Calcium in PDB 4lpk: Crystal Structure of K-Ras Wt, Gdp-Bound

The structure of Crystal Structure of K-Ras Wt, Gdp-Bound, PDB code: 4lpk 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)	20.96 / 1.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.282, 84.282, 41.267, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 19.2

The structure of Crystal Structure of K-Ras Wt, Gdp-Bound also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of K-Ras Wt, Gdp-Bound (pdb code 4lpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of K-Ras Wt, Gdp-Bound, PDB code: 4lpk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of K-Ras Wt, Gdp-Bound


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 K-Ras Wt, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:20.4 occ:1.00 O3B A:GDP201 2.4 29.7 1.0 O A:HOH306 2.4 27.6 1.0 OG A:SER17 2.4 9.8 1.0 O A:HOH302 2.4 26.1 1.0 O A:HOH305 2.5 21.0 1.0 O A:HOH322 2.5 28.7 1.0 HB2 A:SER17 3.4 11.6 1.0 HA A:PRO34 3.5 17.3 1.0 CB A:SER17 3.5 9.7 1.0 PB A:GDP201 3.6 28.7 1.0 H A:SER17 3.6 10.8 1.0 O1B A:GDP201 3.6 27.9 1.0 HD2 A:TYR32 3.7 20.2 1.0 O1A A:GDP201 4.0 27.5 1.0 HB2 A:LYS16 4.0 14.1 1.0 HE2 A:LYS16 4.1 12.5 1.0 HB3 A:SER17 4.1 11.6 1.0 HB3 A:TYR32 4.2 19.3 1.0 N A:SER17 4.2 9.0 1.0 OD2 A:ASP57 4.2 15.4 1.0 CA A:SER17 4.4 9.2 1.0 CA A:PRO34 4.4 14.4 1.0 O A:ASP33 4.4 12.4 1.0 OD1 A:ASP57 4.5 16.2 1.0 O2B A:GDP201 4.5 27.5 1.0 HB2 A:ALA59 4.5 24.3 1.0 O A:PRO34 4.5 15.6 1.0 CD2 A:TYR32 4.5 16.9 1.0 O A:THR58 4.6 12.8 1.0 O A:ILE36 4.6 14.0 1.0 HA A:SER17 4.6 11.1 1.0 O3A A:GDP201 4.7 28.1 1.0 CG A:ASP57 4.7 14.2 1.0 PA A:GDP201 4.7 27.6 1.0 C A:PRO34 4.8 15.4 1.0 HA A:ALA59 4.8 18.2 1.0 HZ1 A:LYS16 4.8 14.5 1.0 O2A A:GDP201 4.9 27.1 1.0 HZ3 A:LYS16 5.0 14.5 1.0 CB A:LYS16 5.0 11.8 1.0 O A:TYR32 5.0 18.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of K-Ras Wt, Gdp-Bound


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 K-Ras Wt, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:25.2 occ:1.00 O B:HOH310 2.2 21.1 1.0 O B:HOH307 2.3 23.4 1.0 OG B:SER17 2.4 12.1 1.0 O B:HOH312 2.4 21.6 1.0 O B:HOH309 2.4 21.9 1.0 O1B B:GDP201 2.4 30.9 1.0 HD2 B:TYR32 3.3 16.4 1.0 HB2 B:SER17 3.4 13.5 1.0 HA B:PRO34 3.4 17.6 1.0 CB B:SER17 3.5 11.2 1.0 H B:SER17 3.6 11.0 1.0 PB B:GDP201 3.6 29.9 1.0 O2B B:GDP201 3.7 30.2 1.0 HB2 B:LYS16 4.0 14.5 1.0 HE2 B:TYR32 4.0 17.5 1.0 OD2 B:ASP57 4.1 14.7 1.0 O1A B:GDP201 4.1 31.6 1.0 CD2 B:TYR32 4.1 13.7 1.0 HE2 B:LYS16 4.1 11.6 1.0 HB3 B:SER17 4.1 13.5 1.0 N B:SER17 4.2 9.2 1.0 O B:ASP33 4.2 10.8 1.0 O B:PRO34 4.2 16.2 1.0 CA B:PRO34 4.3 14.6 1.0 O B:ILE36 4.3 12.6 1.0 CA B:SER17 4.4 10.0 1.0 HA B:ALA59 4.4 16.2 1.0 OD1 B:ASP57 4.4 14.5 1.0 CE2 B:TYR32 4.5 14.6 1.0 HB2 B:ALA59 4.5 16.7 1.0 C B:PRO34 4.6 16.1 1.0 O3B B:GDP201 4.6 29.7 1.0 O B:THR58 4.6 12.3 1.0 HA B:SER17 4.6 12.0 1.0 CG B:ASP57 4.7 11.5 1.0 O3A B:GDP201 4.7 31.1 1.0 HZ1 B:LYS16 4.7 14.5 1.0 PA B:GDP201 4.8 29.3 1.0 HB3 B:TYR32 4.8 16.1 1.0 HZ3 B:LYS16 4.9 14.5 1.0 O2A B:GDP201 4.9 29.1 1.0 O B:TYR32 4.9 14.3 1.0 CB B:LYS16 4.9 12.1 1.0 CE B:LYS16 5.0 9.7 1.0 C B:ASP33 5.0 11.0 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