Magnesium in PDB 5vbm: Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp, PDB code: 5vbm was solved by D.R.Gentile, M.L.Jenkins, S.M.Moss, J.E.Burke, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.55 / 1.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.600, 41.180, 111.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.6

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp (pdb code 5vbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp, PDB code: 5vbm:

Magnesium binding site 1 out of 1 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:11.4 occ:1.00 O3B A:GDP202 2.0 11.0 1.0 O A:HOH320 2.0 12.5 1.0 O A:HOH323 2.1 12.3 1.0 OG A:SER17 2.1 11.9 1.0 O A:HOH346 2.1 13.7 1.0 O A:HOH334 2.1 13.9 1.0 HB2 A:SER17 3.1 12.9 1.0 CB A:SER17 3.1 10.8 1.0 H A:SER17 3.3 10.9 0.5 H A:SER17 3.3 10.9 0.5 PB A:GDP202 3.3 10.9 1.0 O2B A:GDP202 3.5 13.4 1.0 HA A:PRO34 3.5 26.0 1.0 HD2 A:TYR32 3.8 19.0 1.0 HB3 A:SER17 3.8 12.9 1.0 N A:SER17 3.9 9.1 1.0 OD2 A:ASP57 4.0 15.2 1.0 HB2 A:LYS16 4.1 12.1 0.5 CA A:SER17 4.1 10.2 1.0 HB2 A:LYS16 4.1 12.1 0.5 HA A:ALA59 4.1 25.7 1.0 O2A A:GDP202 4.2 12.6 1.0 O A:PRO34 4.3 20.0 1.0 OD1 A:ASP57 4.3 13.8 1.0 O A:ASP33 4.3 18.5 1.0 O3A A:GDP202 4.3 10.9 1.0 HA A:SER17 4.4 12.3 1.0 CA A:PRO34 4.4 21.7 1.0 O A:ILE36 4.4 12.7 1.0 O1B A:GDP202 4.4 11.8 1.0 HE2 A:LYS16 4.4 18.3 0.5 O A:THR58 4.4 17.2 1.0 CG A:ASP57 4.5 13.3 1.0 HE3 A:LYS16 4.5 16.9 0.5 PA A:GDP202 4.5 12.8 1.0 C A:PRO34 4.6 20.7 1.0 O1A A:GDP202 4.7 14.0 1.0 CD2 A:TYR32 4.7 15.8 1.0 O A:TYR32 4.8 21.8 1.0 HB3 A:TYR32 4.9 22.7 1.0 HE2 A:TYR32 5.0 20.0 1.0 CB A:LYS16 5.0 10.1 0.5 CB A:LYS16 5.0 10.1 0.5 C A:LYS16 5.0 9.0 0.5 C A:LYS16 5.0 9.0 0.5

D.R.Gentile, M.K.Rathinaswamy, M.L.Jenkins, S.M.Moss, B.D.Siempelkamp, A.R.Renslo, J.E.Burke, K.M.Shokat. Ras Binder Induces A Modified Switch-II Pocket in Gtp and Gdp States. Cell Chem Biol V. 24 1455 2017.
ISSN: ESSN 2451-9456
PubMed: 29033317
DOI: 10.1016/J.CHEMBIOL.2017.08.025