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

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp, PDB code: 5vbz 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)	51.60 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.840, 75.440, 93.630, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.3

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp (pdb code 5vbz). 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 Gppnhp, PDB code: 5vbz:
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 Gppnhp


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 Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:32.6 occ:1.00 F15 C:92V301 0.0 32.6 1.0 C14 C:92V301 1.3 31.9 1.0 F16 C:92V301 2.2 32.6 1.0 F17 C:92V301 2.2 32.3 1.0 C02 C:92V301 2.3 28.0 1.0 H071 C:92V301 2.5 21.1 1.0 C01 C:92V301 3.2 27.2 1.0 C07 C:92V301 3.2 17.6 1.0 O19 C:92V301 3.2 21.9 1.0 N03 C:92V301 3.2 23.6 1.0 C06 C:92V301 3.6 18.8 1.0 C18 C:92V301 3.7 23.1 1.0 HE1 C:TYR96 3.8 28.0 1.0 CE1 C:TYR96 4.0 23.3 1.0 HG3 C:GLN99 4.0 29.7 1.0 HB3 C:GLN95 4.3 39.7 1.0 C08 C:92V301 4.3 21.5 1.0 N04 C:92V301 4.3 24.6 1.0 C05 C:92V301 4.3 25.5 1.0 CD1 C:TYR96 4.4 21.0 1.0 HD1 C:TYR96 4.4 25.2 1.0 H081 C:92V301 4.5 25.8 1.0 CZ C:TYR96 4.5 24.2 1.0 HG2 C:GLN99 4.7 29.7 1.0 CG C:GLN99 4.8 24.8 1.0 OH C:TYR96 4.8 26.9 1.0 HA C:TYR96 4.9 25.7 1.0 C11 C:92V301 5.0 17.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp


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 Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:32.6 occ:1.00 F16 C:92V301 0.0 32.6 1.0 C14 C:92V301 1.3 31.9 1.0 F17 C:92V301 2.2 32.3 1.0 F15 C:92V301 2.2 32.6 1.0 C02 C:92V301 2.3 28.0 1.0 HB3 C:GLN95 2.8 39.7 1.0 H071 C:92V301 2.8 21.1 1.0 N03 C:92V301 2.9 23.6 1.0 C06 C:92V301 2.9 18.8 1.0 HG3 C:GLN99 2.9 29.7 1.0 C07 C:92V301 2.9 17.6 1.0 HG2 C:GLN99 3.0 29.7 1.0 CG C:GLN99 3.4 24.8 1.0 C01 C:92V301 3.5 27.2 1.0 O C:GLN95 3.7 18.7 1.0 HB2 C:GLN99 3.7 21.6 1.0 CB C:GLN95 3.8 33.1 1.0 C08 C:92V301 3.8 21.5 1.0 C11 C:92V301 3.8 17.5 1.0 HA C:TYR96 3.8 25.7 1.0 C C:GLN95 3.9 20.8 1.0 HB2 C:GLN95 4.1 39.7 1.0 CB C:GLN99 4.1 18.0 1.0 N04 C:92V301 4.2 24.6 1.0 H081 C:92V301 4.2 25.8 1.0 OE1 C:GLN95 4.2 49.2 1.0 O19 C:92V301 4.3 21.9 1.0 H111 C:92V301 4.3 21.0 1.0 N C:TYR96 4.3 25.3 1.0 C18 C:92V301 4.3 23.1 1.0 CA C:GLN95 4.3 27.0 1.0 HE21 C:GLN99 4.5 40.2 1.0 C05 C:92V301 4.5 25.5 1.0 C10 C:92V301 4.5 20.7 1.0 C09 C:92V301 4.5 23.1 1.0 HA C:GLN95 4.5 32.4 1.0 CD C:GLN99 4.6 28.9 1.0 CA C:TYR96 4.6 21.4 1.0 HD1 C:TYR96 4.6 25.2 1.0 HB3 C:GLN99 4.7 21.6 1.0 CD1 C:TYR96 4.7 21.0 1.0 CG C:GLN95 4.7 43.6 1.0 HG3 C:GLN95 4.7 52.3 1.0 H C:TYR96 4.8 30.3 1.0 NE2 C:GLN99 4.9 33.5 1.0 CD C:GLN95 4.9 50.5 1.0 H C:GLN99 4.9 22.0 1.0 CE1 C:TYR96 4.9 23.3 1.0 HE1 C:TYR96 5.0 28.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp


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 Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:32.3 occ:1.00 F17 C:92V301 0.0 32.3 1.0 C14 C:92V301 1.4 31.9 1.0 F16 C:92V301 2.2 32.6 1.0 F15 C:92V301 2.2 32.6 1.0 C02 C:92V301 2.3 28.0 1.0 O19 C:92V301 2.4 21.9 1.0 HG3 C:GLN99 2.5 29.7 1.0 C18 C:92V301 2.8 23.1 1.0 C01 C:92V301 2.8 27.2 1.0 HD1 C:TYR96 3.1 25.2 1.0 CG C:GLN99 3.3 24.8 1.0 HB2 C:GLN99 3.3 21.6 1.0 HA C:TYR96 3.3 25.7 1.0 HG2 C:GLN99 3.5 29.7 1.0 CD1 C:TYR96 3.5 21.0 1.0 N03 C:92V301 3.6 23.6 1.0 HE1 C:TYR96 3.6 28.0 1.0 CB C:GLN99 3.7 18.0 1.0 HB3 C:GLN99 3.8 21.6 1.0 CE1 C:TYR96 3.8 23.3 1.0 N20 C:92V301 4.0 23.6 1.0 H221 C:92V301 4.0 34.9 1.0 C05 C:92V301 4.1 25.5 1.0 H071 C:92V301 4.2 21.1 1.0 CA C:TYR96 4.3 21.4 1.0 C06 C:92V301 4.3 18.8 1.0 CG C:TYR96 4.4 21.2 1.0 O C:GLN95 4.5 18.7 1.0 N04 C:92V301 4.5 24.6 1.0 CD C:GLN99 4.5 28.9 1.0 C07 C:92V301 4.5 17.6 1.0 HB3 C:GLN95 4.6 39.7 1.0 H201 C:92V301 4.6 28.3 1.0 H212 C:92V301 4.7 32.9 1.0 N C:TYR96 4.7 25.3 1.0 C21 C:92V301 4.7 27.4 1.0 C C:GLN95 4.7 20.8 1.0 C22 C:92V301 4.8 29.1 1.0 CZ C:TYR96 4.8 24.2 1.0 CB C:TYR96 4.9 20.8 1.0 H051 C:92V301 4.9 30.6 1.0 OE1 C:GLN99 5.0 26.6 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