Fluorine in PDB 6vkk: Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib

All present enzymatic activity of Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib:
2.4.2.30;

The structure of Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib, PDB code: 6vkk was solved by J.D.Steffen, J.M.Pascal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.267, 107.902, 142.845, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 26.1

The binding sites of Fluorine atom in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib (pdb code 6vkk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib, PDB code: 6vkk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib


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 Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:33.6 occ:1.00 F1 A:RPB1101 0.0 33.6 1.0 C2 A:RPB1101 1.4 32.9 1.0 C1 A:RPB1101 2.3 33.3 1.0 C3 A:RPB1101 2.3 32.9 1.0 O A:PHE897 3.0 29.4 1.0 CB A:ALA898 3.3 32.3 1.0 C A:PHE897 3.3 30.0 1.0 N A:ALA898 3.4 30.3 1.0 CA A:ALA898 3.5 31.4 1.0 CE A:LYS903 3.5 34.0 1.0 CB A:GLU988 3.5 33.5 1.0 C6 A:RPB1101 3.6 33.0 1.0 C4 A:RPB1101 3.6 32.6 1.0 CD A:LYS903 3.8 34.4 1.0 CG A:LYS903 3.9 33.7 1.0 C5 A:RPB1101 4.1 32.3 1.0 CA A:GLU988 4.2 33.4 1.0 NZ A:LYS903 4.2 35.7 1.0 CA A:PHE897 4.3 29.7 1.0 O A:ASN987 4.3 36.1 1.0 N A:PHE897 4.4 29.3 1.0 OE2 A:GLU988 4.5 34.2 1.0 CD A:GLU988 4.7 34.7 1.0 CG A:GLU988 4.8 34.2 1.0 OG A:SER904 4.8 34.6 1.0 C7 A:RPB1101 4.8 31.9 1.0 CB A:LYS903 4.8 34.2 1.0 N2 A:RPB1101 4.8 33.1 1.0 O1 A:RPB1101 4.9 31.6 1.0 C A:TYR896 4.9 30.5 1.0 C A:ALA898 5.0 32.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib


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 Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ D:F1101 b:40.2 occ:1.00 F1 D:RPB1101 0.0 40.2 1.0 C2 D:RPB1101 1.4 39.6 1.0 C1 D:RPB1101 2.3 38.5 1.0 C3 D:RPB1101 2.3 39.1 1.0 O D:PHE897 3.0 39.1 1.0 CB D:ALA898 3.2 42.7 1.0 C D:PHE897 3.2 38.9 1.0 N D:ALA898 3.3 39.8 1.0 CA D:ALA898 3.4 41.5 1.0 C6 D:RPB1101 3.6 38.8 1.0 CE D:LYS903 3.6 46.9 1.0 C4 D:RPB1101 3.6 38.9 1.0 CG D:GLU988 3.7 46.8 1.0 CD D:LYS903 3.8 47.9 1.0 CG D:LYS903 3.9 47.9 1.0 C5 D:RPB1101 4.1 38.9 1.0 CA D:PHE897 4.2 37.6 1.0 NZ D:LYS903 4.2 47.1 1.0 CA D:GLU988 4.3 45.5 1.0 O D:ASN987 4.3 45.5 1.0 N D:PHE897 4.3 37.4 1.0 CB D:GLU988 4.5 46.6 1.0 CD D:GLU988 4.5 47.4 1.0 OE2 D:GLU988 4.5 47.2 1.0 OG D:SER904 4.7 44.7 1.0 C7 D:RPB1101 4.8 39.3 1.0 CB D:LYS903 4.8 49.5 1.0 N2 D:RPB1101 4.9 39.0 1.0 O1 D:RPB1101 4.9 40.2 1.0 C D:TYR896 4.9 37.5 1.0 C D:ALA898 4.9 42.3 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ C:F1101 b:40.6 occ:1.00 F1 C:RPB1101 0.0 40.6 1.0 C2 C:RPB1101 1.4 38.9 1.0 C3 C:RPB1101 2.3 39.8 1.0 C1 C:RPB1101 2.3 39.5 1.0 O C:PHE897 3.0 37.0 1.0 C C:PHE897 3.3 37.5 1.0 CB C:ALA898 3.3 40.9 1.0 N C:ALA898 3.4 37.7 1.0 CA C:ALA898 3.5 39.2 1.0 CE C:LYS903 3.5 46.6 1.0 C6 C:RPB1101 3.6 39.7 1.0 CG C:GLU988 3.6 46.2 1.0 C4 C:RPB1101 3.6 39.5 1.0 CD C:LYS903 3.7 46.3 1.0 CG C:LYS903 3.9 46.2 1.0 NZ C:LYS903 4.1 46.5 1.0 C5 C:RPB1101 4.1 40.1 1.0 CA C:GLU988 4.2 42.7 1.0 O C:ASN987 4.2 44.3 1.0 CA C:PHE897 4.2 37.0 1.0 CB C:GLU988 4.3 45.4 1.0 N C:PHE897 4.3 37.2 1.0 CD C:GLU988 4.4 47.5 1.0 OE2 C:GLU988 4.4 48.9 1.0 C7 C:RPB1101 4.8 39.9 1.0 OG C:SER904 4.9 42.3 1.0 N2 C:RPB1101 4.9 40.9 1.0 O1 C:RPB1101 4.9 39.2 1.0 CB C:LYS903 4.9 46.6 1.0 C C:TYR896 4.9 37.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Parp-1 Cat Domain Bound to Inhibitor Rucaparib within 5.0Å range: probe atom residue distance (Å) B Occ B:F1202 b:37.6 occ:1.00 F1 B:RPB1202 0.0 37.6 1.0 C2 B:RPB1202 1.4 35.6 1.0 C1 B:RPB1202 2.3 35.2 1.0 C3 B:RPB1202 2.3 34.8 1.0 O B:PHE897 3.0 32.7 1.0 CB B:ALA898 3.3 34.5 1.0 C B:PHE897 3.3 32.6 1.0 N B:ALA898 3.4 33.0 1.0 CA B:ALA898 3.4 34.3 1.0 CE B:LYS903 3.5 37.8 1.0 C6 B:RPB1202 3.6 36.2 1.0 C4 B:RPB1202 3.6 34.8 1.0 CD B:LYS903 3.7 38.0 1.0 CG B:GLU988 3.7 41.2 1.0 CG B:LYS903 3.9 37.9 1.0 C5 B:RPB1202 4.1 35.2 1.0 NZ B:LYS903 4.1 37.7 1.0 O B:ASN987 4.2 38.5 1.0 CA B:PHE897 4.3 31.5 1.0 CA B:GLU988 4.3 38.3 1.0 N B:PHE897 4.4 32.2 1.0 CB B:GLU988 4.4 40.2 1.0 CD B:GLU988 4.5 41.2 1.0 OE2 B:GLU988 4.5 41.8 1.0 OG B:SER904 4.7 33.0 1.0 CB B:LYS903 4.8 37.9 1.0 C7 B:RPB1202 4.8 34.8 1.0 N2 B:RPB1202 4.9 36.6 1.0 O1 B:RPB1202 4.9 34.7 1.0 C B:TYR896 5.0 32.6 1.0 C B:ALA898 5.0 34.5 1.0

L.Zandarashvili, M.F.Langelier, U.K.Velagapudi, M.A.Hancock, J.D.Steffen, R.Billur, Z.M.Hannan, A.J.Wicks, D.B.Krastev, S.J.Pettitt, C.J.Lord, T.T.Talele, J.M.Pascal, B.E.Black. Structural Basis For Allosteric Parp-1 Retention on Dna Breaks. Science V. 368 2020.
ISSN: ESSN 1095-9203
PubMed: 32241924
DOI: 10.1126/SCIENCE.AAX6367