Calcium in PDB 6b0y: Crystal Structure of Small Molecule Ars-917 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Ars-917 Covalently Bound to K-Ras G12C, PDB code: 6b0y was solved by R.Hansen, U.Peters, A.Babbar, Y.Chen, J.Feng, M.R.Janes, L.-S.Li, P.Ren, Y.Liu, P.P.Zarrinkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.94 / 1.43
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.430, 39.660, 61.850, 77.45, 81.71, 77.12
R / Rfree (%)	17.4 / 20.7

The structure of Crystal Structure of Small Molecule Ars-917 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 Ars-917 Covalently Bound to K-Ras G12C (pdb code 6b0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Ars-917 Covalently Bound to K-Ras G12C, PDB code: 6b0y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Small Molecule Ars-917 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 Ars-917 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:7.3 occ:1.00 O A:HOH321 2.3 9.1 1.0 O A:HOH339 2.3 9.9 1.0 O1B A:GDP205 2.3 8.0 1.0 O A:HOH331 2.3 9.3 1.0 OG A:SER17 2.4 7.9 1.0 O A:HOH359 2.4 10.3 1.0 CB A:SER17 3.5 7.4 1.0 PB A:GDP205 3.5 7.6 1.0 O2B A:GDP205 3.7 8.3 1.0 N A:SER17 4.0 6.3 1.0 O A:ASP33 4.2 12.5 1.0 OD2 A:ASP57 4.2 13.2 1.0 O2A A:GDP205 4.3 9.9 1.0 CA A:SER17 4.3 6.8 1.0 CB A:ALA59 4.4 10.1 1.0 OD1 A:ASP57 4.4 11.1 1.0 O A:PRO34 4.4 11.9 1.0 O3A A:GDP205 4.5 8.3 1.0 O A:THR58 4.6 8.8 1.0 O3B A:GDP205 4.6 7.5 1.0 O A:ILE36 4.6 12.2 1.0 CA A:PRO34 4.6 13.8 1.0 C A:PRO34 4.7 12.9 1.0 CD2 A:TYR32 4.7 12.5 1.0 CG A:ASP57 4.7 11.4 1.0 PA A:GDP205 4.7 8.7 1.0 O1A A:GDP205 4.9 8.5 1.0 CB A:LYS16 4.9 5.7 1.0 O A:HOH346 5.0 15.8 1.0 CE A:LYS16 5.0 6.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Small Molecule Ars-917 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 Ars-917 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:11.4 occ:1.00 O A:GLY138 2.3 7.7 1.0 O A:HOH442 2.5 13.1 1.0 O A:HOH323 2.5 11.8 1.0 O A:HOH334 2.7 15.9 1.0 C A:GLY138 3.4 6.6 1.0 CA A:GLY138 4.0 6.7 1.0 O A:HOH421 4.4 22.7 1.0 O A:HOH328 4.5 9.3 1.0 N A:ILE139 4.5 6.1 1.0 O A:HOH340 4.6 16.6 1.0 OE1 A:GLU162 4.6 12.7 1.0 CG2 A:ILE139 4.7 6.2 1.0 O A:TYR137 4.8 7.2 1.0 CA A:ILE139 4.8 6.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Small Molecule Ars-917 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 Ars-917 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:7.4 occ:1.00 O3B B:GDP206 2.3 7.6 1.0 OG B:SER17 2.3 7.1 1.0 O B:HOH356 2.3 10.1 1.0 O B:HOH349 2.3 10.3 1.0 O B:HOH319 2.4 10.1 1.0 O B:HOH348 2.4 8.0 1.0 CB B:SER17 3.4 6.3 1.0 PB B:GDP206 3.5 6.6 1.0 O1B B:GDP206 3.7 7.6 1.0 N B:SER17 4.0 5.8 1.0 CA B:SER17 4.3 6.1 1.0 OD2 B:ASP57 4.3 13.0 1.0 O B:ASP33 4.3 14.3 1.0 O1A B:GDP206 4.4 9.7 1.0 OD1 B:ASP57 4.4 12.3 1.0 O B:PRO34 4.4 18.8 1.0 CB B:ALA59 4.5 13.6 1.0 O3A B:GDP206 4.5 8.4 1.0 O2B B:GDP206 4.6 6.6 1.0 O B:ILE36 4.6 16.2 1.0 O B:THR58 4.6 10.3 1.0 CA B:PRO34 4.6 15.3 1.0 C B:PRO34 4.7 18.1 1.0 CG B:ASP57 4.7 11.1 1.0 CD2 B:TYR32 4.7 11.2 1.0 PA B:GDP206 4.8 8.5 1.0 CB B:LYS16 4.9 5.8 1.0 O2A B:GDP206 4.9 8.8 1.0 CE B:LYS16 4.9 6.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Small Molecule Ars-917 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 Ars-917 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:8.9 occ:1.00 O B:HOH309 2.2 15.4 0.5 O B:GLY138 2.3 7.3 1.0 O B:HOH320 2.5 13.4 1.0 O B:HOH441 2.5 10.0 1.0 O B:HOH309 2.5 11.3 0.5 O B:HOH388 2.5 15.9 1.0 C B:GLY138 3.5 6.8 1.0 CA B:GLY138 4.1 7.2 1.0 OD2 B:ASP108 4.4 20.2 1.0 O B:HOH330 4.6 9.7 1.0 N B:ILE139 4.6 6.5 1.0 OD1 B:ASP108 4.6 19.4 1.0 OE1 B:GLU162 4.6 12.1 1.0 O B:HOH384 4.6 18.5 1.0 O B:HOH381 4.7 12.9 1.0 O B:TYR137 4.8 6.8 1.0 CA B:ILE139 4.8 6.5 1.0 CG B:ASP108 4.9 18.1 1.0 CG2 B:ILE139 4.9 6.2 1.0

R.Hansen, U.Peters, A.Babbar, Y.Chen, J.Feng, M.R.Janes, L.S.Li, P.Ren, Y.Liu, P.P.Zarrinkar. The Reactivity-Driven Biochemical Mechanism of Covalent KRASG12CINHIBITORS. Nat. Struct. Mol. Biol. V. 25 454 2018.
ISSN: ESSN 1545-9985
PubMed: 29760531
DOI: 10.1038/S41594-018-0061-5