Fluorine in PDB 6dte: Glcnac-Inspired Cyclophellitol Bound to Nagz

All present enzymatic activity of Glcnac-Inspired Cyclophellitol Bound to Nagz:
3.2.1.52;

The structure of Glcnac-Inspired Cyclophellitol Bound to Nagz, PDB code: 6dte was solved by B.L.Mark, J.L.Winogrodzki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.23 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.910, 88.140, 67.310, 90.00, 92.03, 90.00
R / Rfree (%)	15.4 / 20.2

The binding sites of Fluorine atom in the Glcnac-Inspired Cyclophellitol Bound to Nagz (pdb code 6dte). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Glcnac-Inspired Cyclophellitol Bound to Nagz, PDB code: 6dte:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:12.0 occ:1.00 F81 A:H9J401 0.0 12.0 1.0 C8 A:H9J401 1.3 11.6 1.0 F82 A:H9J401 2.1 11.4 1.0 F83 A:H9J401 2.2 11.9 1.0 C7 A:H9J401 2.3 11.0 1.0 O7 A:H9J401 2.9 11.2 1.0 HE1 A:HIS183 2.9 17.5 1.0 HG21 A:VAL136 2.9 15.4 1.0 OG A:SER182 3.0 12.9 1.0 HG A:SER182 3.1 15.5 1.0 HE3 A:MET257 3.2 16.6 1.0 N2 A:H9J401 3.2 10.5 1.0 CE1 A:HIS183 3.2 14.6 1.0 HG22 A:VAL136 3.3 15.4 1.0 HN2 A:H9J401 3.3 12.6 1.0 ND1 A:HIS183 3.4 14.6 1.0 HG12 A:VAL136 3.5 15.6 1.0 CG2 A:VAL136 3.5 12.8 1.0 HE2 A:MET257 3.6 16.6 1.0 CE A:MET257 3.8 13.8 1.0 HH12 A:ARG140 3.9 12.2 1.0 H A:SER182 4.0 17.5 1.0 NE2 A:HIS175 4.0 11.1 1.0 OD1 A:ASP181 4.2 15.6 1.0 H A:HIS183 4.2 18.7 1.0 HG23 A:VAL136 4.2 15.4 1.0 NE2 A:HIS183 4.2 14.6 1.0 HD2 A:HIS175 4.2 14.7 1.0 CG1 A:VAL136 4.3 13.0 1.0 CD2 A:HIS175 4.3 12.2 1.0 HE1 A:MET257 4.3 16.6 1.0 O A:HOH570 4.4 11.8 1.0 CB A:SER182 4.4 14.9 1.0 H2 A:H9J401 4.4 12.9 1.0 OD2 A:ASP253 4.4 11.0 1.0 C2 A:H9J401 4.5 10.8 1.0 HG13 A:VAL136 4.5 15.6 1.0 CG A:HIS183 4.5 15.3 1.0 CB A:VAL136 4.5 13.2 1.0 N A:SER182 4.6 14.6 1.0 HE2 A:HIS183 4.6 17.5 1.0 HD13 A:ILE137 4.6 11.6 1.0 N A:HIS183 4.7 15.6 1.0 NH1 A:ARG140 4.7 10.2 1.0 HE2 A:HIS171 4.7 11.0 1.0 HD11 A:ILE137 4.8 11.6 1.0 CE1 A:HIS175 4.8 12.2 1.0 NE2 A:HIS171 4.8 9.2 1.0 HH22 A:ARG140 4.8 11.6 1.0 HB2 A:SER182 4.8 17.8 1.0 CD2 A:HIS183 4.9 14.8 1.0 CA A:SER182 4.9 15.2 1.0 H1 A:H9J401 4.9 12.7 1.0 HB3 A:SER182 4.9 17.8 1.0 HB A:VAL136 5.0 15.8 1.0

Fluorine binding site 2 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:11.4 occ:1.00 F82 A:H9J401 0.0 11.4 1.0 C8 A:H9J401 1.3 11.6 1.0 F81 A:H9J401 2.1 12.0 1.0 F83 A:H9J401 2.2 11.9 1.0 C7 A:H9J401 2.4 11.0 1.0 HN2 A:H9J401 2.4 12.6 1.0 N2 A:H9J401 2.7 10.5 1.0 HD2 A:HIS175 2.7 14.7 1.0 HG A:SER182 2.9 15.5 1.0 O A:HOH570 3.1 11.8 1.0 CD2 A:HIS175 3.2 12.2 1.0 CD2 A:HIS171 3.3 10.1 1.0 OG A:SER182 3.4 12.9 1.0 OD2 A:ASP253 3.4 11.0 1.0 NE2 A:HIS171 3.4 9.2 1.0 HD2 A:HIS171 3.4 12.2 1.0 O7 A:H9J401 3.4 11.2 1.0 HE3 A:MET257 3.5 16.6 1.0 HE2 A:HIS171 3.6 11.0 1.0 NE2 A:HIS175 3.6 11.1 1.0 CG A:HIS171 3.7 8.4 1.0 CE1 A:HIS171 3.8 9.1 1.0 ND1 A:HIS171 4.0 9.1 1.0 C2 A:H9J401 4.1 10.8 1.0 HD11 A:ILE137 4.2 11.6 1.0 CG A:HIS175 4.2 10.8 1.0 HE1 A:HIS171 4.3 10.9 1.0 HB3 A:HIS171 4.3 12.2 1.0 CE A:MET257 4.4 13.8 1.0 HB2 A:HIS171 4.4 12.2 1.0 CB A:HIS171 4.5 10.2 1.0 H2 A:H9J401 4.5 12.9 1.0 CG A:ASP253 4.5 11.6 1.0 HG12 A:VAL136 4.5 15.6 1.0 HA A:ALA217 4.5 13.3 1.0 HD1 A:HIS171 4.5 10.9 1.0 HE2 A:MET257 4.6 16.6 1.0 CE1 A:HIS175 4.7 12.2 1.0 HE1 A:HIS183 4.7 17.5 1.0 HB2 A:HIS175 4.7 11.6 1.0 HD13 A:ILE137 4.7 11.6 1.0 H A:HIS218 4.7 15.8 1.0 CB A:SER182 4.7 14.9 1.0 H1 A:H9J401 4.8 12.7 1.0 HH12 A:ARG140 4.8 12.2 1.0 O3 A:H9J401 4.8 8.9 1.0 H3 A:H9J401 4.9 13.0 1.0 HH22 A:ARG140 4.9 11.6 1.0 HG21 A:VAL136 4.9 15.4 1.0 C3 A:H9J401 4.9 10.8 1.0 CD1 A:ILE137 4.9 9.6 1.0 HE1 A:MET257 4.9 16.6 1.0 HG22 A:VAL136 4.9 15.4 1.0 C1 A:H9J401 4.9 10.6 1.0 HB1 A:ALA217 4.9 13.6 1.0 CB A:HIS175 4.9 9.6 1.0 ND1 A:HIS175 5.0 11.0 1.0 HB2 A:SER182 5.0 17.8 1.0 HB3 A:SER182 5.0 17.8 1.0

Fluorine binding site 3 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:11.9 occ:1.00 F83 A:H9J401 0.0 11.9 1.0 C8 A:H9J401 1.3 11.6 1.0 F82 A:H9J401 2.2 11.4 1.0 F81 A:H9J401 2.2 12.0 1.0 C7 A:H9J401 2.3 11.0 1.0 O7 A:H9J401 2.7 11.2 1.0 HD13 A:ILE137 2.8 11.6 1.0 HD11 A:ILE137 2.8 11.6 1.0 HH12 A:ARG140 2.9 12.2 1.0 HG22 A:VAL136 3.2 15.4 1.0 HG12 A:VAL136 3.2 15.6 1.0 CD1 A:ILE137 3.2 9.6 1.0 CE1 A:HIS171 3.3 9.1 1.0 HE1 A:HIS171 3.3 10.9 1.0 NE2 A:HIS171 3.4 9.2 1.0 HE2 A:HIS171 3.5 11.0 1.0 N2 A:H9J401 3.5 10.5 1.0 NH1 A:ARG140 3.5 10.2 1.0 HH22 A:ARG140 3.6 11.6 1.0 HN2 A:H9J401 3.7 12.6 1.0 HD12 A:ILE137 3.7 11.6 1.0 HG21 A:VAL136 3.8 15.4 1.0 ND1 A:HIS171 3.8 9.1 1.0 HD2 A:HIS175 3.9 14.7 1.0 CG2 A:VAL136 3.9 12.8 1.0 CD2 A:HIS175 3.9 12.2 1.0 HH11 A:ARG140 4.0 12.2 1.0 CD2 A:HIS171 4.0 10.1 1.0 HE1 A:HIS183 4.0 17.5 1.0 NH2 A:ARG140 4.1 9.7 1.0 CG1 A:VAL136 4.1 13.0 1.0 CZ A:ARG140 4.2 10.6 1.0 HD1 A:HIS171 4.2 10.9 1.0 CG A:HIS171 4.2 8.4 1.0 NE2 A:HIS175 4.2 11.1 1.0 HG12 A:ILE137 4.4 14.7 1.0 CG A:HIS175 4.4 10.8 1.0 HG A:SER182 4.4 15.5 1.0 CG1 A:ILE137 4.4 12.2 1.0 HD2 A:HIS171 4.5 12.2 1.0 HG11 A:VAL136 4.6 15.6 1.0 OG A:SER182 4.6 12.9 1.0 HB3 A:HIS175 4.6 11.6 1.0 HG23 A:VAL136 4.7 15.4 1.0 HO3 A:H9J401 4.7 10.6 1.0 CB A:VAL136 4.7 13.2 1.0 HG13 A:VAL136 4.7 15.6 1.0 O3 A:H9J401 4.7 8.9 1.0 C2 A:H9J401 4.7 10.8 1.0 CE1 A:HIS183 4.7 14.6 1.0 H2 A:H9J401 4.8 12.9 1.0 HA A:ILE137 4.8 13.8 1.0 HH21 A:ARG140 4.8 11.6 1.0 CE1 A:HIS175 4.8 12.2 1.0 O A:VAL136 4.9 11.7 1.0 ND1 A:HIS175 4.9 11.0 1.0 C A:VAL136 4.9 12.2 1.0 HG13 A:ILE137 5.0 14.7 1.0 CB A:HIS175 5.0 9.6 1.0 HE3 A:MET257 5.0 16.6 1.0 HB2 A:HIS175 5.0 11.6 1.0

Fluorine binding site 4 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:13.3 occ:1.00 F81 B:H9J401 0.0 13.3 1.0 C8 B:H9J401 1.3 14.2 1.0 F82 B:H9J401 2.1 13.9 1.0 F83 B:H9J401 2.2 12.5 1.0 C7 B:H9J401 2.3 13.4 1.0 O7 B:H9J401 2.6 14.5 1.0 HD12 B:ILE137 2.8 15.0 1.0 HH12 B:ARG140 2.9 16.0 1.0 HD13 B:ILE137 3.0 15.0 1.0 HG23 B:VAL136 3.0 19.6 1.0 CE1 B:HIS171 3.1 11.2 1.0 HE1 B:HIS171 3.1 13.4 1.0 NE2 B:HIS171 3.3 12.1 1.0 CD1 B:ILE137 3.3 12.5 1.0 HE2 B:HIS171 3.4 14.6 1.0 N2 B:H9J401 3.5 13.3 1.0 NH1 B:ARG140 3.5 13.3 1.0 HH22 B:ARG140 3.6 13.8 1.0 HG11 B:VAL136 3.6 17.7 1.0 HN2 B:H9J401 3.7 16.0 1.0 ND1 B:HIS171 3.7 11.9 1.0 HD11 B:ILE137 3.8 15.0 1.0 HD2 B:HIS175 3.9 17.3 1.0 CD2 B:HIS171 3.9 11.7 1.0 HG12 B:VAL136 3.9 17.7 1.0 CG2 B:VAL136 3.9 16.3 1.0 HH11 B:ARG140 4.0 16.0 1.0 CD2 B:HIS175 4.0 14.4 1.0 NH2 B:ARG140 4.1 11.5 1.0 HE1 B:HIS183 4.1 22.2 1.0 HD1 B:HIS171 4.1 14.3 1.0 CZ B:ARG140 4.1 13.0 1.0 CG B:HIS171 4.2 11.0 1.0 CG1 B:VAL136 4.2 14.8 1.0 HG21 B:VAL136 4.3 19.6 1.0 NE2 B:HIS175 4.3 16.4 1.0 HG B:SER182 4.3 20.7 1.0 CG B:HIS175 4.4 13.3 1.0 HD2 B:HIS171 4.5 14.0 1.0 HG22 B:VAL136 4.5 19.6 1.0 HG12 B:ILE137 4.5 14.7 1.0 HO3 B:H9J401 4.6 16.3 1.0 CG1 B:ILE137 4.6 12.3 1.0 HB3 B:HIS175 4.6 15.6 1.0 O3 B:H9J401 4.7 13.6 1.0 C2 B:H9J401 4.7 12.9 1.0 CB B:VAL136 4.7 16.2 1.0 H2 B:H9J401 4.7 15.5 1.0 OG B:SER182 4.7 17.2 1.0 HH21 B:ARG140 4.8 13.8 1.0 CE1 B:HIS183 4.8 18.5 1.0 CE1 B:HIS175 4.9 15.7 1.0 HA B:ILE137 4.9 15.4 1.0 O B:VAL136 4.9 12.7 1.0 HE1 B:MET257 4.9 20.6 1.0 ND1 B:HIS175 4.9 13.7 1.0 CB B:HIS175 5.0 13.0 1.0 HB2 B:HIS175 5.0 15.6 1.0

Fluorine binding site 5 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:13.9 occ:1.00 F82 B:H9J401 0.0 13.9 1.0 C8 B:H9J401 1.3 14.2 1.0 F81 B:H9J401 2.1 13.3 1.0 F83 B:H9J401 2.2 12.5 1.0 C7 B:H9J401 2.4 13.4 1.0 HG23 B:VAL136 2.6 19.6 1.0 HG B:SER182 2.8 20.7 1.0 O7 B:H9J401 2.9 14.5 1.0 HE1 B:HIS183 2.9 22.2 1.0 OG B:SER182 3.1 17.2 1.0 HE1 B:MET257 3.2 20.6 1.0 CE1 B:HIS183 3.3 18.5 1.0 N2 B:H9J401 3.3 13.3 1.0 HD1 B:HIS183 3.4 23.8 1.0 HN2 B:H9J401 3.4 16.0 1.0 CG2 B:VAL136 3.5 16.3 1.0 HG22 B:VAL136 3.5 19.6 1.0 HG12 B:VAL136 3.5 17.7 1.0 ND1 B:HIS183 3.5 19.9 1.0 HE3 B:MET257 3.7 20.6 1.0 H B:SER182 3.8 22.2 1.0 HH12 B:ARG140 3.9 16.0 1.0 CE B:MET257 3.9 17.2 1.0 NE2 B:HIS175 4.0 16.4 1.0 OD1 B:ASP181 4.0 16.8 1.0 HG11 B:VAL136 4.0 17.7 1.0 HG21 B:VAL136 4.1 19.6 1.0 CG1 B:VAL136 4.1 14.8 1.0 HD2 B:HIS175 4.2 17.3 1.0 CD2 B:HIS175 4.2 14.4 1.0 NE2 B:HIS183 4.3 18.9 1.0 H B:HIS183 4.3 22.7 1.0 HE2 B:MET257 4.3 20.6 1.0 O B:HOH599 4.4 14.8 1.0 CB B:VAL136 4.4 16.2 1.0 N B:SER182 4.5 18.5 1.0 CB B:SER182 4.5 18.1 1.0 H2 B:H9J401 4.5 15.5 1.0 OD2 B:ASP253 4.5 15.1 1.0 HD12 B:ILE137 4.6 15.0 1.0 C2 B:H9J401 4.6 12.9 1.0 CG B:HIS183 4.6 19.1 1.0 NH1 B:ARG140 4.7 13.3 1.0 HE2 B:HIS171 4.7 14.6 1.0 CE1 B:HIS175 4.7 15.7 1.0 N B:HIS183 4.8 18.9 1.0 NE2 B:HIS171 4.8 12.1 1.0 HD13 B:ILE137 4.8 15.0 1.0 HB B:VAL136 4.8 19.4 1.0 HH22 B:ARG140 4.8 13.8 1.0 CA B:SER182 4.9 18.6 1.0 HA B:ASP181 4.9 22.6 1.0 HB3 B:SER182 5.0 21.7 1.0 HB2 B:SER182 5.0 21.7 1.0 CD2 B:HIS183 5.0 19.8 1.0

Fluorine binding site 6 out of 6 in the Glcnac-Inspired Cyclophellitol Bound to Nagz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Glcnac-Inspired Cyclophellitol Bound to Nagz within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:12.5 occ:1.00 F83 B:H9J401 0.0 12.5 1.0 C8 B:H9J401 1.3 14.2 1.0 F81 B:H9J401 2.2 13.3 1.0 F82 B:H9J401 2.2 13.9 1.0 C7 B:H9J401 2.3 13.4 1.0 HN2 B:H9J401 2.4 16.0 1.0 N2 B:H9J401 2.7 13.3 1.0 HD2 B:HIS175 2.8 17.3 1.0 O B:HOH599 3.0 14.8 1.0 CD2 B:HIS175 3.2 14.4 1.0 CD2 B:HIS171 3.3 11.7 1.0 HG B:SER182 3.3 20.7 1.0 HE1 B:MET257 3.4 20.6 1.0 NE2 B:HIS171 3.4 12.1 1.0 OD2 B:ASP253 3.4 15.1 1.0 OG B:SER182 3.4 17.2 1.0 O7 B:H9J401 3.4 14.5 1.0 HD2 B:HIS171 3.4 14.0 1.0 HE2 B:HIS171 3.5 14.6 1.0 NE2 B:HIS175 3.6 16.4 1.0 CG B:HIS171 3.7 11.0 1.0 CE1 B:HIS171 3.8 11.2 1.0 ND1 B:HIS171 4.0 11.9 1.0 C2 B:H9J401 4.1 12.9 1.0 CG B:HIS175 4.2 13.3 1.0 CE B:MET257 4.3 17.2 1.0 HE1 B:HIS171 4.3 13.4 1.0 HD13 B:ILE137 4.3 15.0 1.0 HB3 B:HIS171 4.4 13.0 1.0 HG23 B:VAL136 4.4 19.6 1.0 H2 B:H9J401 4.5 15.5 1.0 CG B:ASP253 4.5 14.4 1.0 CB B:HIS171 4.5 10.8 1.0 HB2 B:HIS171 4.5 13.0 1.0 HD1 B:HIS171 4.5 14.3 1.0 HE3 B:MET257 4.6 20.6 1.0 HA B:ALA217 4.6 16.1 1.0 HE1 B:HIS183 4.6 22.2 1.0 CE1 B:HIS175 4.7 15.7 1.0 HB2 B:HIS175 4.7 15.6 1.0 H B:HIS218 4.7 20.1 1.0 CB B:SER182 4.7 18.1 1.0 HE2 B:MET257 4.8 20.6 1.0 H1 B:H9J401 4.8 16.9 1.0 HH12 B:ARG140 4.8 16.0 1.0 HD12 B:ILE137 4.8 15.0 1.0 O3 B:H9J401 4.8 13.6 1.0 HG12 B:VAL136 4.9 17.7 1.0 HH22 B:ARG140 4.9 13.8 1.0 C3 B:H9J401 4.9 12.3 1.0 H3 B:H9J401 4.9 14.7 1.0 C1 B:H9J401 4.9 14.1 1.0 H B:SER182 4.9 22.2 1.0 HO3 B:H9J401 5.0 16.3 1.0 CB B:HIS175 5.0 13.0 1.0

L.A.Ho, J.L.Winogrodzki, A.W.Debowski, Z.Madden, D.J.Vocadlo, B.L.Mark, K.A.Stubbs. A Mechanism-Based Glcnac-Inspired Cyclophellitol Inactivator of the Peptidoglycan Recycling Enzyme Nagz Reverses Resistance to Beta-Lactams in Pseudomonas Aeruginosa. Chem. Commun. (Camb.) V. 54 10630 2018.
ISSN: ESSN 1364-548X
PubMed: 30178799
DOI: 10.1039/C8CC05281F