Fluorine in PDB 7t0a: Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F

Enzymatic activity of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F

All present enzymatic activity of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F:
2.5.1.58;

Protein crystallography data

The structure of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F, PDB code: 7t0a was solved by Y.Wang, Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.93 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.21, 141.21, 129.822, 90, 90, 90
R / Rfree (%) 18.7 / 21.3

Other elements in 7t0a:

The structure of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Bromine (Br) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F (pdb code 7t0a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F, PDB code: 7t0a:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7t0a

Go back to Fluorine Binding Sites List in 7t0a
Fluorine binding site 1 out of 3 in the Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:44.6
occ:1.00
 F34 B:XMY605 0.0 44.6 1.0
C33 B:XMY605 1.4 40.5 1.0
F36 B:XMY605 2.2 52.3 1.0
F35 B:XMY605 2.3 48.3 1.0
O32 B:XMY605 2.3 38.0 1.0
C28 B:XMY605 2.9 45.3 1.0
C29 B:XMY605 2.9 46.0 1.0
CH2 B:TRP90 3.4 27.9 1.0
CH2 B:TRP329 3.5 28.6 1.0
CZ2 B:TRP90 4.1 29.6 1.0
CE2 B:TYR200 4.1 29.4 1.0
C27 B:XMY605 4.1 33.0 1.0
CZ3 B:TRP90 4.2 28.2 1.0
C30 B:XMY605 4.2 43.5 1.0
CZ3 B:TRP329 4.2 27.4 1.0
CD2 B:TYR200 4.3 29.1 1.0
SG B:CYS201 4.3 25.4 1.0
CZ2 B:TRP329 4.5 30.7 1.0
C1 B:EDO611 4.6 53.3 1.0
SG B:CYS272 4.9 30.2 1.0
CE2 B:TYR144 4.9 29.5 1.0
O B:HOH849 5.0 33.4 1.0

Fluorine binding site 2 out of 3 in 7t0a

Go back to Fluorine Binding Sites List in 7t0a
Fluorine binding site 2 out of 3 in the Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:48.3
occ:1.00
 F35 B:XMY605 0.0 48.3 1.0
C33 B:XMY605 1.4 40.5 1.0
F36 B:XMY605 2.2 52.3 1.0
F34 B:XMY605 2.3 44.6 1.0
O32 B:XMY605 2.3 38.0 1.0
C29 B:XMY605 2.9 46.0 1.0
C28 B:XMY605 2.9 45.3 1.0
SG B:CYS201 3.1 25.4 1.0
CG B:LEU141 3.5 32.9 1.0
CD2 B:LEU141 3.8 29.1 1.0
CZ2 B:TRP90 3.8 29.6 1.0
CB B:ARG197 3.9 27.3 1.0
CH2 B:TRP90 3.9 27.9 1.0
O B:ARG197 4.1 22.8 1.0
CD1 B:LEU141 4.2 26.7 1.0
C30 B:XMY605 4.2 43.5 1.0
C27 B:XMY605 4.2 33.0 1.0
CG B:ARG197 4.4 37.5 1.0
CA B:ARG197 4.4 26.1 1.0
CB B:LEU141 4.5 26.2 1.0
C B:ARG197 4.6 29.4 1.0
CD2 B:TYR200 4.6 29.1 1.0
CD B:ARG197 4.7 30.0 1.0
CB B:CYS201 4.8 24.3 1.0
CE2 B:TRP90 5.0 35.5 1.0

Fluorine binding site 3 out of 3 in 7t0a

Go back to Fluorine Binding Sites List in 7t0a
Fluorine binding site 3 out of 3 in the Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryptococcus Neoformans Protein Farnesyltransferase Co-Crystallized with Fpp and Inhibitor 2F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:52.3
occ:1.00
 F36 B:XMY605 0.0 52.3 1.0
C33 B:XMY605 1.4 40.5 1.0
F34 B:XMY605 2.2 44.6 1.0
F35 B:XMY605 2.2 48.3 1.0
O32 B:XMY605 2.3 38.0 1.0
SG B:CYS272 2.9 30.2 1.0
CD2 B:TYR200 3.4 29.1 1.0
C28 B:XMY605 3.6 45.3 1.0
CB B:ARG197 3.9 27.3 1.0
CE2 B:TYR200 3.9 29.4 1.0
CA B:ARG197 3.9 26.1 1.0
CG B:ARG197 4.0 37.5 1.0
SG B:CYS201 4.1 25.4 1.0
O B:ARG197 4.1 22.8 1.0
C29 B:XMY605 4.2 46.0 1.0
CG B:TYR200 4.3 22.2 1.0
CH2 B:TRP329 4.3 28.6 1.0
O B:HOH812 4.5 28.9 1.0
CZ3 B:TRP329 4.5 27.4 1.0
C B:ARG197 4.5 29.4 1.0
CB B:CYS272 4.5 24.2 1.0
CB B:TYR200 4.5 25.2 1.0
C27 B:XMY605 4.7 33.0 1.0
BR23 B:XMY605 4.8 53.6 1.0
CD B:ARG197 4.9 30.0 1.0

Reference:

Y.Wang, F.Xu, C.B.Nichols, Y.Shi, H.W.Hellinga, J.A.Alspaugh, M.D.Distefano, L.S.Beese. Structure-Guided Discovery of Potent Antifungals That Prevent Ras Signaling By Inhibiting Protein Farnesyltransferase. J.Med.Chem. V. 65 13753 2022.
ISSN: ISSN 0022-2623
PubMed: 36218371
DOI: 10.1021/ACS.JMEDCHEM.2C00902
Page generated: Fri Aug 2 13:11:09 2024

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