Fluorine in PDB 8jgd: Gdp-Bound Kras G12C in Complex with Yk-8S

All present enzymatic activity of Gdp-Bound Kras G12C in Complex with Yk-8S:
3.6.5.2;

The structure of Gdp-Bound Kras G12C in Complex with Yk-8S, PDB code: 8jgd was solved by Z.M.Zhang, R.L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 1.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.284, 82.284, 97.479, 90, 90, 120
R / Rfree (%)	16.8 / 20.1

The structure of Gdp-Bound Kras G12C in Complex with Yk-8S also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Gdp-Bound Kras G12C in Complex with Yk-8S (pdb code 8jgd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Gdp-Bound Kras G12C in Complex with Yk-8S, PDB code: 8jgd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Gdp-Bound Kras G12C in Complex with Yk-8S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Gdp-Bound Kras G12C in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:22.9 occ:1.00 FBS A:DWI203 0.0 22.9 1.0 CBM A:DWI203 1.4 24.5 1.0 CBN A:DWI203 2.3 19.9 1.0 CBL A:DWI203 2.3 22.6 1.0 NBO A:DWI203 2.9 20.3 1.0 CBK A:DWI203 3.0 17.7 1.0 CBP A:DWI203 3.1 21.5 1.0 O A:HOH441 3.3 21.6 1.0 CBR A:DWI203 3.4 19.4 1.0 O A:HOH480 3.7 50.6 1.0 CBQ A:DWI203 3.7 19.5 1.0 OD1 A:ASP92 4.4 20.3 1.0 CBJ A:DWI203 4.5 15.6 1.0 NZ A:LYS88 4.5 34.8 1.0 OBI A:DWI203 4.8 19.4 1.0

Fluorine binding site 2 out of 3 in the Gdp-Bound Kras G12C in Complex with Yk-8S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Gdp-Bound Kras G12C in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:16.1 occ:1.00 FAT A:DWI203 0.0 16.1 1.0 CAO A:DWI203 1.4 18.4 1.0 C6 A:DWI203 2.2 15.4 1.0 CAN A:DWI203 2.3 19.1 1.0 CAF A:DWI203 2.7 17.3 1.0 N1 A:DWI203 3.0 14.3 1.0 OH A:TYR64 3.1 21.2 1.0 CAA A:DWI203 3.1 11.4 1.0 NAS A:DWI203 3.3 17.6 1.0 CG A:GLN99 3.4 13.6 1.0 CAE A:DWI203 3.4 14.7 1.0 CE1 A:TYR64 3.4 23.4 1.0 NE2 A:HIS95 3.4 16.1 1.0 CAG A:DWI203 3.5 11.6 1.0 CZ A:TYR64 3.6 20.8 1.0 CAL A:DWI203 3.7 10.5 1.0 C5 A:DWI203 3.7 13.6 1.0 CB A:GLN99 3.8 13.1 1.0 CAR A:DWI203 3.9 13.5 1.0 CAB A:DWI203 4.0 12.8 1.0 CE1 A:HIS95 4.0 19.7 1.0 CAM A:DWI203 4.2 10.4 1.0 CAD A:DWI203 4.3 15.8 1.0 C2 A:DWI203 4.3 15.5 1.0 CD A:GLN99 4.3 19.1 1.0 CD2 A:HIS95 4.4 15.0 1.0 CAC A:DWI203 4.4 17.9 1.0 CAH A:DWI203 4.6 14.6 1.0 CD1 A:TYR64 4.6 24.4 1.0 OE1 A:GLN99 4.7 19.1 1.0 CD1 A:TYR96 4.7 11.0 1.0 CE1 A:TYR96 4.8 13.6 1.0 CE2 A:TYR64 4.9 24.8 1.0 CAJ A:DWI203 4.9 12.2 1.0 C4 A:DWI203 4.9 16.4 1.0 OE2 A:GLU62 5.0 22.9 1.0

Fluorine binding site 3 out of 3 in the Gdp-Bound Kras G12C in Complex with Yk-8S


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Gdp-Bound Kras G12C in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:17.5 occ:1.00 FAK A:DWI203 0.0 17.5 1.0 CAH A:DWI203 1.3 14.6 1.0 CAG A:DWI203 2.3 11.6 1.0 CAI A:DWI203 2.4 15.9 1.0 CAL A:DWI203 2.7 10.5 1.0 CG1 A:ILE100 3.3 10.9 1.0 CG1 A:VAL9 3.5 11.4 1.0 CAM A:DWI203 3.6 10.4 1.0 CAA A:DWI203 3.6 11.4 1.0 CAJ A:DWI203 3.6 12.2 1.0 CE2 A:PHE78 3.8 11.7 1.0 CD1 A:ILE100 3.8 12.6 1.0 CD2 A:PHE78 3.9 10.7 1.0 CAB A:DWI203 4.1 12.8 1.0 CB A:VAL9 4.2 10.5 1.0 O A:TYR96 4.4 12.8 1.0 CG2 A:VAL9 4.4 10.4 1.0 SD A:MET72 4.5 23.0 1.0 CB A:ILE100 4.6 12.0 1.0 N A:ILE100 4.6 11.6 1.0 CA A:ILE100 4.7 12.8 1.0 CAF A:DWI203 4.8 17.3 1.0 CD1 A:TYR96 4.8 11.0 1.0 CB A:GLN99 4.9 13.1 1.0 CZ A:PHE78 4.9 13.7 1.0 CG A:PHE78 4.9 9.9 1.0

Z.Yu, X.He, R.Wang, X.Xu, Z.Zhang, K.Ding, Z.M.Zhang, Y.Tan, Z.Li. Simultaneous Covalent Modification of K-Ras(G12D) and K-Ras(G12C) with Tunable Oxirane Electrophiles. J.Am.Chem.Soc. V. 145 20403 2023.
ISSN: ESSN 1520-5126
PubMed: 37534597
DOI: 10.1021/JACS.3C05899