Fluorine in PDB 8jhl: Gdp-Bound Kras G12D in Complex with Yk-8S

The structure of Gdp-Bound Kras G12D in Complex with Yk-8S, PDB code: 8jhl 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)	41.18 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.353, 82.353, 97.912, 90, 90, 120
R / Rfree (%)	16.5 / 20.8

The structure of Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S (pdb code 8jhl). 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 G12D in Complex with Yk-8S, PDB code: 8jhl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:32.9 occ:1.00 FBT A:DNU203 0.0 32.9 1.0 CBN A:DNU203 1.3 37.6 1.0 CBO A:DNU203 2.3 34.7 1.0 CBM A:DNU203 2.3 34.4 1.0 O A:HOH392 2.9 28.1 1.0 NBP A:DNU203 2.9 33.4 1.0 CBL A:DNU203 3.1 35.5 1.0 CBQ A:DNU203 3.1 25.9 1.0 CBS A:DNU203 3.5 32.4 1.0 CBR A:DNU203 3.9 21.7 1.0 OD1 A:ASP92 4.2 25.2 1.0 NZ A:LYS88 4.3 49.2 1.0 CBK A:DNU203 4.5 26.1 1.0 OBI A:DNU203 4.7 28.4 1.0 CG A:HIS95 4.8 24.1 1.0 CG A:ASP92 5.0 27.6 1.0 CD2 A:HIS95 5.0 23.6 1.0

Fluorine binding site 2 out of 3 in the Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:26.1 occ:1.00 FAT A:DNU203 0.0 26.1 1.0 CAO A:DNU203 1.3 27.5 1.0 C6 A:DNU203 2.3 26.4 1.0 CAN A:DNU203 2.4 28.9 1.0 N1 A:DNU203 2.7 28.2 1.0 CAF A:DNU203 2.7 27.4 1.0 CAA A:DNU203 3.0 23.7 1.0 CAL A:DNU203 3.1 22.3 1.0 CAG A:DNU203 3.2 20.6 1.0 OH A:TYR64 3.2 28.3 1.0 CAM A:DNU203 3.5 25.2 1.0 NE2 A:HIS95 3.5 24.6 1.0 NAS A:DNU203 3.6 25.9 1.0 CAE A:DNU203 3.6 31.2 1.0 CE1 A:TYR64 3.6 32.6 1.0 C5 A:DNU203 3.6 29.3 1.0 CG A:GLN99 3.7 18.6 1.0 CZ A:TYR64 3.8 32.5 1.0 CAR A:DNU203 4.0 26.2 1.0 C2 A:DNU203 4.1 27.5 1.0 CB A:GLN99 4.1 17.3 1.0 CAB A:DNU203 4.1 26.1 1.0 CE1 A:HIS95 4.1 30.9 1.0 CE1 A:TYR96 4.3 24.8 1.0 CD1 A:TYR96 4.3 23.3 1.0 CAH A:DNU203 4.3 17.8 1.0 CD2 A:HIS95 4.5 23.6 1.0 CAD A:DNU203 4.5 29.1 1.0 CD A:GLN99 4.6 26.6 1.0 CAC A:DNU203 4.7 28.0 1.0 C4 A:DNU203 4.8 33.3 1.0 CD1 A:TYR64 4.8 29.9 1.0 N3 A:DNU203 4.9 31.2 1.0 OE1 A:GLN99 4.9 25.7 1.0 OBI A:DNU203 4.9 28.4 1.0 FAK A:DNU203 5.0 20.0 1.0

Fluorine binding site 3 out of 3 in the Gdp-Bound Kras G12D 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 G12D in Complex with Yk-8S within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:20.0 occ:1.00 FAK A:DNU203 0.0 20.0 1.0 CAH A:DNU203 1.4 17.8 1.0 CAG A:DNU203 2.4 20.6 1.0 CAI A:DNU203 2.4 21.6 1.0 CAL A:DNU203 2.7 22.3 1.0 CG1 A:ILE100 3.3 13.5 1.0 CAM A:DNU203 3.4 25.2 1.0 CG1 A:VAL9 3.4 15.8 1.0 CAJ A:DNU203 3.7 24.9 1.0 CAA A:DNU203 3.7 23.7 1.0 CD1 A:ILE100 3.9 13.6 1.0 CB A:VAL9 4.1 20.3 1.0 CAB A:DNU203 4.1 26.1 1.0 CG2 A:VAL9 4.2 13.4 1.0 CE2 A:PHE78 4.2 16.8 1.0 CD2 A:PHE78 4.2 18.5 1.0 O A:TYR96 4.3 18.9 1.0 SD A:MET72 4.6 31.6 1.0 CD1 A:TYR96 4.6 23.3 1.0 N A:ILE100 4.6 18.1 1.0 CB A:ILE100 4.6 14.7 1.0 CB A:GLN99 4.7 17.3 1.0 CA A:ILE100 4.8 20.0 1.0 CB A:TYR96 4.9 14.4 1.0 CAF A:DNU203 4.9 27.4 1.0 FAT A:DNU203 5.0 26.1 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