Fluorine 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:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C Gdp, PDB code: 5vbm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F203 b:17.2 occ:1.00 F15 A:92V203 0.0 17.2 1.0 C14 A:92V203 1.3 18.2 1.0 F16 A:92V203 2.1 16.6 1.0 F17 A:92V203 2.2 18.4 1.0 C02 A:92V203 2.3 16.2 1.0 HA A:TYR96 2.8 14.3 1.0 N03 A:92V203 2.8 18.8 1.0 HB3 A:HIS95 2.8 20.1 1.0 C06 A:92V203 2.9 16.6 1.0 HB2 A:HIS95 3.0 20.1 1.0 C A:HIS95 3.1 12.7 1.0 O A:HIS95 3.1 15.0 1.0 C07 A:92V203 3.2 15.4 1.0 N A:TYR96 3.2 13.3 1.0 H071 A:92V203 3.2 18.5 1.0 CB A:HIS95 3.3 16.8 1.0 CA A:TYR96 3.4 11.9 1.0 CD1 A:TYR96 3.5 13.4 1.0 C01 A:92V203 3.6 18.2 1.0 H A:TYR96 3.6 16.0 1.0 CG A:TYR96 3.6 12.5 1.0 C11 A:92V203 3.6 16.5 1.0 HD1 A:TYR96 3.7 16.1 1.0 CE1 A:TYR96 3.7 15.1 1.0 CA A:HIS95 3.8 13.8 1.0 H111 A:92V203 4.0 19.8 1.0 CD2 A:TYR96 4.0 17.0 1.0 HB2 A:GLN99 4.0 17.9 1.0 C08 A:92V203 4.0 19.0 1.0 HB3 A:GLN99 4.1 17.9 1.0 HE1 A:TYR96 4.1 18.2 1.0 CZ A:TYR96 4.1 14.8 1.0 N04 A:92V203 4.1 21.3 1.0 CB A:TYR96 4.1 11.7 1.0 O A:HOH339 4.2 19.8 1.0 CE2 A:TYR96 4.2 15.6 1.0 C18 A:92V203 4.3 18.2 1.0 HA A:HIS95 4.3 16.6 1.0 C10 A:92V203 4.4 16.1 1.0 C05 A:92V203 4.5 22.0 1.0 HD2 A:TYR96 4.5 20.4 1.0 CB A:GLN99 4.5 14.9 1.0 H081 A:92V203 4.6 22.8 1.0 C09 A:92V203 4.6 16.1 1.0 O19 A:92V203 4.6 20.2 1.0 CG A:HIS95 4.7 17.8 1.0 C A:TYR96 4.7 13.8 1.0 H221 A:92V203 4.7 52.9 1.0 HB3 A:TYR96 4.7 14.0 1.0 HG2 A:GLN99 4.8 21.6 1.0 H A:GLN99 4.8 16.2 1.0 HB2 A:TYR96 4.8 14.0 1.0 HE2 A:TYR96 4.8 18.8 1.0 N A:HIS95 4.9 13.9 1.0 OH A:TYR96 5.0 20.8 1.0

Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F binding site number 2 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:F203 b:16.6 occ:1.00 F16 A:92V203 0.0 16.6 1.0 C14 A:92V203 1.3 18.2 1.0 F15 A:92V203 2.1 17.2 1.0 F17 A:92V203 2.1 18.4 1.0 C02 A:92V203 2.3 16.2 1.0 HA A:TYR96 2.6 14.3 1.0 HB3 A:GLN99 2.6 17.9 1.0 H221 A:92V203 2.7 52.9 1.0 C18 A:92V203 2.8 18.2 1.0 O19 A:92V203 2.8 20.2 1.0 C01 A:92V203 2.9 18.2 1.0 HD1 A:TYR96 3.0 16.1 1.0 HG2 A:GLN99 3.0 21.6 1.0 HB2 A:GLN99 3.1 17.9 1.0 CB A:GLN99 3.2 14.9 1.0 CD1 A:TYR96 3.4 13.4 1.0 CA A:TYR96 3.5 11.9 1.0 N20 A:92V203 3.5 21.8 1.0 N03 A:92V203 3.6 18.8 1.0 CG A:GLN99 3.6 18.0 1.0 C22 A:92V203 3.6 44.1 1.0 O A:HIS95 3.7 15.0 1.0 CE1 A:TYR96 3.9 15.1 1.0 H201 A:92V203 3.9 26.2 1.0 HE1 A:TYR96 4.0 18.2 1.0 CG A:TYR96 4.0 12.5 1.0 H222 A:92V203 4.0 52.9 1.0 N A:TYR96 4.1 13.3 1.0 HG3 A:GLN99 4.1 21.6 1.0 C A:HIS95 4.1 12.7 1.0 C21 A:92V203 4.2 41.1 1.0 O A:HOH311 4.2 27.9 1.0 CB A:TYR96 4.2 11.7 1.0 C05 A:92V203 4.2 22.0 1.0 O A:TYR96 4.3 14.4 1.0 H071 A:92V203 4.3 18.5 1.0 H231 A:92V203 4.3 41.4 1.0 H A:GLN99 4.3 16.2 1.0 HB3 A:TYR96 4.3 14.0 1.0 C06 A:92V203 4.3 16.6 1.0 C A:TYR96 4.4 13.8 1.0 H212 A:92V203 4.5 49.3 1.0 C23 A:92V203 4.5 34.5 1.0 N04 A:92V203 4.5 21.3 1.0 CA A:GLN99 4.6 14.6 1.0 C07 A:92V203 4.6 15.4 1.0 H232 A:92V203 4.6 41.4 1.0 H A:TYR96 4.7 16.0 1.0 HB3 A:HIS95 4.8 20.1 1.0 CD A:GLN99 4.8 23.5 1.0 CZ A:TYR96 4.9 14.8 1.0 N A:GLN99 4.9 13.5 1.0 CD2 A:TYR96 4.9 17.0 1.0 O A:HOH339 4.9 19.8 1.0 H A:ILE100 5.0 17.9 1.0 H051 A:92V203 5.0 26.4 1.0 H211 A:92V203 5.0 49.3 1.0

Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F203 b:18.4 occ:1.00 F17 A:92V203 0.0 18.4 1.0 C14 A:92V203 1.3 18.2 1.0 F16 A:92V203 2.1 16.6 1.0 F15 A:92V203 2.2 17.2 1.0 C02 A:92V203 2.3 16.2 1.0 H071 A:92V203 2.5 18.5 1.0 HB2 A:GLN99 2.7 17.9 1.0 C07 A:92V203 3.1 15.4 1.0 N03 A:92V203 3.1 18.8 1.0 HG2 A:GLN99 3.3 21.6 1.0 C01 A:92V203 3.4 18.2 1.0 CB A:GLN99 3.4 14.9 1.0 HB3 A:GLN99 3.4 17.9 1.0 O A:HOH311 3.5 27.9 1.0 C06 A:92V203 3.5 16.6 1.0 O A:HOH339 3.5 19.8 1.0 O A:HIS95 3.6 15.0 1.0 O19 A:92V203 3.6 20.2 1.0 CG A:GLN99 3.8 18.0 1.0 C18 A:92V203 3.8 18.2 1.0 HB3 A:HIS95 3.8 20.1 1.0 HA A:TYR96 4.0 14.3 1.0 HH21 A:ARG102 4.1 28.7 1.0 C08 A:92V203 4.2 19.0 1.0 C A:HIS95 4.2 12.7 1.0 N04 A:92V203 4.3 21.3 1.0 HH22 A:ARG102 4.3 28.7 1.0 CD A:GLN99 4.4 23.5 1.0 OE1 A:GLN99 4.4 21.5 1.0 C05 A:92V203 4.4 22.0 1.0 H081 A:92V203 4.4 22.8 1.0 H A:GLN99 4.5 16.2 1.0 H221 A:92V203 4.6 52.9 1.0 NH2 A:ARG102 4.6 23.9 1.0 HG3 A:GLN99 4.6 21.6 1.0 CB A:HIS95 4.6 16.8 1.0 CA A:GLN99 4.7 14.6 1.0 C11 A:92V203 4.7 16.5 1.0 HB2 A:HIS95 4.7 20.1 1.0 N A:TYR96 4.8 13.3 1.0 CA A:TYR96 4.8 11.9 1.0 HA A:GLN99 4.9 17.6 1.0 HD1 A:TYR96 4.9 16.1 1.0 CA A:HIS95 5.0 13.8 1.0 N A:GLN99 5.0 13.5 1.0

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