Calcium in PDB 5v6v: Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C

The structure of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C, PDB code: 5v6v was solved by L.M.Mcgregor, M.Jenkins, C.Kerwin, J.E.Burke, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.43 / 1.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.230, 39.170, 62.340, 77.34, 81.44, 76.86
R / Rfree (%)	16.8 / 20.2

The structure of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C (pdb code 5v6v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C, PDB code: 5v6v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:15.2 occ:1.00 O2B A:GDP201 2.3 13.6 1.0 O A:HOH430 2.3 20.1 1.0 OG A:SER17 2.4 13.3 1.0 O A:HOH340 2.4 17.8 1.0 O A:HOH348 2.4 17.7 1.0 O A:HOH319 2.4 17.1 1.0 HB2 A:SER17 3.3 16.8 1.0 CB A:SER17 3.4 14.0 1.0 HA A:PRO34 3.5 25.0 1.0 H A:SER17 3.5 16.5 1.0 PB A:GDP201 3.5 13.9 1.0 O1B A:GDP201 3.7 16.2 1.0 HD2 A:TYR32 3.8 20.3 1.0 HB2 A:ALA59 3.8 22.5 1.0 HB3 A:SER17 4.1 16.8 1.0 HE2 A:LYS16 4.1 22.7 1.0 N A:SER17 4.1 13.8 1.0 HB2 A:LYS16 4.1 17.3 1.0 O1A A:GDP201 4.3 17.6 1.0 OD2 A:ASP57 4.3 17.0 1.0 CA A:SER17 4.3 13.1 1.0 CA A:PRO34 4.4 20.8 1.0 O A:ASP33 4.5 21.1 1.0 OD1 A:ASP57 4.5 17.7 1.0 O A:PRO34 4.6 22.0 1.0 O3A A:GDP201 4.6 15.5 1.0 O A:THR58 4.6 16.2 1.0 O3B A:GDP201 4.6 15.7 1.0 O A:ILE36 4.6 16.6 1.0 HA A:SER17 4.7 15.7 1.0 CB A:ALA59 4.7 18.8 1.0 CD2 A:TYR32 4.7 16.9 1.0 HZ1 A:LYS16 4.7 21.0 1.0 HB1 A:ALA59 4.7 22.5 1.0 HB3 A:TYR32 4.8 24.4 1.0 CG A:ASP57 4.8 18.4 1.0 PA A:GDP201 4.8 14.6 1.0 C A:PRO34 4.8 21.4 1.0 O A:HOH438 4.8 20.6 1.0 O2A A:GDP201 4.9 14.3 1.0 HZ3 A:LYS16 4.9 21.0 1.0 CE A:LYS16 5.0 18.9 1.0 O A:HOH328 5.0 23.8 1.0 HB3 A:PRO34 5.0 31.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:15.3 occ:1.00 O A:GLY138 2.2 13.5 1.0 O A:HOH380 2.3 22.7 1.0 O A:HOH443 2.3 16.1 1.0 O A:HOH318 2.4 19.0 1.0 O A:HOH397 2.5 19.7 1.0 C A:GLY138 3.4 14.5 1.0 HA3 A:GLY138 3.5 16.7 1.0 CA A:GLY138 4.0 13.9 1.0 HA A:ILE139 4.1 13.3 1.0 HG22 A:ILE139 4.1 16.9 1.0 HA2 A:GLY138 4.4 16.7 1.0 OD2 A:ASP108 4.4 29.5 1.0 N A:ILE139 4.5 14.2 1.0 OE1 A:GLU162 4.5 19.9 1.0 HG23 A:ILE139 4.5 16.9 1.0 O A:HOH335 4.6 13.9 1.0 O A:HOH332 4.7 19.9 1.0 OD1 A:ASP108 4.7 21.4 1.0 O A:HOH402 4.7 24.9 1.0 O A:TYR137 4.7 19.8 1.0 CA A:ILE139 4.7 11.1 1.0 CG2 A:ILE139 4.8 14.1 1.0 O A:HOH398 4.8 27.2 1.0 O A:HOH444 4.8 36.1 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:47.4 occ:1.00 O A:HOH350 2.4 33.5 1.0 O A:HOH388 2.5 44.8 1.0 OE1 B:GLU63 3.9 30.1 1.0 O A:HOH327 4.0 34.8 1.0 O A:HOH449 4.2 36.2 1.0 HB2 B:GLU63 4.3 38.7 1.0 O B:TYR64 4.6 35.6 1.0 HE2 A:LYS101 4.7 31.7 1.0 OE1 A:GLU98 4.9 21.9 1.0 CD B:GLU63 4.9 34.0 1.0 HE3 A:LYS101 4.9 31.7 1.0 OE2 A:GLU98 4.9 24.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:18.5 occ:1.00 O1B B:GDP202 2.2 17.1 1.0 O B:HOH319 2.3 22.5 1.0 OG B:SER17 2.3 15.6 1.0 O B:HOH318 2.4 18.4 1.0 O B:HOH326 2.4 19.4 1.0 O B:HOH327 2.5 20.6 1.0 HB2 B:SER17 3.3 17.6 1.0 CB B:SER17 3.4 14.7 1.0 PB B:GDP202 3.5 17.6 1.0 H B:SER17 3.5 18.2 1.0 O3B B:GDP202 3.6 19.3 1.0 HA B:PRO34 3.6 38.1 1.0 HB2 B:ALA59 3.8 34.4 1.0 HD2 B:TYR32 3.8 27.9 1.0 HE2 B:LYS16 4.0 24.2 1.0 HB3 B:SER17 4.0 17.6 1.0 HB2 B:LYS16 4.1 18.7 1.0 N B:SER17 4.1 15.2 1.0 OD2 B:ASP57 4.3 20.6 1.0 CA B:SER17 4.3 17.6 1.0 O2A B:GDP202 4.3 22.6 1.0 OD1 B:ASP57 4.4 18.7 1.0 O B:ASP33 4.4 27.6 1.0 O2B B:GDP202 4.5 17.4 1.0 O3A B:GDP202 4.5 19.2 1.0 CA B:PRO34 4.6 31.7 1.0 HA B:SER17 4.6 21.1 1.0 O B:PRO34 4.6 30.2 1.0 O B:ILE36 4.6 24.5 1.0 CB B:ALA59 4.7 28.7 1.0 HB1 B:ALA59 4.7 34.4 1.0 O B:THR58 4.7 17.9 1.0 CG B:ASP57 4.7 21.8 1.0 CD2 B:TYR32 4.7 23.3 1.0 HZ1 B:LYS16 4.7 24.2 1.0 PA B:GDP202 4.8 19.8 1.0 HB3 B:TYR32 4.8 33.8 1.0 O1A B:GDP202 4.8 18.0 1.0 O B:HOH381 4.9 26.1 1.0 C B:PRO34 4.9 29.7 1.0 CE B:LYS16 4.9 20.1 1.0 HZ3 B:LYS16 4.9 24.2 1.0 O B:HOH338 5.0 29.6 1.0 CB B:LYS16 5.0 15.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:25.5 occ:1.00 O B:GLY138 2.3 18.6 1.0 O B:HOH401 2.4 21.3 1.0 O B:HOH358 2.5 27.8 1.0 C B:GLY138 3.4 16.4 1.0 HA3 B:GLY138 3.5 20.7 1.0 HG22 B:ILE139 4.0 17.8 1.0 CA B:GLY138 4.0 17.2 1.0 O B:HOH385 4.1 36.2 1.0 HA B:ILE139 4.2 16.7 1.0 O B:HOH312 4.4 18.5 1.0 HA2 B:GLY138 4.4 20.7 1.0 OE1 B:GLU162 4.5 19.9 1.0 N B:ILE139 4.5 14.1 1.0 HG23 B:ILE139 4.6 17.8 1.0 O B:TYR137 4.7 17.6 1.0 CG2 B:ILE139 4.7 14.8 1.0 O B:HOH321 4.8 24.9 1.0 CA B:ILE139 4.8 13.9 1.0 O B:HOH357 4.9 29.5 1.0 O B:HOH400 5.0 35.7 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:41.7 occ:1.00 O B:GLU3 2.3 33.6 1.0 OE1 B:GLU76 2.4 32.7 1.0 OE2 B:GLU76 2.4 41.4 1.0 CD B:GLU76 2.7 33.4 1.0 HA B:TYR4 3.2 28.0 1.0 C B:GLU3 3.5 35.0 1.0 HD1 B:TYR4 3.6 39.7 1.0 H B:LYS5 3.9 22.4 1.0 CA B:TYR4 4.0 23.3 1.0 HB3 B:GLU3 4.1 41.3 1.0 N B:TYR4 4.2 22.7 1.0 CG B:GLU76 4.2 32.4 1.0 HG2 B:GLU3 4.3 45.5 1.0 H B:GLU3 4.4 39.0 1.0 CD1 B:TYR4 4.4 33.1 1.0 HG3 B:GLU76 4.4 38.9 1.0 N B:LYS5 4.5 18.7 1.0 HG2 B:GLU76 4.6 38.9 1.0 CA B:GLU3 4.6 30.6 1.0 HZ3 B:LYS167 4.6 62.6 1.0 CB B:GLU3 4.7 34.4 1.0 C B:TYR4 4.7 20.6 1.0 N B:GLU3 4.9 32.5 1.0 CG B:GLU3 5.0 37.9 1.0 HE1 B:TYR4 5.0 47.3 1.0 HZ1 B:LYS167 5.0 62.6 1.0

L.M.Mcgregor, M.L.Jenkins, C.Kerwin, J.E.Burke, K.M.Shokat. Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry V. 56 3178 2017.
ISSN: ISSN 1520-4995
PubMed: 28621541
DOI: 10.1021/ACS.BIOCHEM.7B00271