Calcium 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:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Disulfide 4 Covalently Bound to K- Ras G12C, PDB code: 4lv6:
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 4 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 Disulfide 4 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:17.8 occ:1.00 O2B A:GDP204 2.2 14.5 1.0 O A:HOH303 2.2 16.2 1.0 O A:HOH301 2.2 17.6 1.0 O A:HOH306 2.3 17.1 1.0 OG A:SER17 2.3 15.6 1.0 O A:HOH302 2.3 16.3 1.0 HG A:SER17 2.8 18.7 1.0 HB2 A:SER17 3.3 15.3 1.0 CB A:SER17 3.4 12.8 1.0 PB A:GDP204 3.4 14.4 1.0 H A:SER17 3.5 12.7 1.0 HA A:PRO34 3.5 21.7 1.0 O1B A:GDP204 3.6 16.2 1.0 HD2 A:TYR32 3.8 21.1 1.0 HB2 A:ALA59 4.0 24.0 1.0 HB3 A:SER17 4.1 15.3 1.0 N A:SER17 4.1 10.6 1.0 HB2 A:LYS16 4.1 13.9 1.0 OD2 A:ASP57 4.2 22.4 1.0 O1A A:GDP204 4.3 18.3 1.0 HE2 A:LYS16 4.3 17.4 1.0 CA A:SER17 4.3 11.9 1.0 OD1 A:ASP57 4.3 20.3 1.0 O A:HOH316 4.4 26.2 1.0 O A:ASP33 4.5 23.3 1.0 CA A:PRO34 4.5 18.1 1.0 O3B A:GDP204 4.5 13.8 1.0 O3A A:GDP204 4.5 16.3 1.0 O A:ILE36 4.5 17.2 1.0 HA A:SER17 4.6 14.3 1.0 O A:THR58 4.6 17.5 1.0 O A:PRO34 4.6 24.0 1.0 HB3 A:TYR32 4.7 32.5 1.0 CG A:ASP57 4.7 20.4 1.0 HZ1 A:LYS16 4.7 18.9 1.0 CD2 A:TYR32 4.7 17.6 1.0 PA A:GDP204 4.7 16.5 1.0 HZ3 A:LYS16 4.8 18.9 1.0 O2A A:GDP204 4.8 18.7 1.0 C A:PRO34 4.8 22.8 1.0 CB A:ALA59 4.9 20.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca202 b:18.7 occ:1.00 O A:GLY138 2.3 16.2 1.0 O A:HOH325 2.3 21.3 1.0 O A:HOH320 2.4 29.1 1.0 O A:HOH340 2.4 23.3 1.0 O A:HOH309 2.5 18.4 1.0 C A:GLY138 3.4 16.4 1.0 HA3 A:GLY138 3.6 17.9 1.0 CA A:GLY138 4.0 14.9 1.0 HA A:ILE139 4.1 14.7 1.0 HG22 A:ILE139 4.1 17.4 1.0 OD2 A:ASP108 4.4 36.2 1.0 O A:HOH352 4.4 26.9 1.0 OD1 A:ASP108 4.4 27.9 1.0 HA2 A:GLY138 4.5 17.9 1.0 O A:HOH308 4.5 18.8 1.0 N A:ILE139 4.5 13.6 1.0 OE1 A:GLU162 4.6 22.9 1.0 HG23 A:ILE139 4.6 17.4 1.0 O A:TYR137 4.7 16.6 1.0 CA A:ILE139 4.8 12.2 1.0 CG2 A:ILE139 4.8 14.5 1.0 CG A:ASP108 4.8 34.7 1.0 O A:HOH332 5.0 21.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca201 b:21.6 occ:1.00 HG B:SER17 1.9 23.4 1.0 O1B B:GDP204 2.2 18.5 1.0 O B:HOH307 2.2 20.1 1.0 O B:HOH305 2.3 16.9 1.0 O B:HOH308 2.3 20.8 1.0 O B:HOH301 2.3 18.3 1.0 OG B:SER17 2.3 19.5 1.0 HB2 B:SER17 3.2 21.0 1.0 CB B:SER17 3.4 17.5 1.0 PB B:GDP204 3.5 18.0 1.0 H B:SER17 3.5 18.4 1.0 HA B:PRO34 3.5 32.6 1.0 O2B B:GDP204 3.6 19.5 1.0 HD2 B:TYR32 3.8 27.1 1.0 HB2 B:ALA59 3.9 29.2 1.0 HB3 B:SER17 4.0 21.0 1.0 N B:SER17 4.1 15.3 1.0 HB2 B:LYS16 4.1 17.0 1.0 OD1 B:ASP57 4.2 24.4 1.0 OD2 B:ASP57 4.2 24.8 1.0 HE2 B:LYS16 4.2 25.2 1.0 CA B:SER17 4.3 16.3 1.0 O2A B:GDP204 4.3 22.4 1.0 O B:ASP33 4.4 25.2 1.0 O B:ILE36 4.5 23.5 1.0 CA B:PRO34 4.5 27.1 1.0 O B:HOH332 4.5 31.1 1.0 O3A B:GDP204 4.5 19.3 1.0 O3B B:GDP204 4.5 18.0 1.0 HA B:SER17 4.5 19.5 1.0 O B:PRO34 4.6 26.5 1.0 CG B:ASP57 4.6 25.2 1.0 O B:THR58 4.6 22.2 1.0 CD2 B:TYR32 4.7 22.6 1.0 HB3 B:TYR32 4.7 30.9 1.0 PA B:GDP204 4.7 19.0 1.0 HZ3 B:LYS16 4.7 23.6 1.0 C B:PRO34 4.8 26.7 1.0 CB B:ALA59 4.8 24.4 1.0 O1A B:GDP204 4.9 19.7 1.0 HZ2 B:LYS16 4.9 23.6 1.0 HB1 B:ALA59 5.0 29.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca202 b:20.8 occ:1.00 O B:HOH350 2.3 31.0 1.0 O B:GLY138 2.4 16.8 1.0 O B:HOH325 2.4 20.5 1.0 O B:HOH314 2.4 19.7 1.0 O B:HOH326 2.4 23.0 1.0 C B:GLY138 3.5 17.5 1.0 HA3 B:GLY138 3.6 18.2 1.0 HG22 B:ILE139 4.1 18.0 1.0 CA B:GLY138 4.1 15.1 1.0 HA B:ILE139 4.1 15.6 1.0 O B:HOH323 4.5 16.9 1.0 HA2 B:GLY138 4.5 18.2 1.0 N B:ILE139 4.6 14.0 1.0 OE1 B:GLU162 4.6 23.8 1.0 HG23 B:ILE139 4.6 18.0 1.0 O B:HOH344 4.7 25.4 1.0 O B:TYR137 4.8 16.9 1.0 CG2 B:ILE139 4.8 15.0 1.0 CA B:ILE139 4.8 13.0 1.0 O B:HOH347 5.0 28.6 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