Calcium in PDB 6b0v: Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C, PDB code: 6b0v 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)	32.17 / 1.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.140, 39.880, 62.430, 77.00, 81.24, 77.58
R / Rfree (%)	18.2 / 21.8

The structure of Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C (pdb code 6b0v). 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-107 Covalently Bound to K-Ras G12C, PDB code: 6b0v:
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-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:10.8 occ:1.00 O1B A:GDP204 2.3 10.0 1.0 O A:HOH349 2.4 12.0 1.0 O A:HOH354 2.4 11.7 1.0 O A:HOH313 2.4 13.8 1.0 O A:HOH324 2.4 16.1 1.0 OG A:SER17 2.5 10.5 1.0 O A:HOH375 2.5 17.3 1.0 PB A:GDP204 3.5 10.1 1.0 CB A:SER17 3.5 10.0 1.0 O2B A:GDP204 3.8 13.0 1.0 N A:SER17 4.1 8.0 1.0 OD2 A:ASP57 4.3 14.9 1.0 CA A:PRO34 4.3 13.9 1.0 O1 A:C8G203 4.4 13.0 1.0 O A:THR58 4.4 13.6 1.0 CA A:SER17 4.4 8.7 1.0 O2A A:GDP204 4.4 13.3 1.0 OD1 A:ASP57 4.4 13.5 1.0 O A:PRO34 4.5 15.2 1.0 O3B A:GDP204 4.6 10.1 1.0 O A:ILE36 4.6 12.7 1.0 O A:ASP33 4.6 14.2 1.0 O3A A:GDP204 4.7 11.6 1.0 C A:PRO34 4.7 15.0 1.0 CG A:ASP57 4.8 13.2 1.0 CD2 A:TYR32 4.8 15.2 1.0 PA A:GDP204 4.9 12.3 1.0 CE A:LYS16 5.0 11.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:12.4 occ:1.00 O A:HOH305 2.2 24.2 1.0 O A:GLY138 2.3 10.8 1.0 O A:HOH457 2.4 14.1 1.0 O A:HOH337 2.5 13.2 1.0 O A:HOH373 2.5 15.1 1.0 C A:GLY138 3.4 9.2 1.0 CA A:GLY138 4.1 9.6 1.0 OD1 A:ASP108 4.3 35.0 1.0 O A:HOH308 4.4 26.4 1.0 O A:HOH480 4.5 18.8 0.5 O A:HOH316 4.5 10.4 1.0 N A:ILE139 4.6 7.9 1.0 OE1 A:GLU162 4.6 11.8 1.0 O A:HOH355 4.6 14.5 1.0 CG2 A:ILE139 4.7 8.6 1.0 O A:TYR137 4.7 12.4 1.0 CA A:ILE139 4.8 8.2 1.0 O A:HOH391 4.9 15.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:10.2 occ:1.00 O3B B:GDP204 2.3 10.3 1.0 OG B:SER17 2.4 10.8 1.0 O B:HOH347 2.4 12.9 1.0 O B:HOH374 2.4 10.5 1.0 O B:HOH342 2.4 12.8 1.0 O B:HOH354 2.4 10.3 1.0 O B:HOH382 2.6 17.5 1.0 CB B:SER17 3.5 9.3 1.0 PB B:GDP204 3.5 9.8 1.0 O1B B:GDP204 3.8 11.2 1.0 N B:SER17 4.2 8.1 1.0 OD2 B:ASP57 4.3 14.2 1.0 O1A B:GDP204 4.3 12.8 1.0 CA B:PRO34 4.4 14.3 1.0 CA B:SER17 4.4 8.3 1.0 O1 B:C8G203 4.4 12.9 1.0 O B:THR58 4.4 13.2 1.0 OD1 B:ASP57 4.5 15.3 1.0 O B:PRO34 4.5 13.7 1.0 O3A B:GDP204 4.6 11.3 1.0 O B:ASP33 4.6 12.1 1.0 O B:ILE36 4.6 12.2 1.0 O2B B:GDP204 4.6 9.4 1.0 CD2 B:TYR32 4.8 15.5 1.0 CG B:ASP57 4.8 13.7 1.0 C B:PRO34 4.8 13.1 1.0 PA B:GDP204 4.8 11.0 1.0 NZ B:LYS16 5.0 9.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:12.3 occ:1.00 O B:GLY138 2.2 11.4 1.0 O B:HOH356 2.3 17.6 1.0 O B:HOH468 2.4 15.1 1.0 O B:HOH337 2.4 15.0 1.0 O B:HOH415 2.4 25.9 1.0 C B:GLY138 3.4 9.4 1.0 CA B:GLY138 4.0 10.2 1.0 OD1 B:ASP108 4.4 22.8 1.0 OD2 B:ASP108 4.5 24.1 1.0 O B:HOH333 4.5 12.4 1.0 N B:ILE139 4.5 9.1 1.0 OE1 B:GLU162 4.6 12.6 1.0 O B:HOH319 4.6 20.3 1.0 O B:HOH490 4.7 27.6 1.0 O B:HOH400 4.8 17.4 1.0 O B:TYR137 4.8 11.7 1.0 CA B:ILE139 4.8 8.6 1.0 CG2 B:ILE139 4.9 9.9 1.0 CG B:ASP108 4.9 20.1 1.0 O B:HOH379 5.0 16.7 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