Magnesium in PDB 7ewb: Gdp-Bound Kras G12D in Complex with Th-Z835

All present enzymatic activity of Gdp-Bound Kras G12D in Complex with Th-Z835:
3.6.5.2;

The structure of Gdp-Bound Kras G12D in Complex with Th-Z835, PDB code: 7ewb 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)	30.25 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.559, 102.48, 56.126, 90, 106.88, 90
R / Rfree (%)	19.5 / 24.6

The binding sites of Magnesium atom in the Gdp-Bound Kras G12D in Complex with Th-Z835 (pdb code 7ewb). 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-Z835, PDB code: 7ewb:
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-Z835


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-Z835 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:24.2 occ:1.00 O A:HOH435 2.0 23.7 1.0 O A:HOH426 2.0 22.4 1.0 O A:HOH457 2.1 25.1 1.0 O A:HOH433 2.1 20.2 1.0 O3B A:GDP302 2.1 20.6 1.0 OG A:SER17 2.2 17.8 1.0 CB A:SER17 3.1 23.1 1.0 PB A:GDP302 3.3 20.6 1.0 O1B A:GDP302 3.6 19.0 1.0 N A:SER17 4.0 19.7 1.0 OD2 A:ASP57 4.0 23.4 1.0 O1A A:GDP302 4.0 19.3 1.0 CA A:SER17 4.1 23.7 1.0 O A:ASP33 4.1 34.1 1.0 CD2 A:TYR32 4.2 31.5 1.0 OD1 A:ASP57 4.3 23.3 1.0 O A:PRO34 4.3 29.2 1.0 CA A:PRO34 4.3 31.7 1.0 O3A A:GDP302 4.4 17.5 1.0 O2B A:GDP302 4.4 22.1 1.0 CE2 A:TYR32 4.5 38.4 1.0 C A:PRO34 4.5 31.7 1.0 CG A:ASP57 4.5 23.7 1.0 PA A:GDP302 4.6 20.3 1.0 O A:ILE36 4.6 26.2 1.0 O A:THR58 4.6 16.3 1.0 CB A:ALA59 4.7 22.9 1.0 O A:HOH414 4.7 25.9 1.0 O A:HOH418 4.8 22.8 1.0 O2A A:GDP302 4.8 21.1 1.0 O A:TYR32 4.9 34.2 1.0 C A:ASP33 5.0 35.4 1.0 C A:LYS16 5.0 21.1 1.0

Magnesium binding site 2 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z835


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-Z835 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:33.3 occ:1.00 OG B:SER17 2.0 25.1 1.0 O2G B:GNP203 2.0 31.2 1.0 O B:HOH320 2.0 25.1 1.0 O B:HOH322 2.1 34.1 1.0 O2B B:GNP203 2.1 22.9 1.0 O B:HOH315 2.3 36.5 1.0 CB B:SER17 3.1 27.7 1.0 PG B:GNP203 3.3 42.3 1.0 PB B:GNP203 3.5 21.4 1.0 N3B B:GNP203 3.7 25.9 1.0 OD2 B:ASP57 3.8 24.8 1.0 N B:SER17 3.8 25.7 1.0 CA B:SER17 4.0 26.2 1.0 OD1 B:ASP57 4.0 22.6 1.0 O3G B:GNP203 4.1 44.6 1.0 CD2 B:TYR32 4.3 47.7 1.0 O2A B:GNP203 4.3 33.5 1.0 CG B:ASP57 4.3 28.5 1.0 O B:ASP33 4.3 46.9 1.0 O B:THR58 4.4 25.4 1.0 O1G B:GNP203 4.4 47.6 1.0 O1B B:GNP203 4.4 20.7 1.0 CB B:ALA59 4.5 34.9 1.0 O B:PRO34 4.5 45.3 1.0 O B:ILE36 4.5 44.6 1.0 O3A B:GNP203 4.6 23.4 1.0 CE2 B:TYR32 4.6 49.5 1.0 PA B:GNP203 4.7 25.3 1.0 CB B:LYS16 4.8 20.0 1.0 O1A B:GNP203 4.8 28.2 1.0 C B:LYS16 4.9 24.6 1.0 CA B:PRO34 4.9 48.1 1.0 C B:PRO34 4.9 50.6 1.0 NZ B:LYS16 4.9 20.2 1.0

Magnesium binding site 3 out of 3 in the Gdp-Bound Kras G12D in Complex with Th-Z835


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-Z835 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:34.9 occ:1.00 O1G C:GNP203 1.9 44.7 1.0 O1B C:GNP203 2.0 30.6 1.0 O C:HOH303 2.1 40.0 1.0 OG C:SER17 2.2 28.6 1.0 O C:HOH333 2.2 43.1 1.0 O C:HOH309 2.3 31.5 1.0 PB C:GNP203 3.1 28.4 1.0 PG C:GNP203 3.1 49.9 1.0 CB C:SER17 3.2 25.8 1.0 N3B C:GNP203 3.3 26.2 1.0 O2A C:GNP203 3.8 28.7 1.0 N C:SER17 3.8 30.8 1.0 OD2 C:ASP57 4.0 36.3 1.0 O2G C:GNP203 4.1 40.7 1.0 CA C:SER17 4.1 31.3 1.0 O2B C:GNP203 4.1 29.5 1.0 O3A C:GNP203 4.2 28.4 1.0 OD1 C:ASP57 4.2 31.9 1.0 O3G C:GNP203 4.3 49.1 1.0 O C:PRO34 4.3 53.7 1.0 PA C:GNP203 4.3 35.0 1.0 CD2 C:TYR32 4.4 59.4 1.0 CE2 C:TYR32 4.4 57.1 1.0 CA C:PRO34 4.4 60.9 1.0 O C:THR58 4.4 33.9 1.0 CB C:ALA59 4.4 49.5 1.0 O1A C:GNP203 4.5 30.0 1.0 CG C:ASP57 4.5 36.8 1.0 O C:ASP33 4.7 65.1 1.0 C C:PRO34 4.7 59.0 1.0 CB C:LYS16 4.7 23.2 1.0 C C:LYS16 4.8 29.2 1.0 NZ C:LYS16 4.9 27.2 1.0 CE C:LYS16 5.0 25.0 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-Z835 To Be Published.