Fluorine in PDB 5vbe: Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gdp

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gdp, PDB code: 5vbe 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)	46.32 / 1.57
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	92.648, 92.648, 120.532, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.1

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras 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 H-Ras M72C Gdp (pdb code 5vbe). 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 H-Ras M72C Gdp, PDB code: 5vbe:
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 H-Ras 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 H-Ras M72C Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:52.9 occ:1.00 F15 A:92V202 0.0 52.9 1.0 C14 A:92V202 1.3 52.0 1.0 F16 A:92V202 2.1 46.1 1.0 F17 A:92V202 2.2 58.5 1.0 C02 A:92V202 2.3 37.0 1.0 C06 A:92V202 2.8 64.6 1.0 N03 A:92V202 2.8 41.6 1.0 HA A:TYR96 2.9 20.1 1.0 HB3 A:GLN95 3.0 29.4 1.0 C07 A:92V202 3.1 60.3 1.0 C A:GLN95 3.2 18.9 1.0 H071 A:92V202 3.2 72.5 1.0 HB2 A:GLN95 3.2 29.4 1.0 O A:GLN95 3.3 23.4 1.0 N A:TYR96 3.3 17.6 1.0 C11 A:92V202 3.4 85.8 1.0 CB A:GLN95 3.5 24.4 1.0 C01 A:92V202 3.5 43.6 1.0 CA A:TYR96 3.6 17.0 1.0 CD1 A:TYR96 3.7 20.7 1.0 H A:TYR96 3.7 21.2 1.0 H111 A:92V202 3.7 0.1 1.0 HD1 A:TYR96 3.8 25.0 1.0 CG A:TYR96 3.8 19.9 1.0 C08 A:92V202 3.9 59.8 1.0 HB2 A:GLN99 3.9 36.0 1.0 CE1 A:TYR96 3.9 21.7 1.0 CA A:GLN95 4.0 20.4 1.0 O A:HOH366 4.1 36.8 1.0 N04 A:92V202 4.1 36.6 1.0 C10 A:92V202 4.1 66.3 1.0 HB3 A:GLN99 4.2 36.0 1.0 CD2 A:TYR96 4.2 20.0 1.0 C18 A:92V202 4.2 51.2 1.0 HE1 A:TYR96 4.3 26.2 1.0 CB A:TYR96 4.3 18.3 1.0 C09 A:92V202 4.3 63.1 1.0 CZ A:TYR96 4.3 22.7 1.0 H081 A:92V202 4.5 71.9 1.0 C05 A:92V202 4.5 37.0 1.0 O19 A:92V202 4.5 59.3 1.0 HA A:GLN95 4.5 24.6 1.0 CE2 A:TYR96 4.5 21.1 1.0 CB A:GLN99 4.5 29.9 1.0 HG2 A:GLN99 4.7 65.0 1.0 HD2 A:TYR96 4.7 24.2 1.0 C A:TYR96 4.8 19.6 1.0 H101 A:92V202 4.8 79.7 1.0 HB3 A:TYR96 4.9 22.1 1.0 H A:GLN99 4.9 26.1 1.0 CG A:GLN95 4.9 32.0 1.0 HG3 A:GLN95 5.0 38.6 1.0 HB2 A:TYR96 5.0 22.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras 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 H-Ras M72C Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:46.1 occ:1.00 F16 A:92V202 0.0 46.1 1.0 C14 A:92V202 1.3 52.0 1.0 F15 A:92V202 2.1 52.9 1.0 F17 A:92V202 2.2 58.5 1.0 C02 A:92V202 2.3 37.0 1.0 HB3 A:GLN99 2.6 36.0 1.0 C18 A:92V202 2.7 51.2 1.0 O19 A:92V202 2.7 59.3 1.0 HA A:TYR96 2.8 20.1 1.0 C01 A:92V202 2.8 43.6 1.0 HG2 A:GLN99 2.9 65.0 1.0 HB2 A:GLN99 2.9 36.0 1.0 CB A:GLN99 3.1 29.9 1.0 H221 A:92V202 3.2 0.2 1.0 HD1 A:TYR96 3.4 25.0 1.0 CG A:GLN99 3.4 54.1 1.0 N20 A:92V202 3.5 52.2 1.0 N03 A:92V202 3.6 41.6 1.0 CA A:TYR96 3.7 17.0 1.0 O A:GLN95 3.7 23.4 1.0 CD1 A:TYR96 3.8 20.7 1.0 H222 A:92V202 3.8 0.2 1.0 C22 A:92V202 3.9 85.0 1.0 HG3 A:GLN99 3.9 65.0 1.0 H201 A:92V202 4.0 62.8 1.0 C05 A:92V202 4.1 37.0 1.0 C A:GLN95 4.2 18.9 1.0 N A:TYR96 4.2 17.6 1.0 C21 A:92V202 4.2 68.7 1.0 C06 A:92V202 4.3 64.6 1.0 H A:GLN99 4.3 26.1 1.0 CE1 A:TYR96 4.3 21.7 1.0 O A:TYR96 4.4 20.3 1.0 CG A:TYR96 4.4 19.9 1.0 HE1 A:TYR96 4.4 26.2 1.0 H071 A:92V202 4.4 72.5 1.0 N04 A:92V202 4.5 36.6 1.0 CA A:GLN99 4.5 23.8 1.0 CB A:TYR96 4.5 18.3 1.0 C A:TYR96 4.5 19.6 1.0 C07 A:92V202 4.6 60.3 1.0 O A:HOH366 4.6 36.8 1.0 CD A:GLN99 4.7 83.5 1.0 HE21 A:GLN99 4.7 0.8 1.0 HB3 A:TYR96 4.7 22.1 1.0 H212 A:92V202 4.7 82.5 1.0 H A:TYR96 4.8 21.2 1.0 HB3 A:GLN95 4.9 29.4 1.0 N A:GLN99 4.9 21.7 1.0 H051 A:92V202 4.9 44.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras 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 H-Ras M72C Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:58.5 occ:1.00 F17 A:92V202 0.0 58.5 1.0 C14 A:92V202 1.3 52.0 1.0 F16 A:92V202 2.2 46.1 1.0 F15 A:92V202 2.2 52.9 1.0 C02 A:92V202 2.3 37.0 1.0 H071 A:92V202 2.7 72.5 1.0 HB2 A:GLN99 3.1 36.0 1.0 N03 A:92V202 3.2 41.6 1.0 C07 A:92V202 3.2 60.3 1.0 C01 A:92V202 3.3 43.6 1.0 HG2 A:GLN99 3.3 65.0 1.0 O19 A:92V202 3.4 59.3 1.0 C06 A:92V202 3.5 64.6 1.0 O A:HOH366 3.6 36.8 1.0 C18 A:92V202 3.7 51.2 1.0 CB A:GLN99 3.8 29.9 1.0 HB3 A:GLN99 3.8 36.0 1.0 CG A:GLN99 4.0 54.1 1.0 HB3 A:GLN95 4.1 29.4 1.0 O A:GLN95 4.1 23.4 1.0 HE21 A:GLN99 4.1 0.8 1.0 C08 A:92V202 4.2 59.8 1.0 N04 A:92V202 4.3 36.6 1.0 HA A:TYR96 4.4 20.1 1.0 C05 A:92V202 4.4 37.0 1.0 H081 A:92V202 4.5 71.9 1.0 NE2 A:GLN99 4.5 88.8 1.0 CD A:GLN99 4.6 83.5 1.0 C A:GLN95 4.6 18.9 1.0 C11 A:92V202 4.7 85.8 1.0 H221 A:92V202 4.8 0.2 1.0 HG3 A:GLN99 4.8 65.0 1.0 CB A:GLN95 4.9 24.4 1.0 HB2 A:GLN95 4.9 29.4 1.0 N20 A:92V202 5.0 52.2 1.0 H A:GLN99 5.0 26.1 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