Zinc in PDB 8qf8: GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine

The structure of GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine, PDB code: 8qf8 was solved by V.Borlandelli, W.Offen, O.V.Moroz, A.Nin-Hill, N.Mcgregor, L.Binkhorst, Z.Armstrong, A.Ishiwata, M.Artola, C.Rovira, G.J.Davies, H.Overkleeft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.90 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.84, 98.549, 196.584, 90, 90, 90
R / Rfree (%)	19 / 22.1

The binding sites of Zinc atom in the GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine (pdb code 8qf8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine, PDB code: 8qf8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:46.0 occ:1.00 OE1 A:GLU337 2.0 45.2 1.0 SG A:CYS415 2.3 43.2 1.0 SG A:CYS339 2.4 41.1 1.0 SG A:CYS414 2.5 42.0 1.0 HB2 A:CYS339 2.8 41.9 1.0 CD A:GLU337 3.0 40.2 1.0 H A:CYS415 3.1 42.2 1.0 N A:CYS415 3.1 41.4 1.0 HB2 A:CYS414 3.1 39.4 1.0 CB A:CYS339 3.1 41.8 1.0 HG2 A:GLU337 3.2 38.1 1.0 HA A:CYS415 3.3 41.3 1.0 CB A:CYS414 3.3 39.7 1.0 HG3 A:GLU337 3.4 39.1 1.0 H7 A:UI5901 3.4 47.0 1.0 CB A:CYS415 3.4 43.7 1.0 CG A:GLU337 3.4 38.3 1.0 CA A:CYS415 3.5 42.2 1.0 C A:CYS414 3.5 40.5 1.0 HB2 A:CYS415 3.8 44.0 1.0 C2 A:UI5901 3.8 47.1 1.0 HB3 A:CYS339 3.9 41.2 1.0 N A:CYS339 3.9 36.7 1.0 CA A:CYS414 4.0 39.0 1.0 C3 A:UI5901 4.0 48.8 1.0 CA A:CYS339 4.1 39.5 1.0 OE2 A:GLU337 4.2 40.1 1.0 H8 A:UI5901 4.2 48.9 1.0 O A:CYS414 4.2 39.7 1.0 HB3 A:CYS414 4.2 40.4 1.0 HB3 A:CYS415 4.2 43.1 1.0 CZ A:TYR393 4.3 44.3 1.0 CE2 A:TYR393 4.4 44.0 1.0 O1 A:UI5901 4.4 48.5 1.0 CE1 A:TYR393 4.5 43.7 1.0 HA A:CYS339 4.5 38.7 1.0 H A:CYS414 4.6 40.1 1.0 OH A:TYR393 4.6 47.3 1.0 N A:CYS414 4.7 38.5 1.0 HE2 A:TYR393 4.7 43.6 1.0 H A:THR338 4.7 38.2 1.0 HD21 A:ASN264 4.7 45.4 1.0 CD2 A:TYR393 4.7 41.7 1.0 HE1 A:TYR393 4.7 44.2 1.0 CD1 A:TYR393 4.8 43.6 1.0 HA A:CYS414 4.8 38.9 1.0 OG A:SER418 4.8 39.6 1.0 CG A:TYR393 4.9 40.2 1.0 CB A:GLU337 4.9 39.7 1.0 ND2 A:ASN264 5.0 46.0 1.0

Zinc binding site 2 out of 2 in the GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of GH146 Beta-L-Arabinofuranosidase From Bacteroides Thetaioatomicron in Complex with Beta-L-Arabinofurano Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:47.7 occ:1.00 OE1 B:GLU337 2.0 50.3 1.0 SG B:CYS414 2.3 45.2 1.0 SG B:CYS415 2.3 41.2 1.0 SG B:CYS339 2.4 42.8 1.0 HB2 B:CYS339 2.8 43.2 1.0 CD B:GLU337 3.0 45.2 1.0 HB2 B:CYS414 3.1 47.2 1.0 H B:CYS415 3.1 45.1 1.0 N B:CYS415 3.1 45.0 1.0 CB B:CYS339 3.2 44.1 1.0 HG2 B:GLU337 3.2 42.6 1.0 CB B:CYS414 3.2 47.1 1.0 HG3 B:GLU337 3.3 42.4 1.0 HA B:CYS415 3.3 44.3 1.0 CG B:GLU337 3.4 42.5 1.0 CB B:CYS415 3.4 43.4 1.0 CA B:CYS415 3.5 44.2 1.0 C B:CYS414 3.6 46.5 1.0 H7 B:UHU901 3.6 49.3 1.0 HB2 B:CYS415 3.8 43.1 1.0 HB3 B:CYS339 3.9 43.8 1.0 N B:CYS339 4.0 41.4 1.0 CA B:CYS414 4.0 48.1 1.0 H5 B:UHU901 4.0 49.6 1.0 HB3 B:CYS414 4.0 47.7 1.0 OE2 B:GLU337 4.1 45.9 1.0 CA B:CYS339 4.1 41.1 1.0 O B:CYS414 4.2 47.4 1.0 HB3 B:CYS415 4.2 42.8 1.0 CZ B:TYR393 4.4 43.8 1.0 C3 B:UHU901 4.4 50.0 1.0 CE1 B:TYR393 4.5 42.1 1.0 C2 B:UHU901 4.5 50.6 1.0 CE2 B:TYR393 4.5 43.9 1.0 HA B:CYS339 4.6 42.1 1.0 H B:CYS414 4.6 46.4 1.0 N B:CYS414 4.6 45.7 1.0 H B:THR338 4.7 40.3 1.0 HD21 B:ASN264 4.7 48.5 1.0 OH B:TYR393 4.7 44.0 1.0 CD2 B:TYR393 4.8 42.1 1.0 CD1 B:TYR393 4.8 42.6 1.0 HE1 B:TYR393 4.8 42.8 1.0 HE2 B:TYR393 4.8 43.9 1.0 HA B:CYS414 4.8 47.7 1.0 OG B:SER418 4.9 40.9 1.0 CG B:TYR393 4.9 41.0 1.0 ND2 B:ASN264 4.9 48.5 1.0 CB B:GLU337 4.9 41.1 1.0 O1 B:UHU901 5.0 50.2 1.0 O B:HOH1120 5.0 42.4 1.0 HA B:TYR393 5.0 40.7 1.0

V.Borlandelli, W.Offen, O.Moroz, A.Nin-Hill, N.Mcgregor, L.Binkhorst, A.Ishiwata, Z.Armstrong, M.Artola, C.Rovira, G.J.Davies, H.S.Overkleeft. Beta-L- Arabino Furano-Cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes For Retaining Beta-L-Arabinofuranosidases. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 38051515
DOI: 10.1021/ACSCHEMBIO.3C00558