Chlorine in PDB 5fcz: Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)

The structure of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx), PDB code: 5fcz was solved by G.Vadlamani, B.L.Mark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.15 / 2.45
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	133.870, 133.870, 174.913, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 21

The binding sites of Chlorine atom in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) (pdb code 5fcz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx), PDB code: 5fcz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:25.8 occ:1.00 HH A:TYR271 2.3 24.6 1.0 HD3 A:LYS275 3.0 38.3 1.0 O A:HOH977 3.1 27.8 1.0 HE1 A:TYR271 3.1 31.2 1.0 OH A:TYR271 3.1 20.5 1.0 HA3 A:GLY273 3.3 28.6 1.0 HB2 A:LYS275 3.7 27.0 1.0 CE1 A:TYR271 3.8 26.0 1.0 CD A:LYS275 3.9 31.9 1.0 CZ A:TYR271 3.9 27.0 1.0 HG3 A:LYS275 3.9 36.0 1.0 H A:THR274 4.0 35.0 1.0 HD2 A:LYS275 4.2 38.3 1.0 CA A:GLY273 4.3 23.8 1.0 CG A:LYS275 4.3 30.0 1.0 H A:LYS275 4.3 31.5 1.0 CB A:LYS275 4.5 22.5 1.0 HA2 A:GLY273 4.5 28.6 1.0 N A:THR274 4.6 29.1 1.0 N A:LYS275 4.9 26.3 1.0 C A:GLY273 5.0 27.4 1.0

Chlorine binding site 2 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:27.6 occ:1.00 HE A:ARG179 2.4 33.4 1.0 HH11 A:ARG176 2.4 22.2 1.0 HH21 A:ARG179 2.7 25.9 1.0 HD3 A:ARG176 2.9 28.4 1.0 O A:HOH981 2.9 30.6 1.0 NE A:ARG179 3.2 27.9 1.0 NH1 A:ARG176 3.2 18.5 1.0 HB3 A:ASP175 3.3 24.4 1.0 NH2 A:ARG179 3.4 21.6 1.0 HA A:ARG176 3.5 27.6 1.0 HD11 A:ILE495 3.5 30.4 1.0 HH12 A:ARG176 3.5 22.2 1.0 O A:ASP175 3.7 23.6 1.0 CZ A:ARG179 3.7 24.7 1.0 HB2 A:ASP175 3.8 24.4 1.0 O A:HOH749 3.9 25.0 1.0 CD A:ARG176 3.9 23.7 1.0 C A:ASP175 3.9 22.9 1.0 CB A:ASP175 3.9 20.4 1.0 N A:ARG176 4.0 18.5 1.0 HH22 A:ARG121 4.1 35.9 1.0 HH22 A:ARG179 4.2 25.9 1.0 HG3 A:ARG179 4.2 30.4 1.0 CA A:ARG176 4.2 23.0 1.0 CD A:ARG179 4.2 28.4 1.0 HD2 A:ARG179 4.3 34.1 1.0 HD2 A:ARG176 4.3 28.4 1.0 HG2 A:ARG176 4.3 30.8 1.0 CZ A:ARG176 4.3 26.0 1.0 H A:ARG176 4.4 22.2 1.0 CD1 A:ILE495 4.4 25.4 1.0 HD13 A:ILE495 4.5 30.4 1.0 NE A:ARG176 4.5 25.5 1.0 CG A:ARG176 4.6 25.7 1.0 CA A:ASP175 4.6 22.0 1.0 O A:HOH1069 4.7 39.1 1.0 CG A:ARG179 4.7 25.3 1.0 O A:HOH884 4.8 35.3 1.0 NH2 A:ARG121 4.9 29.9 1.0 HG2 A:ARG179 4.9 30.4 1.0 CB A:ARG176 4.9 26.7 1.0 HD12 A:ILE495 5.0 30.4 1.0 HG12 A:ILE495 5.0 40.5 1.0

Chlorine binding site 3 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl607 b:33.9 occ:0.50 H A:VAL276 2.7 36.4 1.0 HZ2 A:LYS275 2.8 34.6 1.0 HG22 A:VAL276 2.9 31.4 1.0 HA A:LYS275 3.0 28.7 1.0 HG2 A:LYS275 3.0 36.0 1.0 HB3 A:LYS275 3.2 27.0 1.0 N A:VAL276 3.5 30.4 1.0 CA A:LYS275 3.7 23.9 1.0 CB A:LYS275 3.7 22.5 1.0 NZ A:LYS275 3.7 28.9 1.0 CG A:LYS275 3.8 30.0 1.0 CG2 A:VAL276 3.9 26.2 1.0 HG13 A:VAL276 3.9 33.8 1.0 HZ1 A:LYS275 4.1 34.6 1.0 C A:LYS275 4.1 28.7 1.0 HZ3 A:LYS275 4.1 34.6 1.0 O A:VAL276 4.3 28.8 1.0 HG23 A:VAL276 4.3 31.4 1.0 HE3 A:LYS275 4.4 39.2 1.0 HG21 A:VAL276 4.4 31.4 1.0 HG3 A:LYS275 4.4 36.0 1.0 CA A:VAL276 4.4 32.4 1.0 CE A:LYS275 4.5 32.7 1.0 CB A:VAL276 4.5 25.2 1.0 HB2 A:LYS275 4.6 27.0 1.0 CG1 A:VAL276 4.7 28.2 1.0 CD A:LYS275 4.7 31.9 1.0 C A:VAL276 4.8 33.0 1.0 O A:THR274 4.8 32.5 1.0 O A:HOH844 4.9 22.5 1.0 O A:HOH971 4.9 22.0 1.0 N A:LYS275 5.0 26.3 1.0

Chlorine binding site 4 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:64.4 occ:1.00 H A:GLY76 2.5 44.0 1.0 HH21 A:ARG44 3.3 41.1 1.0 N A:GLY76 3.4 36.7 1.0 HA2 A:GLY76 3.7 43.0 1.0 HA A:HIS75 3.7 44.5 0.5 HA A:HIS75 3.8 44.5 0.5 NH2 A:ARG44 4.0 34.3 1.0 CA A:GLY76 4.0 35.8 1.0 HB2 A:HIS75 4.1 46.1 0.5 HE1 A:HIS77 4.2 80.1 1.0 HH22 A:ARG44 4.2 41.1 1.0 O A:GLY76 4.2 47.4 1.0 HB3 A:HIS75 4.3 46.1 0.5 C A:HIS75 4.4 37.0 1.0 CA A:HIS75 4.4 37.1 0.5 CA A:HIS75 4.5 37.0 0.5 C A:GLY76 4.5 41.9 1.0 HE A:ARG44 4.5 57.3 1.0 CE1 A:HIS77 4.7 66.7 1.0 CB A:HIS75 4.8 38.4 0.5 ND1 A:HIS77 4.9 68.0 1.0 CB A:HIS75 4.9 38.4 0.5 HA3 A:GLY76 4.9 43.0 1.0 CZ A:ARG44 5.0 44.2 1.0

Chlorine binding site 5 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:51.0 occ:1.00 H A:ALA111 2.7 39.5 1.0 HB2 A:ALA111 3.2 33.1 1.0 HB3 A:ALA110 3.2 30.1 1.0 O A:HOH788 3.3 25.8 1.0 HB3 A:LYS109 3.3 38.0 1.0 O A:HOH807 3.4 24.7 1.0 N A:ALA111 3.5 32.9 1.0 HE1 A:HIS238 3.5 32.6 1.0 H A:ALA110 3.6 31.9 1.0 HD1 A:HIS238 3.8 28.0 1.0 HB3 A:ALA111 3.8 33.1 1.0 CB A:ALA111 3.8 27.6 1.0 HB2 A:LYS109 3.8 38.0 1.0 O A:HOH738 3.9 29.4 1.0 N A:ALA110 4.0 26.6 1.0 CB A:LYS109 4.0 31.6 1.0 CE1 A:HIS238 4.1 27.2 1.0 CB A:ALA110 4.1 25.1 1.0 ND1 A:HIS238 4.2 23.3 1.0 CA A:ALA111 4.2 25.7 1.0 CA A:ALA110 4.4 28.6 1.0 C A:ALA110 4.4 28.4 1.0 O A:HOH1068 4.5 39.9 1.0 HA A:ALA111 4.6 30.9 1.0 HB2 A:ALA110 4.6 30.1 1.0 C A:LYS109 4.6 28.5 1.0 HB1 A:ALA111 4.7 33.1 1.0 HB1 A:ALA110 4.7 30.1 1.0 O A:HOH1052 4.8 34.7 1.0 CA A:LYS109 4.9 34.0 1.0

Chlorine binding site 6 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl610 b:68.2 occ:1.00 HH22 A:ARG306 2.8 38.5 1.0 HZ1 A:LYS184 3.3 34.8 1.0 NH2 A:ARG306 3.5 32.1 1.0 HB1 A:ALA152 3.5 25.8 1.0 O A:HOH905 3.7 22.2 1.0 HD22 A:ASN183 3.7 29.9 1.0 O A:HOH1020 3.7 30.6 1.0 HH21 A:ARG306 3.8 38.5 1.0 HD21 A:ASN183 3.9 29.9 1.0 NZ A:LYS184 4.0 29.0 1.0 ND2 A:ASN183 4.1 24.9 1.0 HZ2 A:LYS184 4.1 34.8 1.0 HH12 A:ARG306 4.1 32.2 1.0 O A:HOH856 4.3 29.0 1.0 O A:ALA152 4.4 25.8 1.0 HZ3 A:LYS184 4.4 34.8 1.0 OE1 A:GLU92 4.4 30.0 1.0 CB A:ALA152 4.5 21.5 1.0 CZ A:ARG306 4.5 31.4 1.0 HG3 A:GLU92 4.5 31.7 1.0 CD A:GLU92 4.5 29.3 1.0 NH1 A:ARG306 4.7 26.8 1.0 O A:HOH1068 4.7 39.9 1.0 HB2 A:ALA152 4.7 25.8 1.0 O A:HOH890 4.8 33.3 1.0 OE2 A:GLU92 4.8 31.6 1.0 HB2 A:ASP91 4.9 43.1 1.0 HA A:ALA152 4.9 30.8 1.0

Chlorine binding site 7 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl611 b:71.4 occ:1.00 HE A:ARG69 2.6 60.9 1.0 HH21 A:ARG69 2.9 81.1 1.0 NE A:ARG69 3.4 50.7 1.0 O A:HOH961 3.5 37.2 1.0 NH2 A:ARG69 3.7 67.6 1.0 HG3 A:ARG69 3.7 44.1 1.0 CZ A:ARG69 4.0 57.9 1.0 HG2 A:ARG69 4.1 44.1 1.0 CG A:ARG69 4.2 36.7 1.0 HB3 A:PRO71 4.3 32.8 1.0 HH22 A:ARG69 4.4 81.1 1.0 CD A:ARG69 4.4 42.7 1.0 HA A:PRO71 4.7 24.9 1.0 HD2 A:ARG69 4.9 51.3 1.0

Chlorine binding site 8 out of 8 in the Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Streptomyces Plicatus N-Acetyl-Beta-Hexosaminidase in Complex with Thio-Naglucal (Tnx) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl612 b:62.4 occ:1.00 HD3 A:PRO135 3.6 41.5 1.0 HA A:PRO135 3.7 52.1 1.0 N A:PRO135 3.9 42.1 1.0 C A:GLN134 4.0 32.9 1.0 HG3 A:PRO135 4.2 41.5 1.0 CD A:PRO135 4.2 34.6 1.0 O A:GLN134 4.3 36.8 1.0 HA A:GLN134 4.3 36.2 1.0 CA A:PRO135 4.3 43.4 1.0 CA A:GLN134 4.5 30.1 1.0 N A:GLN134 4.6 26.6 1.0 CG A:PRO135 4.7 34.5 1.0 O A:ALA133 4.7 36.9 1.0 HB1 A:ALA133 4.8 40.2 1.0 C A:ALA133 4.8 34.7 1.0 H A:GLN134 4.9 32.0 1.0 HB3 A:ALA133 4.9 40.2 1.0

A.G.Santana, G.Vadlamani, B.L.Mark, S.G.Withers. N-Acetyl Glycals Are Tight-Binding and Environmentally Insensitive Inhibitors of Hexosaminidases. Chem.Commun.(Camb.) V. 52 7943 2016.
ISSN: ESSN 1364-548X
PubMed: 27253678
DOI: 10.1039/C6CC02520J