Magnesium in PDB 7ewa: Gdp-Bound Kras G12D in Complex with Th-Z827

All present enzymatic activity of Gdp-Bound Kras G12D in Complex with Th-Z827:
3.6.5.2;

The structure of Gdp-Bound Kras G12D in Complex with Th-Z827, PDB code: 7ewa 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)	33.70 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.691, 102.793, 56.395, 90, 107.1, 90
R / Rfree (%)	20.3 / 25.8

The binding sites of Magnesium atom in the Gdp-Bound Kras G12D in Complex with Th-Z827 (pdb code 7ewa). 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-Z827, PDB code: 7ewa:
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-Z827


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-Z827 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.2 occ:1.00 O A:HOH430 2.0 34.6 1.0 O3B A:GDP302 2.0 33.6 1.0 O A:HOH435 2.1 36.7 1.0 O A:HOH411 2.1 34.2 1.0 O A:HOH404 2.2 33.6 1.0 OG A:SER17 2.4 30.6 1.0 CB A:SER17 3.3 32.4 1.0 PB A:GDP302 3.3 33.3 1.0 O1B A:GDP302 3.5 31.0 1.0 N A:SER17 4.0 32.9 1.0 OD2 A:ASP57 4.0 40.3 1.0 O1A A:GDP302 4.1 36.1 1.0 CA A:SER17 4.1 34.1 1.0 O2B A:GDP302 4.2 33.7 1.0 O A:PRO34 4.3 45.5 1.0 OD1 A:ASP57 4.3 35.5 1.0 O A:ASP33 4.4 44.8 1.0 CA A:PRO34 4.4 42.4 1.0 O A:HOH433 4.4 33.4 1.0 O3A A:GDP302 4.4 33.1 1.0 CD2 A:TYR32 4.5 46.5 1.0 O A:ILE36 4.5 41.4 1.0 O A:THR58 4.6 30.7 1.0 CG A:ASP57 4.6 35.1 1.0 C A:PRO34 4.6 44.7 1.0 PA A:GDP302 4.6 35.2 1.0 CB A:ALA59 4.6 41.0 1.0 O2A A:GDP302 4.7 34.6 1.0 NZ A:LYS16 4.9 30.5 1.0

Magnesium binding site 2 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z827


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-Z827 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:47.9 occ:1.00 O2G B:GNP203 1.9 51.5 1.0 OG B:SER17 1.9 47.0 1.0 O B:HOH303 2.1 51.2 1.0 O B:HOH307 2.2 47.5 1.0 O1B B:GNP203 2.5 43.1 1.0 O B:HOH316 2.5 60.0 1.0 CB B:SER17 3.0 46.4 1.0 PG B:GNP203 3.5 61.8 1.0 OD2 B:ASP57 3.6 50.8 1.0 N B:SER17 3.7 45.2 1.0 PB B:GNP203 3.8 40.3 1.0 CA B:SER17 3.9 45.1 1.0 OD1 B:ASP57 3.9 47.3 1.0 CD1 B:TYR32 3.9 64.8 1.0 N3B B:GNP203 4.1 42.9 1.0 CG B:ASP57 4.1 48.9 1.0 O2A B:GNP203 4.2 39.8 1.0 O B:ASP33 4.2 70.8 1.0 O1G B:GNP203 4.3 56.2 1.0 CE1 B:TYR32 4.3 63.5 1.0 O3G B:GNP203 4.5 65.0 1.0 O B:THR58 4.6 45.6 1.0 O1A B:GNP203 4.6 43.1 1.0 O B:ILE36 4.6 62.2 1.0 CB B:ALA59 4.7 57.6 1.0 PA B:GNP203 4.7 37.8 1.0 C B:LYS16 4.8 42.5 1.0 O2B B:GNP203 4.8 40.7 1.0 O3A B:GNP203 4.8 43.0 1.0 CB B:LYS16 4.8 37.3 1.0 CA B:PRO34 4.9 69.6 1.0 O B:PRO34 4.9 69.2 1.0 O B:HOH304 4.9 56.1 1.0

Magnesium binding site 3 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z827


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-Z827 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:43.9 occ:1.00 O3G C:GNP202 1.9 45.4 1.0 OG C:SER17 2.1 35.7 1.0 O2B C:GNP202 2.2 36.5 1.0 O C:HOH319 2.2 37.3 1.0 O C:HOH303 2.3 36.9 1.0 O C:HOH301 2.3 42.5 1.0 CB C:SER17 3.2 35.0 1.0 PG C:GNP202 3.3 48.6 1.0 PB C:GNP202 3.6 35.6 1.0 N3B C:GNP202 3.7 33.0 1.0 OD2 C:ASP57 3.7 41.7 1.0 N C:SER17 4.0 41.5 1.0 O2A C:GNP202 4.1 30.5 1.0 CA C:SER17 4.1 39.7 1.0 OD1 C:ASP57 4.2 38.4 1.0 O1G C:GNP202 4.2 46.9 1.0 O C:THR58 4.3 40.8 1.0 CG C:ASP57 4.4 41.3 1.0 O2G C:GNP202 4.4 48.1 1.0 O1B C:GNP202 4.5 34.5 1.0 O C:HOH344 4.6 57.0 1.0 O1A C:GNP202 4.6 38.1 1.0 PA C:GNP202 4.6 38.2 1.0 O3A C:GNP202 4.6 33.4 1.0 C C:LYS16 5.0 37.7 1.0 CB C:LYS16 5.0 32.0 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-Z827 To Be Published.