Fluorine in PDB 3qzq: Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir

The structure of Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir, PDB code: 3qzq was solved by J.Wang, T.Fan, X.Yao, Z.Wu, L.Guo, X.Lei, J.Wang, M.Wang, Q.Jin, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.06 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	142.443, 142.443, 69.564, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.4

The binding sites of Fluorine atom in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir (pdb code 3qzq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir, PDB code: 3qzq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:47.1 occ:1.00 F1 A:AG7501 0.0 47.1 1.0 C09 A:AG7501 1.3 43.8 1.0 HB3 A:LYS130 2.3 42.4 1.0 HD2 A:LYS130 2.3 63.1 1.0 C08 A:AG7501 2.4 46.6 1.0 HH22 A:ARG39 2.4 45.8 1.0 C10 A:AG7501 2.4 41.1 1.0 HH21 A:ARG39 2.6 45.8 1.0 H31 A:AG7501 2.6 55.9 1.0 H33 A:AG7501 2.6 49.3 1.0 NH2 A:ARG39 2.7 38.2 1.0 HB2 A:LYS130 2.8 42.4 1.0 CB A:LYS130 2.9 35.3 1.0 HE3 A:LYS130 2.9 77.6 1.0 CD A:LYS130 3.0 52.6 1.0 O A:LEU127 3.3 22.2 1.0 CE A:LYS130 3.3 64.7 1.0 CG A:LYS130 3.3 48.8 1.0 HZ2 A:LYS130 3.4 78.2 1.0 HB3 A:LEU127 3.4 35.5 1.0 HG2 A:LYS130 3.6 58.5 1.0 C07 A:AG7501 3.6 36.2 1.0 C11 A:AG7501 3.6 38.9 1.0 NZ A:LYS130 3.8 65.2 1.0 HD3 A:LYS130 3.9 63.1 1.0 CZ A:ARG39 3.9 39.2 1.0 C06 A:AG7501 4.1 32.2 1.0 O A:HOH455 4.2 41.0 1.0 CA A:LYS130 4.2 26.5 1.0 H A:LYS130 4.2 34.6 1.0 HE2 A:LYS130 4.2 77.6 1.0 HG3 A:LYS130 4.2 58.5 1.0 HB2 A:SER128 4.3 29.5 1.0 HB3 A:HIS40 4.3 30.6 0.5 HH12 A:ARG39 4.4 46.8 1.0 HZ1 A:LYS130 4.4 78.2 1.0 CB A:LEU127 4.4 29.6 1.0 C A:LEU127 4.4 22.9 1.0 H30 A:AG7501 4.4 43.5 1.0 H34 A:AG7501 4.4 46.7 1.0 HZ3 A:LYS130 4.5 78.2 1.0 OD2 A:ASP71 4.5 31.3 1.0 HB2 A:HIS40 4.5 30.1 0.5 NH1 A:ARG39 4.6 39.0 1.0 N A:LYS130 4.6 28.8 1.0 HD23 A:LEU127 4.6 33.4 1.0 O A:LYS130 4.6 27.6 1.0 HE A:ARG39 4.6 48.4 1.0 NE A:ARG39 4.7 40.4 1.0 HB2 A:LEU127 4.8 35.5 1.0 C A:LYS130 4.8 25.6 1.0 HG A:LEU127 4.9 38.8 1.0 HA A:LYS130 4.9 31.8 1.0

Fluorine binding site 2 out of 4 in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:50.2 occ:1.00 F1 B:AG7501 0.0 50.2 1.0 C09 B:AG7501 1.3 46.3 1.0 HD2 B:LYS130 2.2 60.7 1.0 HB3 B:LYS130 2.3 40.1 1.0 HH21 B:ARG39 2.3 42.2 1.0 C10 B:AG7501 2.4 40.5 1.0 C08 B:AG7501 2.4 48.5 1.0 HH22 B:ARG39 2.5 42.2 1.0 H33 B:AG7501 2.6 48.6 1.0 H31 B:AG7501 2.6 58.2 1.0 NH2 B:ARG39 2.6 35.2 1.0 CD B:LYS130 3.0 50.6 1.0 CB B:LYS130 3.0 33.4 1.0 HB2 B:LYS130 3.0 40.1 1.0 HE3 B:LYS130 3.1 81.3 1.0 CG B:LYS130 3.4 46.9 1.0 HZ2 B:LYS130 3.4 86.1 1.0 O B:LEU127 3.4 25.2 1.0 CE B:LYS130 3.4 67.8 1.0 HB3 B:LEU127 3.4 37.8 1.0 HG2 B:LYS130 3.5 56.3 1.0 C11 B:AG7501 3.6 40.5 1.0 C07 B:AG7501 3.6 40.8 1.0 HD3 B:LYS130 3.7 60.7 1.0 CZ B:ARG39 3.8 37.9 1.0 NZ B:LYS130 3.9 71.8 1.0 C06 B:AG7501 4.1 33.5 1.0 HB3 B:HIS40 4.2 30.8 0.5 HB2 B:SER128 4.2 31.0 1.0 H B:LYS130 4.3 35.3 1.0 HG3 B:LYS130 4.3 56.3 1.0 HE B:ARG39 4.3 43.6 1.0 HE2 B:LYS130 4.3 81.3 1.0 HD23 B:LEU127 4.3 39.3 1.0 CA B:LYS130 4.4 28.9 1.0 CB B:LEU127 4.4 31.5 1.0 H34 B:AG7501 4.4 48.6 1.0 H30 B:AG7501 4.4 49.0 1.0 OD2 B:ASP71 4.5 27.9 1.0 HZ3 B:LYS130 4.5 86.1 1.0 NE B:ARG39 4.5 36.3 1.0 C B:LEU127 4.5 24.4 1.0 HZ1 B:LYS130 4.5 86.1 1.0 HH12 B:ARG39 4.5 47.3 1.0 HG B:LEU127 4.5 35.5 1.0 HB2 B:HIS40 4.6 29.8 0.5 NH1 B:ARG39 4.6 39.4 1.0 O B:LYS130 4.7 30.0 1.0 N B:LYS130 4.7 29.4 1.0 HB2 B:LEU127 4.9 37.8 1.0 HD2 B:HIS40 4.9 27.3 0.5 CG B:LEU127 4.9 29.6 1.0 C B:LYS130 4.9 28.5 1.0 HD1 B:HIS40 5.0 29.9 0.5

Fluorine binding site 3 out of 4 in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:42.6 occ:1.00 F1 C:AG7501 0.0 42.6 1.0 C09 C:AG7501 1.3 40.2 1.0 C08 C:AG7501 2.4 39.4 1.0 C10 C:AG7501 2.4 40.0 1.0 HH22 C:ARG39 2.4 42.1 1.0 HD2 C:LYS130 2.4 68.0 1.0 HH21 C:ARG39 2.5 42.1 1.0 H31 C:AG7501 2.6 47.2 1.0 H33 C:AG7501 2.6 48.0 1.0 NH2 C:ARG39 2.7 35.1 1.0 HB3 C:LYS130 2.8 42.6 1.0 HB2 C:LYS130 2.9 42.6 1.0 CB C:LYS130 3.2 35.5 1.0 CD C:LYS130 3.2 56.7 1.0 HE3 C:LYS130 3.3 83.3 1.0 O C:LEU127 3.5 17.2 1.0 HZ2 C:LYS130 3.5 75.2 1.0 C11 C:AG7501 3.6 34.8 1.0 C07 C:AG7501 3.6 34.0 1.0 CG C:LYS130 3.7 47.1 1.0 CE C:LYS130 3.7 69.4 1.0 O C:HOH209 3.8 34.8 1.0 HG2 C:LYS130 3.8 56.5 1.0 CZ C:ARG39 3.9 34.8 1.0 HD3 C:LYS130 4.0 68.0 1.0 HB2 C:SER128 4.0 25.8 1.0 NZ C:LYS130 4.1 62.7 1.0 C06 C:AG7501 4.1 29.7 1.0 HB3 C:HIS40 4.1 25.2 0.4 HG C:LEU127 4.2 26.7 1.0 HB3 C:LEU127 4.3 24.9 1.0 H34 C:AG7501 4.4 41.7 1.0 H30 C:AG7501 4.4 40.9 1.0 HH12 C:ARG39 4.4 43.5 1.0 H C:LYS130 4.5 32.6 1.0 HD23 C:LEU127 4.5 30.6 1.0 HG3 C:LYS130 4.6 56.5 1.0 HE C:ARG39 4.6 37.0 1.0 HE2 C:LYS130 4.6 83.3 1.0 NH1 C:ARG39 4.6 36.3 1.0 CA C:LYS130 4.6 28.9 1.0 C C:LEU127 4.6 16.8 1.0 HZ1 C:LYS130 4.6 75.2 1.0 OD1 C:ASP71 4.7 31.0 1.0 HZ3 C:LYS130 4.7 75.2 1.0 NE C:ARG39 4.7 30.8 1.0 HB2 C:HIS40 4.7 22.4 0.6 O C:SER128 4.9 23.1 1.0 N C:LYS130 4.9 27.2 1.0 CB C:SER128 4.9 21.5 1.0 CG C:LEU127 4.9 22.2 1.0 HD1 C:HIS40 5.0 33.8 0.6

Fluorine binding site 4 out of 4 in the Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Enterovirus 71 3C Protease Mutant E71D in Complex with Rupintrivir within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:51.0 occ:1.00 F1 D:AG7501 0.0 51.0 1.0 C09 D:AG7501 1.3 50.9 1.0 C10 D:AG7501 2.4 49.6 1.0 C08 D:AG7501 2.4 51.3 1.0 HH22 D:ARG39 2.4 47.3 1.0 HH21 D:ARG39 2.4 47.3 1.0 H33 D:AG7501 2.6 59.5 1.0 H31 D:AG7501 2.6 61.6 1.0 HB3 D:LYS130 2.7 34.8 1.0 NH2 D:ARG39 2.7 39.5 1.0 HB2 D:LYS130 3.0 34.8 1.0 CB D:LYS130 3.2 29.0 1.0 HG2 D:LYS130 3.3 49.7 1.0 HD3 D:LYS130 3.3 55.7 1.0 O D:LEU127 3.5 22.8 1.0 CG D:LYS130 3.6 41.4 1.0 C11 D:AG7501 3.6 44.5 1.0 C07 D:AG7501 3.6 43.6 1.0 CZ D:ARG39 3.9 38.1 1.0 HB2 D:SER128 3.9 28.1 1.0 CD D:LYS130 3.9 46.4 1.0 O D:HOH517 3.9 39.8 1.0 C06 D:AG7501 4.1 36.4 1.0 HB3 D:LEU127 4.1 28.4 1.0 HB3 D:HIS40 4.3 29.5 0.4 H34 D:AG7501 4.4 53.4 1.0 H30 D:AG7501 4.4 52.4 1.0 H D:LYS130 4.4 36.2 1.0 HG D:LEU127 4.4 31.0 1.0 HH12 D:ARG39 4.5 45.1 1.0 HG3 D:LYS130 4.5 49.7 1.0 HE D:ARG39 4.5 39.9 1.0 HD2 D:LYS130 4.5 55.7 1.0 CA D:LYS130 4.6 28.4 1.0 C D:LEU127 4.6 20.4 1.0 NH1 D:ARG39 4.7 37.6 1.0 O D:SER128 4.7 22.0 1.0 NE D:ARG39 4.7 33.3 1.0 HB2 D:HIS40 4.7 29.6 0.6 HD23 D:LEU127 4.7 38.0 1.0 HE2 D:LYS130 4.8 62.1 1.0 CB D:SER128 4.8 23.4 1.0 N D:LYS130 4.8 30.2 1.0 OD2 D:ASP71 4.8 29.9 1.0 HB3 D:SER128 4.9 28.1 1.0 CE D:LYS130 5.0 51.8 1.0 CB D:LEU127 5.0 23.7 1.0

J.Wang, T.Fan, X.Yao, Z.Wu, L.Guo, X.Lei, J.Wang, M.Wang, Q.Jin, S.Cui. Crystal Structures of Enterovirus 71 3C Protease Complexed with Rupintrivir Reveal the Roles of Catalytically Important Residues. J.Virol. V. 85 10021 2011.
ISSN: ISSN 0022-538X
PubMed: 21813612
DOI: 10.1128/JVI.05107-11