Calcium in PDB 4luc: Crystal Structure of Small Molecule Disulfide 6 Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Disulfide 6 Bound to K-Ras G12C, PDB code: 4luc was solved by J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.37 / 1.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	32.822, 39.083, 62.457, 77.86, 81.54, 77.55
R / Rfree (%)	15.2 / 16.9

The structure of Crystal Structure of Small Molecule Disulfide 6 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 Disulfide 6 Bound to K-Ras G12C (pdb code 4luc). 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 Disulfide 6 Bound to K-Ras G12C, PDB code: 4luc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Small Molecule Disulfide 6 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 Disulfide 6 Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:13.8 occ:1.00 O3B A:GDP204 2.2 12.5 1.0 O A:HOH305 2.2 14.3 1.0 O A:HOH308 2.2 15.2 1.0 O A:HOH307 2.2 12.7 1.0 OG A:SER17 2.2 12.7 1.0 O A:HOH303 2.3 12.7 1.0 HB2 A:SER17 3.3 13.5 1.0 CB A:SER17 3.3 11.3 1.0 PB A:GDP204 3.4 11.6 1.0 H A:SER17 3.4 12.7 1.0 HA A:PRO34 3.5 20.3 1.0 O2B A:GDP204 3.6 12.6 1.0 HD2 A:TYR32 3.8 18.6 1.0 HB3 A:SER17 4.0 13.5 1.0 HB2 A:LYS16 4.0 13.8 1.0 HB2 A:ALA59 4.0 23.5 1.0 N A:SER17 4.0 10.6 1.0 HE2 A:LYS16 4.1 18.8 1.0 OD2 A:ASP57 4.2 16.3 1.0 O1A A:GDP204 4.2 15.8 1.0 CA A:SER17 4.2 9.8 1.0 OD1 A:ASP57 4.3 16.2 1.0 O A:PRO34 4.4 18.8 1.0 O A:ILE36 4.4 15.2 1.0 O3A A:GDP204 4.4 12.8 1.0 O A:ASP33 4.4 19.0 1.0 CA A:PRO34 4.4 16.9 1.0 O1B A:GDP204 4.5 10.9 1.0 HA A:SER17 4.5 11.8 1.0 C A:PRO34 4.6 16.9 1.0 O A:THR58 4.6 15.8 1.0 CG A:ASP57 4.7 15.2 1.0 HZ1 A:LYS16 4.7 18.3 1.0 PA A:GDP204 4.7 12.9 1.0 CD2 A:TYR32 4.7 15.5 1.0 HB3 A:TYR32 4.8 25.2 1.0 HB1 A:ALA59 4.9 23.5 1.0 O2A A:GDP204 4.9 14.4 1.0 CB A:ALA59 4.9 19.6 1.0 HZ3 A:LYS16 4.9 18.3 1.0 CB A:LYS16 5.0 11.5 1.0 CE A:LYS16 5.0 15.6 1.0 O A:HOH353 5.0 25.0 1.0 O A:HOH334 5.0 17.8 1.0 HE2 A:TYR32 5.0 19.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Small Molecule Disulfide 6 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 Disulfide 6 Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:14.0 occ:1.00 O A:GLY138 2.3 10.6 1.0 O A:HOH346 2.3 24.8 1.0 O A:HOH318 2.4 19.0 1.0 O A:HOH306 2.4 14.5 1.0 O A:HOH320 2.5 16.9 1.0 C A:GLY138 3.4 10.1 1.0 HA3 A:GLY138 3.6 12.9 1.0 CA A:GLY138 4.1 10.7 1.0 HG22 A:ILE139 4.1 12.8 1.0 HA A:ILE139 4.1 10.6 1.0 OD2 A:ASP108 4.3 33.2 1.0 OD1 A:ASP108 4.5 22.3 1.0 HA2 A:GLY138 4.5 12.9 1.0 N A:ILE139 4.5 9.8 1.0 O A:HOH310 4.5 13.9 1.0 HG23 A:ILE139 4.6 12.8 1.0 O A:HOH358 4.6 25.9 1.0 OE1 A:GLU162 4.6 18.1 1.0 O A:HOH350 4.7 20.2 1.0 O A:HOH421 4.7 34.1 1.0 O A:TYR137 4.7 11.9 1.0 CG2 A:ILE139 4.8 10.6 1.0 O B:HOH440 4.8 27.1 1.0 CA A:ILE139 4.8 8.8 1.0 CG A:ASP108 4.8 26.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Small Molecule Disulfide 6 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 Disulfide 6 Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:14.9 occ:1.00 O B:HOH308 2.2 14.9 1.0 O1B B:GDP204 2.2 13.4 1.0 O B:HOH306 2.2 13.0 1.0 O B:HOH302 2.2 13.1 1.0 OG B:SER17 2.3 14.6 1.0 O B:HOH309 2.3 15.8 1.0 HB2 B:SER17 3.3 15.1 1.0 CB B:SER17 3.3 12.6 1.0 PB B:GDP204 3.4 13.4 1.0 H B:SER17 3.5 14.5 1.0 HA B:PRO34 3.6 24.4 1.0 O2B B:GDP204 3.6 14.4 1.0 HD2 B:TYR32 3.8 20.6 1.0 HE2 B:LYS16 3.9 23.0 1.0 HB2 B:LYS16 4.0 15.7 1.0 HB3 B:SER17 4.0 15.1 1.0 HB2 B:ALA59 4.0 23.8 1.0 N B:SER17 4.1 12.1 1.0 OD2 B:ASP57 4.2 19.2 1.0 O1A B:GDP204 4.2 15.3 1.0 CA B:SER17 4.3 11.7 1.0 OD1 B:ASP57 4.3 16.9 1.0 O B:PRO34 4.4 19.4 1.0 O3A B:GDP204 4.4 14.7 1.0 O B:ASP33 4.5 18.7 1.0 CA B:PRO34 4.5 20.3 1.0 O B:ILE36 4.5 16.0 1.0 HA B:SER17 4.5 14.0 1.0 O3B B:GDP204 4.6 13.1 1.0 CG B:ASP57 4.6 17.3 1.0 O B:THR58 4.6 16.3 1.0 C B:PRO34 4.7 20.1 1.0 PA B:GDP204 4.7 13.8 1.0 CD2 B:TYR32 4.7 17.2 1.0 HB3 B:TYR32 4.7 22.4 1.0 HZ1 B:LYS16 4.8 19.9 1.0 O2A B:GDP204 4.8 14.6 1.0 HB1 B:ALA59 4.8 23.8 1.0 CE B:LYS16 4.8 19.2 1.0 CB B:ALA59 4.8 19.9 1.0 CB B:LYS16 4.9 13.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Small Molecule Disulfide 6 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 Disulfide 6 Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:14.7 occ:1.00 O B:GLY138 2.3 13.3 1.0 O B:HOH394 2.4 32.2 1.0 O B:HOH312 2.4 17.1 1.0 O B:HOH311 2.4 15.7 1.0 O B:HOH313 2.4 14.7 1.0 C B:GLY138 3.5 12.3 1.0 HA3 B:GLY138 3.6 13.1 1.0 HG22 B:ILE139 4.0 15.0 1.0 CA B:GLY138 4.1 10.9 1.0 HA B:ILE139 4.1 12.6 1.0 O B:HOH417 4.5 28.6 1.0 HG23 B:ILE139 4.5 15.0 1.0 O B:HOH307 4.5 13.4 1.0 N B:ILE139 4.5 9.9 1.0 HA2 B:GLY138 4.6 13.1 1.0 OE1 B:GLU162 4.6 16.9 1.0 CG2 B:ILE139 4.7 12.5 1.0 O B:HOH325 4.7 16.5 1.0 O B:TYR137 4.7 13.0 1.0 CA B:ILE139 4.8 10.5 1.0 O B:HOH425 4.8 31.6 1.0

J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat. K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity and Effector Interactions. Nature V. 503 548 2013.
ISSN: ISSN 0028-0836
PubMed: 24256730
DOI: 10.1038/NATURE12796