Magnesium in PDB 9bgh: Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977

All present enzymatic activity of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977:
3.6.5.2; 5.2.1.8;

The structure of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bgh was solved by Y.Pourfarjam, Y.Goldgur, A.Cuevas-Navarro, P.Lito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.48 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.483, 81.787, 127.832, 90, 90, 90
R / Rfree (%)	21.8 / 25.1

The structure of Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Aluminium	(Al)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 (pdb code 9bgh). 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 in A Transition State Mimetic Complex with Cypa and Rmc-7977, PDB code: 9bgh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977


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 in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.7 occ:1.00 O1B A:GDP201 2.0 18.8 1.0 OG A:SER17 2.0 18.4 1.0 O A:HOH333 2.1 18.9 1.0 O A:HOH326 2.1 19.6 1.0 OG1 A:THR35 2.1 16.5 1.0 O A:HOH313 2.2 19.9 1.0 CB A:THR35 3.1 19.4 1.0 CB A:SER17 3.1 18.0 1.0 PB A:GDP201 3.2 19.3 1.0 O3B A:GDP201 3.5 21.7 1.0 N A:THR35 3.8 23.8 1.0 N A:SER17 3.8 17.4 1.0 CA A:SER17 4.0 17.3 1.0 CA A:THR35 4.1 23.4 1.0 OD2 A:ASP57 4.1 19.7 1.0 OD1 A:ASP57 4.1 19.7 1.0 CG2 A:THR35 4.1 20.6 1.0 O2A A:GDP201 4.1 21.7 1.0 O2B A:GDP201 4.2 18.8 1.0 O A:HOH371 4.3 32.4 1.0 O3A A:GDP201 4.3 20.3 1.0 O A:ASP33 4.3 23.2 1.0 O A:THR58 4.5 19.4 1.0 CG A:ASP57 4.5 17.4 1.0 PA A:GDP201 4.5 21.1 1.0 CE A:LYS16 4.6 22.4 1.0 CB A:LYS16 4.6 19.1 1.0 O1A A:GDP201 4.7 20.2 1.0 NZ A:LYS16 4.8 25.1 1.0 C A:PRO34 4.8 24.3 1.0 OD1 A:ASP12 4.8 24.5 1.0 C A:LYS16 4.9 18.4 1.0 CA A:PRO34 4.9 23.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977


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 in A Transition State Mimetic Complex with Cypa and Rmc-7977 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:39.6 occ:1.00 O C:HOH320 2.0 30.6 1.0 OG C:SER17 2.1 37.4 1.0 O C:HOH327 2.1 33.5 1.0 O1B C:GDP201 2.1 42.6 1.0 OG1 C:THR35 2.2 37.5 1.0 O C:HOH310 2.2 33.9 1.0 F3 C:AF3203 2.7 45.3 1.0 CB C:SER17 3.1 37.3 1.0 O2B C:GDP201 3.3 44.7 1.0 PB C:GDP201 3.3 44.0 1.0 CB C:THR35 3.3 37.5 1.0 N C:THR35 3.8 40.1 1.0 N C:SER17 3.9 38.8 1.0 O2A C:GDP201 3.9 43.5 1.0 CA C:SER17 4.1 38.9 1.0 CA C:THR35 4.1 38.2 1.0 AL C:AF3203 4.1 43.9 1.0 O C:ASP33 4.1 42.8 1.0 OD2 C:ASP57 4.2 34.7 1.0 O3B C:GDP201 4.4 44.8 1.0 O C:HOH359 4.4 45.6 1.0 O3A C:GDP201 4.4 46.0 1.0 CG2 C:THR35 4.5 35.7 1.0 PA C:GDP201 4.5 44.1 1.0 O1A C:GDP201 4.6 42.3 1.0 C C:PRO34 4.6 41.0 1.0 OD1 C:ASP57 4.6 36.1 1.0 F2 C:AF3203 4.6 48.8 1.0 CA C:PRO34 4.7 43.1 1.0 CG C:ASP57 4.8 34.8 1.0 O C:HOH307 4.8 52.0 1.0 O C:THR58 5.0 40.6 1.0

Y.Pourfarjam, Y.Goldgur, A.Cuevas-Navarro, P.Lito. Crystal Structure of Kras G12D in A Transition State Mimetic Complex with Cypa and Rmc-7977 To Be Published.