Chlorine 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:

Calcium

(Ca)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Small Molecule Disulfide 6 Bound to K-Ras G12C, PDB code: 4luc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203 b:17.5 occ:1.00 CL1 A:20G203 0.0 17.5 1.0 C02 A:20G203 1.7 15.8 1.0 C03 A:20G203 2.7 16.6 1.0 C25 A:20G203 2.7 15.0 1.0 H03 A:20G203 2.8 19.9 1.0 H25 A:20G203 2.8 18.0 1.0 HG11 A:VAL7 2.9 15.1 1.0 HG3 A:MET72 2.9 17.3 1.0 HB2 A:TYR71 3.1 20.2 1.0 HG3 A:ARG68 3.1 16.4 1.0 HG2 A:ARG68 3.3 16.4 1.0 HB3 A:TYR71 3.3 20.2 1.0 HG21 A:THR58 3.3 16.9 1.0 HG2 A:MET72 3.4 17.3 1.0 CB A:TYR71 3.6 16.8 1.0 CG A:MET72 3.6 14.4 1.0 CG A:ARG68 3.6 13.7 1.0 CG1 A:VAL7 3.7 12.6 1.0 HD2 A:TYR71 3.8 26.9 1.0 HE2 A:PHE78 3.9 12.2 1.0 O A:ARG68 3.9 13.8 1.0 C04 A:20G203 3.9 17.1 1.0 HG13 A:VAL7 3.9 15.1 1.0 C24 A:20G203 4.0 14.2 1.0 HG12 A:VAL7 4.0 15.1 1.0 HG12 A:VAL9 4.0 18.5 1.0 H A:MET72 4.1 16.2 1.0 HD3 A:ARG68 4.1 19.6 1.0 HG11 A:VAL9 4.1 18.5 1.0 N A:MET72 4.1 13.5 1.0 HG22 A:THR58 4.1 16.9 1.0 CG2 A:THR58 4.1 14.1 1.0 HA A:MET72 4.2 15.6 1.0 HE2 A:MET72 4.2 20.7 1.0 HD23 A:LEU56 4.2 21.2 1.0 HA A:ARG68 4.3 16.0 1.0 C A:TYR71 4.3 13.3 1.0 HG21 A:VAL7 4.4 13.6 1.0 CD2 A:TYR71 4.4 22.4 1.0 C06 A:20G203 4.4 15.8 1.0 CD A:ARG68 4.4 16.4 1.0 CG A:TYR71 4.5 20.6 1.0 CG1 A:VAL9 4.5 15.4 1.0 CA A:MET72 4.6 13.0 1.0 HG23 A:THR58 4.6 16.9 1.0 CA A:TYR71 4.6 15.1 1.0 CB A:MET72 4.7 13.5 1.0 C A:ARG68 4.7 12.9 1.0 HD21 A:LEU56 4.7 21.2 1.0 CE2 A:PHE78 4.7 10.2 1.0 SD A:MET72 4.8 16.7 1.0 H24 A:20G203 4.8 17.0 1.0 O A:TYR71 4.8 14.8 1.0 CA A:ARG68 4.8 13.3 1.0 CB A:ARG68 4.8 13.8 1.0 O A:HOH363 4.9 28.5 1.0 CB A:VAL7 4.9 9.3 1.0 HD2 A:PHE78 4.9 12.1 1.0 HG13 A:VAL9 4.9 18.5 1.0 CE A:MET72 4.9 17.2 1.0 CD2 A:LEU56 4.9 17.7 1.0 HB A:THR58 5.0 14.9 1.0 HE A:ARG68 5.0 18.5 1.0 HB A:VAL7 5.0 11.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203 b:21.9 occ:1.00 CL2 A:20G203 0.0 21.9 1.0 C04 A:20G203 1.7 17.1 1.0 C03 A:20G203 2.6 16.6 1.0 HG13 A:ILE100 2.6 16.4 1.0 C06 A:20G203 2.6 15.8 1.0 H03 A:20G203 2.7 19.9 1.0 O07 A:20G203 2.8 15.9 1.0 HB3 A:TYR96 2.9 15.4 1.0 HD11 A:ILE100 2.9 16.9 1.0 O A:TYR96 3.1 11.3 1.0 CG1 A:ILE100 3.3 13.7 1.0 OE1 A:GLN99 3.4 24.2 1.0 HB2 A:GLN99 3.4 20.9 1.0 HG21 A:VAL9 3.4 19.4 1.0 HG11 A:VAL9 3.5 18.5 1.0 CD1 A:ILE100 3.5 14.1 1.0 HA A:TYR96 3.5 13.2 1.0 HG12 A:ILE100 3.6 16.4 1.0 HD12 A:ILE100 3.6 16.9 1.0 C A:TYR96 3.7 10.6 1.0 CB A:TYR96 3.7 12.8 1.0 CA A:TYR96 3.8 11.0 1.0 C02 A:20G203 3.9 15.8 1.0 C24 A:20G203 4.0 14.2 1.0 HB A:VAL9 4.0 18.1 1.0 H A:ILE100 4.1 13.7 1.0 SD A:MET72 4.2 16.7 1.0 C08 A:20G203 4.2 15.4 1.0 HB3 A:GLN99 4.2 20.9 1.0 CB A:GLN99 4.2 17.4 1.0 CG2 A:VAL9 4.3 16.2 1.0 CG1 A:VAL9 4.3 15.4 1.0 CD A:GLN99 4.3 44.1 1.0 HD13 A:ILE100 4.4 16.9 1.0 HD3 A:ARG68 4.4 19.6 1.0 HB2 A:TYR96 4.4 15.4 1.0 CB A:VAL9 4.4 15.1 1.0 C25 A:20G203 4.4 15.0 1.0 HG2 A:MET72 4.5 17.3 1.0 N A:ILE100 4.5 11.4 1.0 H08 A:20G203 4.6 18.5 1.0 H08A A:20G203 4.6 18.5 1.0 HE2 A:MET72 4.6 20.7 1.0 HD1 A:TYR96 4.6 17.2 1.0 CG A:TYR96 4.6 14.0 1.0 HG23 A:VAL9 4.6 19.4 1.0 CB A:ILE100 4.7 13.2 1.0 HG12 A:VAL9 4.7 18.5 1.0 H24 A:20G203 4.8 17.0 1.0 O23 A:20G203 4.8 16.4 1.0 N A:ARG97 4.8 10.3 1.0 CG A:GLN99 4.8 30.3 1.0 HB A:ILE100 4.9 15.8 1.0 CE A:MET72 4.9 17.2 1.0 CG A:MET72 4.9 14.4 1.0 HE1 A:MET72 4.9 20.7 1.0 CD1 A:TYR96 5.0 14.3 1.0 HG22 A:VAL9 5.0 19.4 1.0 HG13 A:VAL9 5.0 18.5 1.0 HG3 A:GLN99 5.0 36.4 1.0 HA A:ILE100 5.0 14.3 1.0 HA A:ARG97 5.0 13.1 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203 b:17.9 occ:1.00 CL1 B:20G203 0.0 17.9 1.0 C02 B:20G203 1.7 17.0 1.0 C25 B:20G203 2.7 16.3 1.0 C03 B:20G203 2.7 17.0 1.0 H25 B:20G203 2.8 19.6 1.0 H03 B:20G203 2.8 20.4 1.0 HG3 B:MET72 2.9 17.8 1.0 HG11 B:VAL7 3.0 14.8 1.0 HB2 B:TYR71 3.0 21.9 1.0 HG3 B:ARG68 3.1 19.5 1.0 HB3 B:TYR71 3.2 21.9 1.0 HG21 B:THR58 3.3 17.7 1.0 HG2 B:ARG68 3.3 19.5 1.0 HG2 B:MET72 3.4 17.8 1.0 CB B:TYR71 3.5 18.3 1.0 CG B:MET72 3.6 14.8 1.0 HD2 B:TYR71 3.6 25.0 1.0 CG B:ARG68 3.7 16.3 1.0 HE2 B:PHE78 3.7 13.6 1.0 CG1 B:VAL7 3.8 12.3 1.0 O B:ARG68 3.9 14.6 1.0 C04 B:20G203 3.9 17.4 1.0 C24 B:20G203 4.0 15.8 1.0 HG13 B:VAL7 4.0 14.8 1.0 HG12 B:VAL7 4.1 14.8 1.0 HG12 B:VAL9 4.1 18.5 1.0 HD3 B:ARG68 4.1 18.2 1.0 H B:MET72 4.1 16.9 1.0 HG22 B:THR58 4.1 17.7 1.0 N B:MET72 4.1 14.1 1.0 CG2 B:THR58 4.1 14.8 1.0 HG11 B:VAL9 4.1 18.5 1.0 HE2 B:MET72 4.2 22.5 1.0 HA B:MET72 4.2 16.5 1.0 HA B:ARG68 4.2 19.7 1.0 C B:TYR71 4.3 15.8 1.0 CD2 B:TYR71 4.3 20.9 1.0 CG B:TYR71 4.4 21.6 1.0 HD23 B:LEU56 4.5 22.2 1.0 CD B:ARG68 4.5 15.2 1.0 C06 B:20G203 4.5 15.7 1.0 CA B:MET72 4.5 13.8 1.0 CG1 B:VAL9 4.5 15.4 1.0 HG21 B:VAL7 4.6 14.4 1.0 CA B:TYR71 4.6 15.3 1.0 HG23 B:THR58 4.6 17.7 1.0 CE2 B:PHE78 4.6 11.3 1.0 CB B:MET72 4.6 15.5 1.0 C B:ARG68 4.7 14.7 1.0 O B:TYR71 4.8 15.9 1.0 H24 B:20G203 4.8 19.0 1.0 CA B:ARG68 4.8 16.4 1.0 SD B:MET72 4.8 16.7 1.0 CB B:ARG68 4.8 15.3 1.0 HD2 B:PHE78 4.8 12.9 1.0 CE B:MET72 4.8 18.7 1.0 HD21 B:LEU56 4.9 22.2 1.0 HB B:THR58 4.9 16.8 1.0 HG13 B:VAL9 4.9 18.5 1.0 CB B:VAL7 5.0 10.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203 b:22.8 occ:1.00 CL2 B:20G203 0.0 22.8 1.0 C04 B:20G203 1.7 17.4 1.0 C03 B:20G203 2.6 17.0 1.0 C06 B:20G203 2.7 15.7 1.0 HG13 B:ILE100 2.7 17.1 1.0 H03 B:20G203 2.7 20.4 1.0 HB3 B:TYR96 2.8 17.4 1.0 O07 B:20G203 2.9 14.5 1.0 HD11 B:ILE100 3.0 16.9 1.0 O B:TYR96 3.1 12.3 1.0 OE1 B:GLN99 3.3 18.8 0.5 HB2 B:GLN99 3.4 21.2 0.5 CG1 B:ILE100 3.4 14.3 1.0 HG21 B:VAL9 3.4 17.5 1.0 HA B:TYR96 3.4 15.3 1.0 HG11 B:VAL9 3.5 18.5 1.0 CD1 B:ILE100 3.5 14.1 1.0 HD12 B:ILE100 3.6 16.9 1.0 CB B:TYR96 3.7 14.5 1.0 HG12 B:ILE100 3.7 17.1 1.0 C B:TYR96 3.7 11.1 1.0 CA B:TYR96 3.8 12.7 1.0 HB3 B:GLN99 3.8 21.2 0.5 HB2 B:GLN99 3.9 14.6 0.5 C02 B:20G203 3.9 17.0 1.0 C24 B:20G203 3.9 15.8 1.0 HB B:VAL9 4.0 17.5 1.0 CB B:GLN99 4.0 17.7 0.5 H B:ILE100 4.1 13.3 1.0 CD B:GLN99 4.2 25.4 0.5 C08 B:20G203 4.2 14.0 1.0 CG2 B:VAL9 4.3 14.6 1.0 HB2 B:TYR96 4.3 17.4 1.0 CG1 B:VAL9 4.3 15.4 1.0 SD B:MET72 4.4 16.7 1.0 HD13 B:ILE100 4.4 16.9 1.0 C25 B:20G203 4.4 16.3 1.0 HD3 B:ARG68 4.5 18.2 1.0 CB B:VAL9 4.5 14.6 1.0 HE2 B:MET72 4.5 22.5 1.0 HG2 B:MET72 4.5 17.8 1.0 H08A B:20G203 4.5 16.8 1.0 CG B:TYR96 4.6 15.6 1.0 N B:ILE100 4.6 11.1 1.0 HD1 B:TYR96 4.6 18.3 1.0 HG23 B:VAL9 4.7 17.5 1.0 H08 B:20G203 4.7 16.8 1.0 CB B:ILE100 4.7 12.3 1.0 CG B:GLN99 4.7 20.0 0.5 HG12 B:VAL9 4.7 18.5 1.0 CB B:GLN99 4.7 12.2 0.5 H24 B:20G203 4.7 19.0 1.0 HB3 B:GLN99 4.8 14.6 0.5 O23 B:20G203 4.8 15.9 1.0 N B:ARG97 4.9 10.1 1.0 HG3 B:GLN99 4.9 24.0 0.5 CD1 B:TYR96 4.9 15.2 1.0 HB B:ILE100 4.9 14.8 1.0 CE B:MET72 4.9 18.7 1.0 HD2 B:PHE78 4.9 12.9 1.0 CG B:MET72 5.0 14.8 1.0 HG22 B:VAL9 5.0 17.5 1.0 HG13 B:VAL9 5.0 18.5 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