Chlorine in PDB 4lv6: Crystal Structure of Small Molecule Disulfide 4 Covalently Bound to K- Ras G12C

The structure of Crystal Structure of Small Molecule Disulfide 4 Covalently Bound to K- Ras G12C, PDB code: 4lv6 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)	19.50 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.140, 39.320, 62.790, 77.33, 81.21, 77.35
R / Rfree (%)	15.7 / 18.7

The structure of Crystal Structure of Small Molecule Disulfide 4 Covalently 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 4 Covalently Bound to K- Ras G12C (pdb code 4lv6). 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 4 Covalently Bound to K- Ras G12C, PDB code: 4lv6:
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 4 Covalently 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 4 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:24.0 occ:1.00 CL1 A:20H203 0.0 24.0 1.0 C02 A:20H203 1.7 21.6 1.0 C24 A:20H203 2.7 21.3 1.0 C03 A:20H203 2.7 19.2 1.0 H03 A:20H203 2.8 23.1 1.0 H24 A:20H203 2.8 25.6 1.0 HG11 A:VAL7 3.0 16.5 1.0 HG3 A:ARG68 3.1 25.1 1.0 HG3 A:MET72 3.1 19.5 1.0 HG2 A:ARG68 3.2 25.1 1.0 HG21 A:THR58 3.2 18.6 1.0 HB3 A:TYR71 3.3 26.7 1.0 HB2 A:TYR71 3.3 26.7 1.0 HG2 A:MET72 3.4 19.5 1.0 CG A:ARG68 3.6 20.9 1.0 CG A:MET72 3.7 16.3 1.0 CB A:TYR71 3.7 22.3 1.0 CG1 A:VAL7 3.8 13.7 1.0 HG12 A:VAL9 3.8 20.5 1.0 O A:ARG68 3.9 18.1 1.0 HD2 A:TYR71 3.9 37.6 1.0 C22 A:20H203 3.9 24.3 1.0 HG13 A:VAL7 4.0 16.5 1.0 HG22 A:THR58 4.0 18.6 1.0 C04 A:20H203 4.0 18.5 1.0 HG12 A:VAL7 4.0 16.5 1.0 HD3 A:ARG68 4.0 31.8 1.0 CG2 A:THR58 4.0 15.5 1.0 HE2 A:PHE78 4.0 18.9 1.0 HE2 A:MET72 4.1 28.2 1.0 HG11 A:VAL9 4.1 20.5 1.0 H A:MET72 4.2 20.5 1.0 HA A:ARG68 4.3 22.9 1.0 N A:MET72 4.3 17.1 1.0 HD23 A:LEU56 4.3 23.3 1.0 CD A:ARG68 4.4 26.5 1.0 CG1 A:VAL9 4.4 17.1 1.0 HA A:MET72 4.4 21.6 1.0 C05 A:20H203 4.5 20.3 1.0 CD2 A:TYR71 4.6 31.3 1.0 C A:TYR71 4.6 20.6 1.0 HG23 A:THR58 4.6 18.6 1.0 CG A:TYR71 4.6 28.5 1.0 O A:HOH402 4.7 30.7 1.0 HG21 A:VAL7 4.7 15.9 1.0 C A:ARG68 4.7 18.8 1.0 SD A:MET72 4.8 22.0 1.0 CA A:MET72 4.8 18.0 1.0 HB A:THR58 4.8 18.2 1.0 HG13 A:VAL9 4.8 20.5 1.0 CB A:MET72 4.8 18.2 1.0 CB A:ARG68 4.8 24.5 1.0 CE A:MET72 4.8 23.5 1.0 CA A:TYR71 4.8 22.0 1.0 CA A:ARG68 4.8 19.1 1.0 H04 A:20H203 4.8 22.2 1.0 HD21 A:LEU56 4.8 23.3 1.0 HE A:ARG68 4.9 30.7 1.0 CE2 A:PHE78 4.9 15.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Small Molecule Disulfide 4 Covalently 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 4 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:34.9 occ:1.00 CL2 A:20H203 0.0 34.9 1.0 C22 A:20H203 1.7 24.3 1.0 C24 A:20H203 2.6 21.3 1.0 C05 A:20H203 2.7 20.3 1.0 HG13 A:ILE100 2.8 21.2 1.0 H24 A:20H203 2.8 25.6 1.0 HB3 A:TYR96 2.9 17.9 1.0 O06 A:20H203 2.9 21.6 1.0 O A:TYR96 3.1 16.2 1.0 HB2 A:GLN99 3.2 21.4 1.0 HA A:TYR96 3.3 18.6 1.0 HD11 A:ILE100 3.4 20.6 1.0 CG1 A:ILE100 3.6 17.7 1.0 O A:HOH425 3.7 43.0 1.0 CB A:TYR96 3.7 14.9 1.0 HG11 A:VAL9 3.7 20.5 1.0 CA A:TYR96 3.7 15.5 1.0 C A:TYR96 3.7 16.0 1.0 CD1 A:ILE100 3.8 17.1 1.0 HD12 A:ILE100 3.9 20.6 1.0 HG21 A:VAL9 3.9 27.8 1.0 HG12 A:ILE100 3.9 21.2 1.0 C02 A:20H203 3.9 21.6 1.0 C04 A:20H203 3.9 18.5 1.0 HB A:VAL9 4.0 27.3 1.0 H A:ILE100 4.0 17.8 1.0 SD A:MET72 4.1 22.0 1.0 CB A:GLN99 4.1 17.9 1.0 HB3 A:GLN99 4.3 21.4 1.0 HD1 A:TYR96 4.3 22.5 1.0 C07 A:20H203 4.3 19.2 1.0 HE2 A:MET72 4.3 28.2 1.0 HB2 A:TYR96 4.4 17.9 1.0 HD3 A:ARG68 4.4 31.8 1.0 N A:ILE100 4.4 14.8 1.0 C03 A:20H203 4.4 19.2 1.0 CG1 A:VAL9 4.4 17.1 1.0 CG A:TYR96 4.5 17.9 1.0 CB A:VAL9 4.6 22.8 1.0 HE1 A:MET72 4.6 28.2 1.0 CE A:MET72 4.6 23.5 1.0 CG2 A:VAL9 4.6 23.2 1.0 H07A A:20H203 4.6 23.1 1.0 CD1 A:TYR96 4.7 18.8 1.0 HG2 A:MET72 4.7 19.5 1.0 HG12 A:VAL9 4.7 20.5 1.0 HD13 A:ILE100 4.7 20.6 1.0 CB A:ILE100 4.8 16.3 1.0 H07 A:20H203 4.8 23.1 1.0 H04 A:20H203 4.8 22.2 1.0 HG3 A:GLN99 4.9 32.9 1.0 H A:GLN99 4.9 17.4 1.0 N A:ARG97 4.9 12.3 1.0 HA A:ILE100 4.9 17.2 1.0 HG2 A:GLN99 4.9 32.9 1.0 CG A:GLN99 5.0 27.4 1.0 HB A:ILE100 5.0 19.5 1.0 CA A:ILE100 5.0 14.3 1.0 C A:GLN99 5.0 12.0 1.0 HG23 A:VAL9 5.0 27.8 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Small Molecule Disulfide 4 Covalently 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 4 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:27.3 occ:1.00 CL1 B:20H203 0.0 27.3 1.0 C02 B:20H203 1.7 26.0 1.0 C24 B:20H203 2.7 26.1 1.0 C03 B:20H203 2.7 23.3 1.0 H03 B:20H203 2.8 27.9 1.0 H24 B:20H203 2.8 31.3 1.0 HG3 B:MET72 3.0 25.5 1.0 HG11 B:VAL7 3.0 17.9 1.0 HG3 B:ARG68 3.1 37.5 1.0 HB2 B:TYR71 3.2 27.2 1.0 HG21 B:THR58 3.2 23.5 1.0 HB3 B:TYR71 3.3 27.2 1.0 HG2 B:MET72 3.3 25.5 1.0 HG2 B:ARG68 3.5 37.5 1.0 CG B:MET72 3.6 21.3 1.0 CB B:TYR71 3.7 22.7 1.0 CG B:ARG68 3.7 31.3 1.0 CG1 B:VAL7 3.8 15.0 1.0 HD2 B:TYR71 3.9 41.9 1.0 C22 B:20H203 3.9 27.9 1.0 HG12 B:VAL9 3.9 22.5 1.0 HE2 B:MET72 3.9 31.2 1.0 HG22 B:THR58 4.0 23.5 1.0 O B:ARG68 4.0 20.4 1.0 C04 B:20H203 4.0 22.9 1.0 CG2 B:THR58 4.0 19.6 1.0 HG13 B:VAL7 4.0 17.9 1.0 HE2 B:PHE78 4.1 17.8 1.0 HG12 B:VAL7 4.1 17.9 1.0 H B:MET72 4.1 24.2 1.0 HG11 B:VAL9 4.2 22.5 1.0 N B:MET72 4.2 20.2 1.0 HD3 B:ARG68 4.2 33.6 1.0 HA B:MET72 4.3 23.6 1.0 HA B:ARG68 4.3 29.3 1.0 HD23 B:LEU56 4.5 26.0 1.0 C B:TYR71 4.5 20.7 1.0 C05 B:20H203 4.5 24.5 1.0 CG1 B:VAL9 4.5 18.8 1.0 CD B:ARG68 4.5 28.0 1.0 CD2 B:TYR71 4.6 34.9 1.0 HG23 B:THR58 4.6 23.5 1.0 CG B:TYR71 4.6 27.2 1.0 CA B:MET72 4.7 19.7 1.0 CE B:MET72 4.7 26.0 1.0 HE B:ARG68 4.7 39.2 1.0 SD B:MET72 4.7 21.4 1.0 CB B:MET72 4.7 19.4 1.0 HB B:THR58 4.7 24.1 1.0 HG21 B:VAL7 4.7 18.5 1.0 CA B:TYR71 4.7 23.5 1.0 O B:HOH385 4.8 37.9 1.0 C B:ARG68 4.8 22.5 1.0 HD21 B:LEU56 4.8 26.0 1.0 H04 B:20H203 4.8 27.5 1.0 CB B:ARG68 4.9 22.0 1.0 CA B:ARG68 4.9 24.4 1.0 HE3 B:MET72 4.9 31.2 1.0 CE2 B:PHE78 5.0 14.8 1.0 CB B:THR58 5.0 20.0 1.0 HG13 B:VAL9 5.0 22.5 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Small Molecule Disulfide 4 Covalently 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 4 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:36.2 occ:1.00 CL2 B:20H203 0.0 36.2 1.0 C22 B:20H203 1.7 27.9 1.0 C24 B:20H203 2.6 26.1 1.0 C05 B:20H203 2.7 24.5 1.0 H24 B:20H203 2.8 31.3 1.0 HG13 B:ILE100 2.9 25.7 1.0 HB3 B:TYR96 2.9 20.4 1.0 O06 B:20H203 2.9 24.6 1.0 O B:TYR96 3.1 18.1 1.0 HB2 B:GLN99 3.1 24.2 1.0 HA B:TYR96 3.2 21.4 1.0 HD11 B:ILE100 3.4 20.8 1.0 O B:HOH410 3.7 39.5 1.0 CA B:TYR96 3.7 17.8 1.0 C B:TYR96 3.7 15.8 1.0 CB B:TYR96 3.7 17.0 1.0 CG1 B:ILE100 3.7 21.4 1.0 HG11 B:VAL9 3.8 22.5 1.0 C02 B:20H203 3.9 26.0 1.0 CD1 B:ILE100 3.9 17.4 1.0 C04 B:20H203 3.9 22.9 1.0 HG21 B:VAL9 4.0 29.8 1.0 HG12 B:ILE100 4.0 25.7 1.0 CB B:GLN99 4.0 20.2 1.0 HB3 B:GLN99 4.0 24.2 1.0 HD12 B:ILE100 4.0 20.8 1.0 H B:ILE100 4.0 19.3 1.0 HB B:VAL9 4.1 32.2 1.0 HE2 B:MET72 4.1 31.2 1.0 SD B:MET72 4.1 21.4 1.0 HD1 B:TYR96 4.3 25.1 1.0 C07 B:20H203 4.3 24.1 1.0 HB2 B:TYR96 4.4 20.4 1.0 HE1 B:MET72 4.4 31.2 1.0 C03 B:20H203 4.4 23.3 1.0 N B:ILE100 4.5 16.1 1.0 HD3 B:ARG68 4.5 33.6 1.0 CE B:MET72 4.5 26.0 1.0 CG B:TYR96 4.5 16.7 1.0 HG3 B:GLN99 4.6 34.4 1.0 CG1 B:VAL9 4.6 18.8 1.0 CB B:VAL9 4.7 26.8 1.0 CD1 B:TYR96 4.7 20.9 1.0 H07A B:20H203 4.7 29.0 1.0 HG2 B:MET72 4.7 25.5 1.0 CG2 B:VAL9 4.7 24.8 1.0 CG B:GLN99 4.8 28.6 1.0 H07 B:20H203 4.8 29.0 1.0 HD13 B:ILE100 4.8 20.8 1.0 H04 B:20H203 4.8 27.5 1.0 N B:ARG97 4.9 14.2 1.0 H B:GLN99 4.9 20.9 1.0 HG12 B:VAL9 4.9 22.5 1.0 CB B:ILE100 4.9 17.4 1.0 CA B:GLN99 5.0 16.5 1.0 C B:GLN99 5.0 15.4 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