Fluorine in PDB 6c2o: Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir

The structure of Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir, PDB code: 6c2o was solved by A.N.Matthew, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.444, 58.950, 59.994, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 14.4

The structure of Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir (pdb code 6c2o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir, PDB code: 6c2o:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir


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 Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:18.8 occ:0.93 F1 A:TSV1201 0.0 18.8 0.9 H16 A:TSV1201 0.4 13.1 0.1 C16 A:TSV1201 1.3 10.9 0.1 C21 A:TSV1201 1.3 13.7 0.9 C24 A:TSV1201 2.4 10.1 0.1 C26 A:TSV1201 2.4 11.8 0.9 C14 A:TSV1201 2.4 11.4 0.1 C17 A:TSV1201 2.5 14.9 0.9 H17 A:TSV1201 2.7 17.9 0.9 H14 A:TSV1201 2.7 13.6 0.1 H6B A:TSV1201 2.8 16.4 0.1 H6B A:TSV1201 2.8 17.3 0.9 C12 A:TSV1201 3.0 10.0 0.1 H6A A:TSV1201 3.0 16.4 0.1 H6A A:TSV1201 3.0 17.3 0.9 H12 A:TSV1201 3.1 12.0 0.1 C31 A:TSV1201 3.1 11.3 0.9 H31 A:TSV1201 3.2 13.5 0.9 C6 A:TSV1201 3.2 13.6 0.1 HE A:ARG1155 3.2 11.4 1.0 C6 A:TSV1201 3.2 14.4 0.9 H6 A:TSV1201 3.2 16.4 0.1 H6 A:TSV1201 3.2 17.3 0.9 O A:HOH1433 3.3 36.2 1.0 OD1 A:ASP1168 3.3 25.3 1.0 O A:HOH1537 3.4 38.4 1.0 HG2 A:ARG1155 3.5 8.5 1.0 NE A:ARG1155 3.5 9.5 1.0 HD2 A:ARG1155 3.6 9.0 1.0 C26 A:TSV1201 3.7 9.4 0.1 CG A:ASP1168 3.7 16.9 1.0 HB3 A:ALA1156 3.8 8.6 1.0 C24 A:TSV1201 3.8 12.0 0.9 C17 A:TSV1201 3.8 10.6 0.1 C14 A:TSV1201 3.8 14.3 0.9 HB2 A:ALA1156 3.9 8.6 1.0 CD A:ARG1155 3.9 7.5 1.0 OD2 A:ASP1168 4.0 22.3 1.0 O A:HOH1529 4.1 38.7 1.0 CZ A:ARG1155 4.1 10.1 1.0 HH11 A:ARG1155 4.1 16.4 1.0 CG A:ARG1155 4.2 7.1 1.0 C21 A:TSV1201 4.2 9.1 0.1 CB A:ALA1156 4.2 7.1 1.0 C16 A:TSV1201 4.3 14.1 0.9 NH1 A:ARG1155 4.3 13.6 1.0 N4 A:TSV1201 4.4 10.1 0.9 HB3 A:ASP1168 4.4 10.9 1.0 N4 A:TSV1201 4.4 10.0 0.1 H17 A:TSV1201 4.5 12.7 0.1 H14 A:TSV1201 4.6 17.2 0.9 CB A:ASP1168 4.6 9.1 1.0 HB1 A:ALA1156 4.6 8.6 1.0 C9 A:TSV1201 4.7 13.4 0.1 C9 A:TSV1201 4.7 13.5 0.9 C12 A:TSV1201 4.8 10.3 0.9 HB3 A:ARG1155 4.8 7.7 1.0 HG3 A:ARG1155 4.8 8.5 1.0 C31 A:TSV1201 4.8 9.5 0.1 HD3 A:ARG1155 4.9 9.0 1.0 HB2 A:ASP1168 4.9 10.9 1.0 NH2 A:ARG1155 4.9 10.0 1.0 H7A A:TSV1201 4.9 17.0 0.1 HH12 A:ARG1155 5.0 16.4 1.0 H7A A:TSV1201 5.0 20.1 0.9

Fluorine binding site 2 out of 2 in the Crystal Structure of Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir


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 Hcv NS3/4A Protease Variant Y56H in Complex with Danoprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:6.2 occ:0.07 F1 A:TSV1201 0.0 6.2 0.1 H16 A:TSV1201 0.3 16.9 0.9 C16 A:TSV1201 1.2 14.1 0.9 C21 A:TSV1201 1.3 9.1 0.1 C24 A:TSV1201 2.3 12.0 0.9 C26 A:TSV1201 2.4 9.4 0.1 C14 A:TSV1201 2.4 14.3 0.9 C17 A:TSV1201 2.4 10.6 0.1 O A:HOH1340 2.6 25.5 1.0 HB2 A:ASP1081 2.6 8.2 1.0 H17 A:TSV1201 2.7 12.7 0.1 H14 A:TSV1201 2.7 17.2 0.9 C12 A:TSV1201 2.9 10.3 0.9 H12 A:TSV1201 2.9 12.4 0.9 C31 A:TSV1201 3.0 9.5 0.1 H31 A:TSV1201 3.0 11.4 0.1 O A:HOH1514 3.2 36.6 1.0 O A:VAL1078 3.2 9.3 1.0 O A:HOH1461 3.2 41.2 1.0 O A:ASP1079 3.4 11.7 1.0 H A:ASP1081 3.4 7.8 1.0 O A:HOH1366 3.5 25.1 1.0 N A:ASP1081 3.6 6.5 1.0 CB A:ASP1081 3.6 6.9 1.0 C26 A:TSV1201 3.6 11.8 0.9 C24 A:TSV1201 3.7 10.1 0.1 C17 A:TSV1201 3.8 14.9 0.9 C14 A:TSV1201 3.8 11.4 0.1 C A:ASP1079 3.8 8.7 1.0 CA A:ASP1081 3.9 5.7 1.0 HA A:ASP1081 4.0 6.9 1.0 C A:LYS1080 4.0 7.2 1.0 HB3 A:ASP1081 4.1 8.2 1.0 HA A:ASP1079 4.1 10.5 1.0 C21 A:TSV1201 4.2 13.7 0.9 HD2 A:ARG1155 4.2 9.0 1.0 C16 A:TSV1201 4.3 10.9 0.1 N4 A:TSV1201 4.3 10.0 0.1 N A:LYS1080 4.3 7.5 1.0 C A:VAL1078 4.3 8.0 1.0 N4 A:TSV1201 4.3 10.1 0.9 HA A:LYS1080 4.4 9.7 1.0 CG A:ASP1081 4.4 7.3 1.0 CA A:ASP1079 4.5 8.7 1.0 CA A:LYS1080 4.5 8.0 1.0 O A:HOH1527 4.5 41.0 1.0 H17 A:TSV1201 4.5 17.9 0.9 H14 A:TSV1201 4.5 13.6 0.1 O A:LYS1080 4.6 8.6 1.0 C12 A:TSV1201 4.7 10.0 0.1 C31 A:TSV1201 4.7 11.3 0.9 HH21 A:ARG1155 4.8 12.0 1.0 H A:LYS1080 4.9 9.0 1.0 N A:ASP1079 4.9 7.8 1.0 OD2 A:ASP1081 5.0 8.4 1.0 OD1 A:ASP1081 5.0 7.9 1.0 HG22 A:VAL1078 5.0 14.9 1.0

A.N.Matthew, C.A.Schiffer. Clinical Signature Variant of Hcv NS3/4A Protease Uses A Novel Mechanism to Confer Resistance To Be Published.