9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Gdp-Bound Kras G12D in Complex with Th-Z816, PDB code: 7ew9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z816


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdp-Bound Kras G12D in Complex with Th-Z816 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.5 occ:1.00 O A:HOH427 2.0 27.6 1.0 O3B A:GDP303 2.0 28.9 1.0 O A:HOH407 2.1 30.4 1.0 O A:HOH421 2.2 33.1 1.0 OG A:SER17 2.2 30.9 1.0 O A:HOH428 2.5 33.3 1.0 CB A:SER17 3.2 31.8 1.0 PB A:GDP303 3.2 29.7 1.0 O1B A:GDP303 3.4 30.4 1.0 N A:SER17 3.9 26.0 1.0 O1A A:GDP303 4.1 31.3 1.0 CA A:SER17 4.1 29.6 1.0 OD1 A:ASP57 4.2 30.4 1.0 OD2 A:ASP57 4.2 36.4 1.0 O2B A:GDP303 4.3 26.2 1.0 O3A A:GDP303 4.3 26.3 1.0 O A:PRO34 4.3 38.4 1.0 O A:THR58 4.4 26.6 1.0 O A:ASP33 4.4 42.8 1.0 CA A:PRO34 4.5 42.9 1.0 O A:HOH433 4.5 32.9 1.0 CB A:ALA59 4.5 39.0 1.0 PA A:GDP303 4.5 27.8 1.0 O2A A:GDP303 4.6 32.7 1.0 CG A:ASP57 4.6 29.3 1.0 C A:PRO34 4.6 41.8 1.0 CD2 A:TYR32 4.7 39.4 1.0 O A:ILE36 4.8 36.3 1.0 O A:HOH449 4.9 35.6 1.0 NZ A:LYS16 4.9 27.2 1.0 CB A:LYS16 4.9 22.1 1.0 C A:LYS16 5.0 26.7 1.0

Magnesium binding site 2 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z816


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gdp-Bound Kras G12D in Complex with Th-Z816 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:37.1 occ:1.00 O B:HOH424 2.1 38.6 1.0 O B:HOH405 2.1 35.3 1.0 O B:HOH445 2.1 44.0 1.0 O B:HOH407 2.1 37.1 1.0 O1B B:GDP303 2.2 30.4 1.0 OG B:SER17 2.2 33.7 1.0 CB B:SER17 3.1 33.4 1.0 PB B:GDP303 3.3 31.0 1.0 O3B B:GDP303 3.5 32.1 1.0 N B:SER17 3.8 37.6 1.0 OD1 B:ASP57 4.0 36.4 1.0 CA B:SER17 4.0 35.9 1.0 OD2 B:ASP57 4.1 37.3 1.0 O2A B:GDP303 4.1 32.8 1.0 O B:THR58 4.2 34.6 1.0 O B:ASP33 4.3 55.0 1.0 O2B B:GDP303 4.4 31.2 1.0 CG B:ASP57 4.4 35.7 1.0 O3A B:GDP303 4.4 29.3 1.0 O B:HOH431 4.5 37.0 1.0 CB B:ALA59 4.5 45.1 1.0 PA B:GDP303 4.6 33.6 1.0 O B:PRO34 4.6 50.8 1.0 CD2 B:TYR32 4.6 50.6 1.0 CB B:LYS16 4.6 27.9 1.0 O1A B:GDP303 4.6 37.1 1.0 O B:ILE36 4.7 50.4 1.0 CA B:PRO34 4.8 52.0 1.0 CE2 B:TYR32 4.8 45.5 1.0 C B:LYS16 4.8 34.5 1.0 CE B:LYS16 4.9 29.3 1.0 C B:PRO34 4.9 52.3 1.0

Magnesium binding site 3 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z816


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gdp-Bound Kras G12D in Complex with Th-Z816 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:40.0 occ:1.00 O2B C:GDP302 2.0 34.3 1.0 O C:HOH412 2.0 39.0 1.0 O C:HOH445 2.1 52.7 1.0 OG C:SER17 2.2 34.6 1.0 O C:HOH409 2.2 41.5 1.0 O C:HOH405 2.2 33.8 1.0 CB C:SER17 3.2 32.7 1.0 PB C:GDP302 3.2 34.0 1.0 O3B C:GDP302 3.4 34.6 1.0 N C:SER17 3.9 30.1 1.0 CA C:PRO34 4.0 69.2 1.0 OD2 C:ASP57 4.0 33.9 1.0 CA C:SER17 4.1 30.1 1.0 O1A C:GDP302 4.2 37.2 1.0 OD1 C:ASP57 4.2 37.9 1.0 CB C:ALA59 4.2 57.9 1.0 O1B C:GDP302 4.3 33.1 1.0 O3A C:GDP302 4.3 32.3 1.0 O C:ASP33 4.4 71.5 1.0 O C:THR58 4.4 42.7 1.0 CG C:ASP57 4.5 37.3 1.0 PA C:GDP302 4.5 30.8 1.0 CB C:PRO34 4.6 68.9 1.0 O2A C:GDP302 4.6 34.8 1.0 C C:PRO34 4.7 71.8 1.0 NZ C:LYS16 4.7 34.7 1.0 O C:PRO34 4.7 70.6 1.0 N C:PRO34 4.8 73.0 1.0 O C:TYR32 4.8 79.8 1.0 CB C:LYS16 4.8 32.5 1.0 C C:LYS16 4.9 34.2 1.0 O C:HOH441 4.9 43.2 1.0 C C:ASP33 4.9 77.6 1.0

P.Shen, Y.Yang, Y.Y.Yang, L.Zhang, Y.Zhang, C.C.Chen, R.T.Guo. Gdp-Bound Kras G12D in Complex with Th-Z816 To Be Published.