Chlorine in PDB 4m22: Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C, PDB code: 4m22 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)	23.67 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.906, 83.457, 86.924, 90.00, 109.29, 90.00
R / Rfree (%)	17.9 / 21.6

The structure of Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Chlorine atom in the Crystal Structure of Small Molecule Acrylamide 16 Covalently Bound to K-Ras G12C (pdb code 4m22). 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 Acrylamide 16 Covalently Bound to K-Ras G12C, PDB code: 4m22:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Small Molecule Acrylamide 16 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 Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:44.2 occ:1.00 CL1 B:22C202 0.0 44.2 1.0 C02 B:22C202 1.7 31.2 1.0 C08 B:22C202 2.7 30.8 1.0 C03 B:22C202 2.7 31.8 1.0 O B:HOH303 2.9 17.3 1.0 O09 B:22C202 2.9 29.4 1.0 HD3 B:ARG68 3.0 26.9 1.0 HA3 B:GLY60 3.1 24.7 1.0 HH B:TYR71 3.1 26.7 1.0 HA2 B:GLY60 3.1 24.7 1.0 O B:HOH304 3.2 22.6 1.0 HD2 B:ARG68 3.3 26.9 1.0 HB B:THR58 3.3 23.0 1.0 H B:GLY60 3.3 23.9 1.0 OH B:TYR71 3.4 22.3 1.0 CA B:GLY60 3.4 20.6 1.0 N B:GLY60 3.5 19.9 1.0 CD B:ARG68 3.6 22.4 1.0 OG1 B:THR58 3.8 18.7 1.0 C07 B:22C202 4.0 31.5 1.0 C04 B:22C202 4.0 32.2 1.0 CB B:THR58 4.0 19.2 1.0 HE1 B:TYR96 4.1 31.3 1.0 C20 B:22C202 4.3 20.7 1.0 NE B:ARG68 4.3 23.8 1.0 C10 B:22C202 4.4 28.0 1.0 C B:ALA59 4.4 20.9 1.0 HG12 B:VAL9 4.5 26.4 1.0 C06 B:22C202 4.5 32.0 1.0 HG21 B:THR58 4.5 23.7 1.0 HG1 B:THR58 4.6 22.4 1.0 H B:ALA59 4.6 26.9 1.0 HH11 B:ARG68 4.6 29.5 1.0 HG2 B:ARG68 4.6 27.5 1.0 HB B:VAL9 4.7 24.4 1.0 N B:ALA59 4.7 22.4 1.0 CZ B:TYR71 4.7 22.3 1.0 HE B:ARG68 4.7 28.6 1.0 C21 B:22C202 4.7 21.5 1.0 HH B:TYR96 4.8 33.0 1.0 CG B:ARG68 4.8 22.9 1.0 OE1 B:GLU62 4.8 26.2 1.0 CG2 B:THR58 4.8 19.8 1.0 CE1 B:TYR96 4.8 26.1 1.0 C B:GLY60 4.9 20.9 1.0 H B:GLY10 4.9 20.0 1.0 C B:THR58 5.0 20.5 1.0 CZ B:ARG68 5.0 24.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Small Molecule Acrylamide 16 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 Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:32.1 occ:1.00 CL2 B:22C202 0.0 32.1 1.0 C04 B:22C202 1.7 32.2 1.0 HE2 B:MET72 2.7 32.8 1.0 C06 B:22C202 2.7 32.0 1.0 C03 B:22C202 2.7 31.8 1.0 HE1 B:MET72 3.0 32.8 1.0 HA B:TYR96 3.2 28.1 1.0 HD1 B:TYR96 3.3 30.6 1.0 HB2 B:GLN99 3.3 32.7 1.0 CE B:MET72 3.3 27.4 1.0 HG13 B:ILE100 3.4 23.2 1.0 HB3 B:TYR96 3.5 28.0 1.0 O B:TYR96 3.6 23.9 1.0 CD1 B:TYR96 3.6 25.5 1.0 HG11 B:VAL9 3.7 26.4 1.0 CA B:TYR96 3.8 23.4 1.0 HD11 B:ILE100 3.8 21.6 1.0 HG21 B:VAL9 3.9 23.5 1.0 CB B:TYR96 3.9 23.4 1.0 HE3 B:MET72 4.0 32.8 1.0 HB B:VAL9 4.0 24.4 1.0 CG B:TYR96 4.0 26.0 1.0 C02 B:22C202 4.0 31.2 1.0 C07 B:22C202 4.0 31.5 1.0 CB B:GLN99 4.1 27.3 1.0 C B:TYR96 4.1 23.9 1.0 HB3 B:GLN99 4.1 32.7 1.0 CG1 B:ILE100 4.2 19.4 1.0 HG3 B:GLN99 4.3 36.8 1.0 CD1 B:ILE100 4.4 18.0 1.0 HG12 B:ILE100 4.4 23.2 1.0 CE1 B:TYR96 4.4 26.1 1.0 HG2 B:GLN99 4.5 36.8 1.0 CG1 B:VAL9 4.5 22.0 1.0 HD12 B:ILE100 4.5 21.6 1.0 CG B:GLN99 4.5 30.7 1.0 SD B:MET72 4.5 33.1 1.0 H B:ILE100 4.5 26.9 1.0 C08 B:22C202 4.5 30.8 1.0 CB B:VAL9 4.5 20.3 1.0 HE1 B:TYR96 4.6 31.3 1.0 CG2 B:VAL9 4.6 19.6 1.0 HG12 B:VAL9 4.7 26.4 1.0 HD2 B:ARG68 4.8 26.9 1.0 HH B:TYR71 4.8 26.7 1.0 HB2 B:TYR96 4.9 28.0 1.0 HG23 B:VAL9 5.0 23.5 1.0 CD2 B:TYR96 5.0 28.2 1.0 N B:ILE100 5.0 22.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Small Molecule Acrylamide 16 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 Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:65.8 occ:1.00 CL1 C:22C202 0.0 65.8 1.0 C02 C:22C202 1.7 55.6 1.0 C03 C:22C202 2.7 56.0 1.0 C08 C:22C202 2.7 55.2 1.0 O09 C:22C202 2.9 53.7 1.0 O C:HOH301 3.0 22.4 1.0 O C:HOH337 3.3 32.8 1.0 HH C:TYR71 3.4 59.2 1.0 HB C:THR58 3.5 51.2 1.0 OH C:TYR71 3.5 49.3 1.0 HE1 C:TYR96 3.8 36.9 1.0 O C:ALA59 3.8 54.5 1.0 C04 C:22C202 4.0 56.4 1.0 C14 C:22C202 4.0 42.1 1.0 C07 C:22C202 4.0 55.8 1.0 OG1 C:THR58 4.0 42.7 1.0 C10 C:22C202 4.2 51.3 1.0 CB C:THR58 4.2 42.6 1.0 C13 C:22C202 4.3 43.4 1.0 C06 C:22C202 4.5 56.2 1.0 C C:ALA59 4.5 55.0 1.0 HG21 C:THR58 4.6 49.1 1.0 H C:ALA59 4.7 57.7 1.0 CE1 C:TYR96 4.7 30.8 1.0 C11 C:22C202 4.7 48.0 1.0 N C:ALA59 4.8 48.1 1.0 N12 C:22C202 4.8 44.8 1.0 HG12 C:VAL9 4.8 35.8 1.0 CZ C:TYR71 4.8 48.2 1.0 HG1 C:THR58 4.9 51.2 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Small Molecule Acrylamide 16 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 Acrylamide 16 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:0.4 occ:1.00 CL2 C:22C202 0.0 0.4 1.0 C04 C:22C202 1.7 56.4 1.0 C03 C:22C202 2.7 56.0 1.0 C06 C:22C202 2.7 56.2 1.0 HD1 C:TYR96 3.0 36.9 1.0 HG13 C:ILE100 3.6 41.7 1.0 HG11 C:VAL9 3.6 35.8 1.0 HB2 C:GLN99 3.6 63.5 1.0 SD C:MET72 3.7 59.3 1.0 HA C:TYR96 3.7 37.3 1.0 CD1 C:TYR96 3.8 30.7 1.0 HB3 C:GLN99 3.8 63.5 1.0 HE2 C:MET72 3.9 69.7 1.0 C02 C:22C202 4.0 55.6 1.0 C07 C:22C202 4.0 55.8 1.0 OE1 C:GLN99 4.0 62.4 1.0 HH C:TYR71 4.1 59.2 1.0 HG12 C:ILE100 4.1 41.7 1.0 HB3 C:TYR96 4.1 35.3 1.0 HD11 C:ILE100 4.1 39.0 1.0 HB C:VAL9 4.1 32.8 1.0 CB C:GLN99 4.2 53.0 1.0 O C:TYR96 4.2 33.7 1.0 CE C:MET72 4.2 58.1 1.0 CG1 C:ILE100 4.2 34.8 1.0 HE1 C:MET72 4.2 69.7 1.0 HG21 C:VAL9 4.3 31.0 1.0 CG1 C:VAL9 4.4 29.8 1.0 CD C:GLN99 4.4 60.1 1.0 HG2 C:MET72 4.4 60.7 1.0 HE1 C:TYR96 4.4 36.9 1.0 CA C:TYR96 4.4 31.1 1.0 HG12 C:VAL9 4.5 35.8 1.0 C08 C:22C202 4.5 55.2 1.0 HG3 C:MET72 4.5 60.7 1.0 CG C:MET72 4.5 50.6 1.0 CB C:TYR96 4.6 29.4 1.0 CE1 C:TYR96 4.6 30.8 1.0 HE2 C:TYR71 4.6 55.8 1.0 CG C:TYR96 4.6 29.7 1.0 CB C:VAL9 4.7 27.4 1.0 CD1 C:ILE100 4.7 32.5 1.0 H C:ILE100 4.7 46.7 1.0 C C:TYR96 4.8 32.4 1.0 OH C:TYR71 4.8 49.3 1.0 NE2 C:GLN99 4.8 59.7 1.0 CG C:GLN99 4.9 57.7 1.0 HE22 C:GLN99 4.9 71.6 1.0 CG2 C:VAL9 5.0 25.8 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