Calcium in PDB 5v9u: Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u was solved by M.R.Janes, J.Zhang, L.-S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, J.Feng, J.H.Chen, S.Li, D.Brehmer, L.Darjania, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, Y.Wang, Y.Yao, X.Deng, P.Zarrinkar, D.Dashyant, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.03 / 1.38
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.440, 39.740, 61.780, 77.48, 81.97, 77.20
R / Rfree (%)	14.9 / 18.9

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C (pdb code 5v9u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:4.2 occ:1.00 O1B A:GDP206 2.3 4.0 1.0 O A:HOH336 2.3 9.0 1.0 OG A:SER17 2.3 8.8 1.0 O A:HOH370 2.4 9.5 1.0 O A:HOH347 2.4 10.2 1.0 O A:HOH378 2.4 10.0 1.0 CB A:SER17 3.4 8.6 1.0 PB A:GDP206 3.5 4.6 1.0 O2B A:GDP206 3.7 4.8 1.0 N A:SER17 4.0 7.7 1.0 O A:ASP33 4.2 13.2 1.0 OD2 A:ASP57 4.2 10.4 1.0 CA A:SER17 4.3 8.3 1.0 O2A A:GDP206 4.3 6.1 1.0 CB A:ALA59 4.3 11.6 1.0 O A:PRO34 4.4 12.3 1.0 OD1 A:ASP57 4.4 10.0 1.0 O3A A:GDP206 4.5 4.8 1.0 O3B A:GDP206 4.6 3.8 1.0 O A:THR58 4.6 9.3 1.0 O A:ILE36 4.7 11.5 1.0 CA A:PRO34 4.7 12.9 1.0 CD2 A:TYR32 4.7 14.3 1.0 C A:PRO34 4.7 12.9 1.0 PA A:GDP206 4.7 5.4 1.0 CG A:ASP57 4.7 9.8 1.0 CE A:LYS16 4.8 8.2 1.0 O1A A:GDP206 4.9 5.5 1.0 CB A:LYS16 4.9 7.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:8.8 occ:1.00 O A:GLY138 2.4 8.4 1.0 O A:HOH344 2.4 11.9 1.0 O A:HOH473 2.4 13.4 1.0 O A:HOH391 2.6 17.6 1.0 C A:GLY138 3.5 7.7 1.0 CA A:GLY138 4.1 8.1 1.0 OD1 A:ASP108 4.3 42.6 1.0 O A:HOH331 4.5 9.8 1.0 O A:HOH458 4.6 23.8 1.0 N A:ILE139 4.6 7.3 1.0 O A:HOH441 4.6 41.5 1.0 OE1 A:GLU162 4.6 11.5 1.0 O A:HOH363 4.7 17.6 1.0 CG2 A:ILE139 4.7 7.2 1.0 O A:TYR137 4.8 8.7 1.0 CA A:ILE139 4.8 7.3 1.0 O A:HOH377 5.0 24.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:7.1 occ:0.50 CA A:CA203 0.0 7.1 0.5 CA A:CA203 1.6 19.6 0.5 O A:HOH442 2.1 34.0 1.0 OD1 A:ASP105 2.5 16.6 1.0 O A:HOH390 2.6 22.0 1.0 OD2 A:ASP105 2.7 15.8 1.0 CG A:ASP105 2.9 14.9 1.0 O A:HOH351 4.2 32.9 1.0 CB A:ASP105 4.4 13.6 1.0 O A:ASP105 4.4 13.5 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:19.6 occ:0.50 CA A:CA203 0.0 19.6 0.5 CA A:CA203 1.6 7.1 0.5 OD2 A:ASP105 2.4 15.8 1.0 OD1 A:ASP105 2.8 16.6 1.0 CG A:ASP105 2.9 14.9 1.0 O A:HOH442 3.5 34.0 1.0 O A:HOH390 3.9 22.0 1.0 CB A:ASP105 4.3 13.6 1.0 O A:HOH388 4.4 24.1 1.0 O A:HOH351 4.6 32.9 1.0 O B:HOH317 4.9 30.1 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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 Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:9.6 occ:0.50 CA A:CA207 0.0 9.6 0.5 CA A:CA207 1.8 12.5 0.5 O B:HOH401 2.2 18.8 1.0 O B:HOH344 2.4 26.5 1.0 OE1 B:GLU63 2.5 15.3 1.0 O A:HOH364 2.7 24.7 1.0 OE2 A:GLU107 3.4 41.3 1.0 CD B:GLU63 3.5 15.2 1.0 OE1 A:GLU107 3.7 39.1 1.0 CD A:GLU107 4.0 36.1 1.0 NZ A:LYS101 4.2 24.6 1.0 O B:TYR64 4.2 18.8 1.0 CG B:GLU63 4.3 14.0 1.0 CB B:GLU63 4.3 14.7 1.0 OE2 B:GLU63 4.4 15.9 1.0 O A:HOH454 4.5 30.8 1.0 O A:HOH402 4.6 16.6 1.0 O A:HOH312 4.7 34.7 1.0 OE2 A:GLU98 4.7 10.7 1.0 CE A:LYS101 4.8 24.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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 Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:12.5 occ:0.50 CA A:CA207 0.0 12.5 0.5 CA A:CA207 1.8 9.6 0.5 O B:HOH401 2.1 18.8 1.0 O A:HOH364 2.1 24.7 1.0 OE1 A:GLU107 2.2 39.1 1.0 NZ A:LYS101 2.6 24.6 1.0 OE2 A:GLU107 2.8 41.3 1.0 CD A:GLU107 2.9 36.1 1.0 CE A:LYS101 3.3 24.6 1.0 O B:HOH344 3.6 26.5 1.0 OE1 B:GLU63 4.0 15.3 1.0 O A:HOH454 4.1 30.8 1.0 O A:HOH402 4.3 16.6 1.0 OE2 A:GLU98 4.3 10.7 1.0 CG A:GLU107 4.4 33.4 1.0 OE1 A:GLU98 4.5 13.1 1.0 CD A:LYS101 4.6 21.3 1.0 CD A:GLU98 4.8 10.6 1.0 O A:HOH312 4.9 34.7 1.0 O B:TYR64 4.9 18.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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 7 of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:4.5 occ:1.00 O B:HOH361 2.3 11.9 1.0 O3B B:GDP207 2.3 5.1 1.0 O B:HOH325 2.4 10.7 1.0 OG B:SER17 2.4 9.2 1.0 O B:HOH377 2.4 11.7 1.0 O B:HOH363 2.4 10.8 1.0 CB B:SER17 3.4 9.0 1.0 PB B:GDP207 3.5 4.6 1.0 O1B B:GDP207 3.7 4.7 1.0 N B:SER17 4.1 8.0 1.0 OD2 B:ASP57 4.3 12.6 1.0 CA B:SER17 4.3 8.3 1.0 O B:ASP33 4.3 16.4 1.0 O1A B:GDP207 4.4 6.2 1.0 OD1 B:ASP57 4.4 12.1 1.0 CB B:ALA59 4.4 15.1 1.0 O B:PRO34 4.5 17.3 1.0 O3A B:GDP207 4.5 5.5 1.0 O2B B:GDP207 4.6 4.3 1.0 O B:ILE36 4.6 16.8 1.0 CA B:PRO34 4.6 14.8 1.0 O B:THR58 4.6 12.4 1.0 C B:PRO34 4.7 15.5 1.0 CD2 B:TYR32 4.7 13.9 1.0 CG B:ASP57 4.7 11.6 1.0 PA B:GDP207 4.7 5.5 1.0 O2A B:GDP207 4.8 5.9 1.0 CE B:LYS16 4.9 9.6 1.0 CB B:LYS16 4.9 8.1 1.0 O1 B:91S204 5.0 8.8 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Small Molecule Ars-1620 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 8 of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:5.3 occ:1.00 O B:GLY138 2.3 10.2 1.0 O B:HOH335 2.4 12.8 1.0 O B:HOH463 2.4 12.3 1.0 O B:HOH412 2.4 20.0 0.5 O B:HOH437 2.5 17.9 1.0 O B:HOH412 2.7 16.5 0.5 C B:GLY138 3.5 9.4 1.0 CA B:GLY138 4.1 9.5 1.0 OD2 B:ASP108 4.5 21.0 1.0 O B:HOH338 4.5 11.0 1.0 N B:ILE139 4.6 9.0 1.0 O B:HOH370 4.6 14.2 1.0 OE1 B:GLU162 4.6 13.3 1.0 O B:HOH309 4.6 32.3 1.0 OD1 B:ASP108 4.6 22.4 1.0 O B:HOH400 4.7 20.7 1.0 O B:TYR137 4.8 9.5 1.0 CA B:ILE139 4.8 8.9 1.0 CG2 B:ILE139 4.9 8.2 1.0 CG B:ASP108 5.0 19.6 1.0

M.R.Janes, J.Zhang, L.S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, L.Darjania, J.Feng, J.H.Chen, S.Li, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, K.Yu, Y.Wang, Y.Yao, X.Deng, P.P.Zarrinkar, D.Brehmer, D.Dhanak, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu. Targeting Kras Mutant Cancers with A Covalent G12C-Specific Inhibitor. Cell V. 172 578 2018.
ISSN: ISSN 1097-4172
PubMed: 29373830
DOI: 10.1016/J.CELL.2018.01.006