Fluorine in PDB 7tlg: Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)

All present enzymatic activity of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S):
3.6.5.2;

The structure of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S), PDB code: 7tlg was solved by Z.Ziyang, K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.35 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.55, 66.53, 60.8, 90, 101.89, 90
R / Rfree (%)	17.9 / 23.3

The structure of Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S) (pdb code 7tlg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S), PDB code: 7tlg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)


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 Beta-Lactone 5 Covalently Bound to K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:13.7 occ:1.00 F13 A:I7H202 0.0 13.7 1.0 C12 A:I7H202 1.4 15.6 1.0 C14 A:I7H202 2.3 11.9 1.0 C11 A:I7H202 2.5 15.3 1.0 N40 A:I7H202 2.7 11.2 1.0 C10 A:I7H202 2.9 14.4 1.0 CE1 A:TYR64 3.2 16.8 1.0 C41 A:I7H202 3.3 13.5 1.0 NE2 A:HIS95 3.3 13.3 1.0 OH A:TYR64 3.3 18.7 1.0 CL01 A:I7H202 3.5 25.7 1.0 C02 A:I7H202 3.5 16.6 1.0 CG A:GLN99 3.6 14.2 1.0 C09 A:I7H202 3.6 16.0 1.0 C15 A:I7H202 3.6 11.5 1.0 N17 A:I7H202 3.7 15.7 1.0 CZ A:TYR64 3.7 19.1 1.0 H091 A:I7H202 3.8 19.2 1.0 CB A:GLN99 4.0 13.9 1.0 C29 A:I7H202 4.0 15.2 1.0 CE1 A:HIS95 4.0 15.6 1.0 C16 A:I7H202 4.1 15.7 1.0 CD2 A:HIS95 4.2 14.9 1.0 C06 A:I7H202 4.3 13.1 1.0 CD1 A:TYR64 4.3 18.2 1.0 CE1 A:TYR96 4.4 14.7 1.0 CD1 A:TYR96 4.4 12.3 1.0 C08 A:I7H202 4.5 12.7 1.0 CD A:GLN99 4.6 17.5 1.0 C03 A:I7H202 4.6 15.2 1.0 C18 A:I7H202 4.7 14.6 1.0 O30 A:I7H202 4.8 17.2 1.0 C07 A:I7H202 4.8 13.9 1.0 N28 A:I7H202 4.8 13.2 1.0 OE1 A:GLN99 4.9 15.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Small Molecule Beta-Lactone 5 Covalently Bound to K-Ras(G12S)


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 Beta-Lactone 5 Covalently Bound to K-Ras(G12S) within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:25.3 occ:1.00 F13 B:I7H203 0.0 25.3 1.0 C12 B:I7H203 1.4 21.6 1.0 C11 B:I7H203 2.4 17.8 1.0 C14 B:I7H203 2.4 22.3 1.0 C10 B:I7H203 2.7 21.2 1.0 N40 B:I7H203 2.8 19.5 1.0 OH B:TYR64 3.1 23.5 1.0 C41 B:I7H203 3.2 19.6 1.0 CE1 B:TYR64 3.4 17.8 1.0 C09 B:I7H203 3.4 23.7 1.0 NE2 B:HIS95 3.4 20.1 1.0 CG B:GLN99 3.4 21.7 1.0 C02 B:I7H203 3.5 22.8 1.0 CL01 B:I7H203 3.5 27.9 1.0 H091 B:I7H203 3.6 28.4 1.0 N17 B:I7H203 3.6 23.9 1.0 CZ B:TYR64 3.6 18.6 1.0 C15 B:I7H203 3.7 22.1 1.0 CE1 B:HIS95 3.8 28.4 1.0 CB B:GLN99 4.0 21.1 1.0 C16 B:I7H203 4.1 21.6 1.0 C29 B:I7H203 4.2 22.0 1.0 C06 B:I7H203 4.2 18.2 1.0 CD B:GLN99 4.2 26.6 1.0 C08 B:I7H203 4.3 25.8 1.0 CD2 B:HIS95 4.4 22.4 1.0 CE1 B:TYR96 4.5 20.9 1.0 CD1 B:TYR64 4.5 21.9 1.0 OE1 B:GLN99 4.5 27.7 1.0 CD1 B:TYR96 4.6 19.5 1.0 C03 B:I7H203 4.6 18.8 1.0 C07 B:I7H203 4.7 23.4 1.0 C18 B:I7H203 4.8 24.7 1.0 ND1 B:HIS95 4.9 27.6 1.0 CE2 B:TYR64 4.9 20.4 1.0 N28 B:I7H203 5.0 22.7 1.0 O30 B:I7H203 5.0 20.7 1.0

Z.Zhang, K.Z.Guiley, K.M.Shokat. Chemical Acylation of An Acquired Serine Suppresses Oncogenic Signaling of K-Ras(G12S). Nat.Chem.Biol. V. 18 1177 2022.
ISSN: ESSN 1552-4469
PubMed: 35864332
DOI: 10.1038/S41589-022-01065-9