Fluorine in PDB 8v0c: Structure of TDP1 Catalytic Domain Complexed with Compound IB06

The structure of Structure of TDP1 Catalytic Domain Complexed with Compound IB06, PDB code: 8v0c was solved by G.T.Lountos, X.Z.Zhao, I.Barakat, W.Wang, K.Agama, M.R.Al Mahmud, Y.Pommier, T.R.Burke Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.17 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.02, 105.183, 193.625, 90, 90, 90
R / Rfree (%)	17.2 / 20.3

The binding sites of Fluorine atom in the Structure of TDP1 Catalytic Domain Complexed with Compound IB06 (pdb code 8v0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of TDP1 Catalytic Domain Complexed with Compound IB06, PDB code: 8v0c:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of TDP1 Catalytic Domain Complexed with Compound IB06


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of TDP1 Catalytic Domain Complexed with Compound IB06 within 5.0Å range: probe atom residue distance (Å) B Occ A:F706 b:53.7 occ:0.56 F21 A:YE3706 0.0 53.7 0.6 S18 A:YE3706 1.6 55.8 0.6 O19 A:YE3706 1.7 53.0 0.4 O19 A:YE3706 2.4 57.6 0.6 O20 A:YE3706 2.4 60.7 0.6 C17 A:YE3706 2.7 43.5 0.6 SG A:CYS205 2.8 22.1 0.3 S18 A:YE3706 3.0 41.5 0.4 O A:HOH822 3.4 36.2 1.0 CE2 A:TYR204 3.5 20.9 1.0 CZ A:TYR204 3.5 29.8 1.0 O A:TYR204 3.7 15.0 1.0 OH A:TYR204 3.8 40.5 1.0 C17 A:YE3706 3.8 40.7 0.4 CE1 A:TYR204 3.9 22.8 1.0 CB A:CYS205 3.9 14.9 0.7 CD2 A:TYR204 3.9 17.6 1.0 C16 A:YE3706 3.9 40.8 0.6 O20 A:YE3706 4.0 42.3 0.4 CB A:CYS205 4.1 16.3 0.3 CA A:CYS205 4.1 13.9 0.7 CA A:CYS205 4.1 14.3 0.3 C A:TYR204 4.3 12.9 1.0 SG A:CYS205 4.3 19.5 0.7 OD1 A:ASP230 4.3 22.3 1.0 CD1 A:TYR204 4.3 18.1 1.0 O A:HOH1016 4.4 24.5 1.0 CG A:TYR204 4.4 14.5 1.0 O A:HOH818 4.5 32.8 1.0 N A:CYS205 4.5 12.9 0.3 N A:CYS205 4.5 12.9 0.7 O A:HOH983 4.9 16.9 1.0 OD2 A:ASP230 5.0 23.9 1.0 N15 A:YE3706 5.0 34.6 0.6

Fluorine binding site 2 out of 2 in the Structure of TDP1 Catalytic Domain Complexed with Compound IB06


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of TDP1 Catalytic Domain Complexed with Compound IB06 within 5.0Å range: probe atom residue distance (Å) B Occ B:F704 b:57.8 occ:0.50 F21 B:YE3704 0.0 57.8 0.5 S18 B:YE3704 1.6 58.3 0.5 O20 B:YE3704 2.1 56.6 0.5 O19 B:YE3704 2.4 57.1 0.5 O20 B:YE3704 2.4 62.9 0.5 SG B:CYS205 2.5 39.9 0.4 C17 B:YE3704 2.7 47.7 0.5 S18 B:YE3704 3.4 50.4 0.5 CB B:CYS205 3.6 24.7 0.6 SG B:CYS205 3.6 28.3 0.6 O B:HOH807 3.7 49.2 1.0 CB B:CYS205 3.7 26.6 0.4 O B:HOH940 3.8 29.0 1.0 C17 B:YE3704 3.9 44.5 0.5 CA B:CYS205 3.9 26.7 0.6 CA B:CYS205 3.9 26.5 0.4 CE2 B:TYR204 4.0 33.6 1.0 O B:TYR204 4.1 25.5 1.0 C16 B:YE3704 4.1 42.5 0.5 CZ B:TYR204 4.2 47.4 1.0 OH B:TYR204 4.4 66.2 1.0 CD2 B:TYR204 4.5 28.3 1.0 O19 B:YE3704 4.5 47.9 0.5 N B:CYS205 4.5 24.6 0.4 N B:CYS205 4.5 24.7 0.6 C B:TYR204 4.6 24.2 1.0 CE1 B:TYR204 4.7 38.5 1.0 OD1 B:ASP230 4.8 40.0 1.0 N15 B:YE3704 5.0 39.3 0.5 CG B:TYR204 5.0 27.5 1.0

G.T.Lountos, X.Z.Zhao, I.Barakat, W.Wang, K.Agama, M.R.Al Mahmud, Y.Pommier, T.R.Burke Jr.. Structures of TDP1 Complexed with Inhibitors To Be Published.