Magnesium in PDB 5v9l: Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder

The structure of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder, PDB code: 5v9l was solved by K.Westover, J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 1.98
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	85.062, 85.062, 130.542, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 22.6

The structure of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder (pdb code 5v9l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder, PDB code: 5v9l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.9 occ:1.00 O3B A:GDP201 1.9 17.9 1.0 OG A:SER17 2.0 21.3 1.0 O A:HOH301 2.2 18.9 1.0 O A:HOH306 2.2 23.0 1.0 O A:HOH336 2.2 20.6 1.0 O A:HOH322 2.2 23.0 1.0 CB A:SER17 3.1 20.3 1.0 PB A:GDP201 3.2 21.7 1.0 O1B A:GDP201 3.7 27.0 1.0 N A:SER17 3.8 20.2 1.0 CA A:SER17 4.0 21.4 1.0 O1A A:GDP201 4.0 23.1 1.0 OD2 A:ASP57 4.1 34.6 1.0 O3A A:GDP201 4.2 19.6 1.0 OD1 A:ASP57 4.2 27.3 1.0 O2B A:GDP201 4.3 23.4 1.0 O A:ASP33 4.3 40.1 1.0 CD2 A:TYR32 4.4 39.5 1.0 CA A:PRO34 4.4 34.2 1.0 O A:PRO34 4.4 35.0 1.0 PA A:GDP201 4.4 22.4 1.0 CG A:ASP57 4.6 28.7 1.0 O2A A:GDP201 4.6 26.1 1.0 O A:THR58 4.6 33.2 1.0 O A:ILE36 4.6 32.9 1.0 C A:PRO34 4.7 33.8 1.0 CE A:LYS16 4.8 21.2 1.0 O A:HOH315 4.9 26.8 1.0 NZ A:LYS16 4.9 23.6 1.0 CB A:LYS16 4.9 23.8 1.0 C A:LYS16 4.9 24.7 1.0 CE2 A:TYR32 5.0 42.6 1.0 O20 A:91D203 5.0 30.5 1.0

Magnesium binding site 2 out of 3 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.4 occ:1.00 O3B B:GDP201 2.0 20.3 1.0 O B:HOH321 2.0 14.1 1.0 O B:HOH331 2.0 22.1 1.0 O B:HOH312 2.1 14.9 1.0 OG B:SER17 2.1 18.9 1.0 O B:HOH342 2.3 18.9 1.0 PB B:GDP201 3.1 17.7 1.0 CB B:SER17 3.3 16.3 1.0 O1B B:GDP201 3.4 17.8 1.0 N B:SER17 3.9 16.4 1.0 O1A B:GDP201 4.0 15.3 1.0 OD2 B:ASP57 4.1 25.8 1.0 CA B:SER17 4.2 17.4 1.0 O2B B:GDP201 4.2 15.8 1.0 OD1 B:ASP57 4.2 29.5 1.0 O3A B:GDP201 4.2 14.1 1.0 CD1 B:TYR32 4.3 34.9 1.0 PA B:GDP201 4.5 19.1 1.0 CA B:PRO34 4.5 26.1 1.0 O B:THR58 4.5 28.2 1.0 O B:ASP33 4.5 29.9 1.0 CB B:ALA59 4.5 36.0 1.0 CG B:ASP57 4.6 34.2 1.0 O B:TYR32 4.6 27.3 1.0 O2A B:GDP201 4.6 17.8 1.0 CE B:LYS16 4.7 19.4 1.0 CB B:LYS16 4.7 15.9 1.0 NZ B:LYS16 4.7 14.0 1.0 O B:ILE36 4.8 25.8 1.0 O20 B:91D203 4.9 32.0 1.0 CE1 B:TYR32 4.9 36.1 1.0 O B:HOH324 4.9 21.8 1.0 C B:LYS16 4.9 18.6 1.0 O B:PRO34 5.0 39.5 1.0

Magnesium binding site 3 out of 3 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:13.7 occ:1.00 O3B C:GDP201 1.9 10.3 1.0 O C:HOH317 2.1 15.1 1.0 O C:HOH338 2.1 12.4 1.0 O C:HOH323 2.1 14.7 1.0 OG C:SER17 2.2 19.2 1.0 O C:HOH322 2.2 15.4 1.0 PB C:GDP201 3.2 17.8 1.0 CB C:SER17 3.2 20.4 1.0 O1B C:GDP201 3.5 20.6 1.0 N C:SER17 3.8 19.8 1.0 O1A C:GDP201 4.0 19.6 1.0 CA C:SER17 4.1 20.7 1.0 OD2 C:ASP57 4.2 27.6 1.0 O2B C:GDP201 4.2 15.1 1.0 OD1 C:ASP57 4.2 22.1 1.0 O3A C:GDP201 4.3 17.9 1.0 CD1 C:TYR32 4.3 20.9 1.0 CA C:PRO34 4.4 19.3 1.0 O C:ASP33 4.4 18.4 1.0 PA C:GDP201 4.5 22.6 1.0 O C:PRO34 4.5 18.0 1.0 O C:ILE36 4.6 19.7 1.0 O C:THR58 4.6 21.8 1.0 CE1 C:TYR32 4.6 27.7 1.0 CG C:ASP57 4.6 24.1 1.0 O2A C:GDP201 4.7 19.6 1.0 CB C:LYS16 4.7 18.5 1.0 O C:TYR32 4.8 27.6 1.0 C C:PRO34 4.8 15.8 1.0 CE C:LYS16 4.8 15.8 1.0 O C:HOH313 4.8 24.3 1.0 NZ C:LYS16 4.9 15.5 1.0 C C:LYS16 4.9 20.6 1.0 O20 C:91D203 5.0 25.2 1.0

M.Zeng, J.Lu, L.Li, F.Feru, C.Quan, T.W.Gero, S.B.Ficarro, Y.Xiong, C.Ambrogio, R.M.Paranal, M.Catalano, J.Shao, K.K.Wong, J.A.Marto, E.S.Fischer, P.A.Janne, D.A.Scott, K.D.Westover, N.S.Gray. Potent and Selective Covalent Quinazoline Inhibitors of Kras G12C. Cell Chem Biol V. 24 1005 2017.
ISSN: ESSN 2451-9456
PubMed: 28781124
DOI: 10.1016/J.CHEMBIOL.2017.06.017