Chlorine in PDB 7op6: Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine

The structure of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine, PDB code: 7op6 was solved by N.G.S.Mcgregor, T.J.M.Beenakker, C.Kuo, C.Wong, W.A.Offen, Z.Armstrong, J.D.C.Codee, J.M.F.G.Aerts, B.I.Florea, H.S.Overkleeft, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.19 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.92, 116.858, 100.844, 90, 114.15, 90
R / Rfree (%)	18.5 / 23.3

The structure of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine also contains other interesting chemical elements:

Bromine	(Br)	10 atoms
Sodium	(Na)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine (pdb code 7op6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine, PDB code: 7op6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl922 b:47.9 occ:1.00 N A:THR477 3.6 42.0 1.0 CG2 A:THR477 3.7 43.4 1.0 CA A:PHE476 3.8 42.8 1.0 CG2 A:VAL480 3.9 42.5 1.0 CD1 A:PHE476 4.0 42.0 1.0 CB A:PHE476 4.0 43.8 1.0 CB A:PHE172 4.1 36.5 1.0 CB A:VAL480 4.2 42.2 1.0 C A:PHE476 4.2 46.3 1.0 OG1 A:THR477 4.3 43.9 1.0 CG1 A:VAL480 4.4 43.7 1.0 CB A:THR477 4.4 44.1 1.0 CG A:PHE476 4.5 45.5 1.0 CA A:THR477 4.6 44.2 1.0 O A:HOH1238 4.6 43.0 1.0 CG A:PHE172 4.8 34.4 1.0 O A:LYS475 4.9 50.8 1.0

Chlorine binding site 2 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl923 b:56.1 occ:1.00 O A:THR787 3.5 52.0 1.0 N A:THR787 3.6 50.3 1.0 CA A:PRO786 3.7 51.4 1.0 CB A:PRO786 3.8 54.9 1.0 CG A:GLU861 3.9 44.9 0.5 CG A:ARG860 4.0 52.9 1.0 CA A:GLU861 4.1 43.5 1.0 CE1 A:HIS858 4.1 48.5 1.0 N A:GLU861 4.1 41.9 1.0 C A:PRO786 4.2 50.2 1.0 C A:ARG860 4.3 42.5 1.0 CB A:ARG860 4.4 49.5 1.0 O A:ARG860 4.4 38.2 1.0 C A:THR787 4.5 48.8 1.0 CB A:GLU861 4.6 44.4 1.0 NE2 A:HIS858 4.7 50.0 1.0 CA A:THR787 4.7 47.6 1.0 NH1 A:ARG860 5.0 64.6 1.0 CA A:ARG860 5.0 44.0 1.0 N A:PRO786 5.0 53.4 1.0

Chlorine binding site 3 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl924 b:71.7 occ:1.00 O A:HOH1232 2.8 44.1 1.0 O A:HOH1323 3.0 40.1 1.0 ND2 A:ASN390 3.2 26.2 1.0 O A:ASN300 3.2 26.8 1.0 CD1 A:TRP302 4.0 28.6 1.0 NE1 A:TRP302 4.0 29.6 1.0 CG A:ASN390 4.1 25.5 1.0 CB A:ASN390 4.2 25.0 1.0 O A:HOH1290 4.2 34.8 1.0 O A:HOH1159 4.3 37.0 1.0 C A:ASN300 4.3 25.9 1.0 CG A:MET355 4.3 26.1 1.0 CE2 A:TRP302 4.4 27.6 1.0 CG A:TRP302 4.4 29.2 1.0 CA A:GLY301 4.4 27.0 1.0 SD A:MET355 4.6 28.3 1.0 CD2 A:TRP302 4.7 30.2 1.0 C A:GLY301 4.7 29.1 1.0 CE A:LYS358 4.7 26.6 1.0 N A:TRP302 4.7 27.7 1.0 NZ A:LYS358 4.8 29.5 1.0 CB A:ASP697 4.8 30.5 1.0 N A:GLY301 4.8 29.7 1.0 O A:PHE356 4.9 29.9 1.0 O A:ASP697 4.9 33.1 1.0

Chlorine binding site 4 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl925 b:73.9 occ:1.00 O A:HOH1069 2.9 42.5 1.0 O A:HOH1184 3.3 38.7 1.0 N A:PHE775 3.7 34.0 1.0 O A:HOH1362 4.0 40.4 1.0 O A:PHE775 4.0 40.7 1.0 ND1 A:HIS774 4.0 43.5 1.0 CB A:PHE775 4.2 36.9 1.0 CA A:PHE775 4.4 37.4 1.0 CD2 A:PHE775 4.4 38.6 1.0 NH2 A:ARG626 4.4 36.2 0.5 CA A:HIS774 4.5 39.8 1.0 O A:HOH1168 4.5 41.5 1.0 C A:HIS774 4.6 38.5 1.0 CE1 A:HIS774 4.6 49.8 1.0 C A:PHE775 4.6 39.9 1.0 O A:VAL773 4.7 40.0 1.0 CG A:PHE775 4.8 38.5 1.0 O A:HOH1222 4.8 37.3 1.0 CZ A:ARG626 4.9 35.6 0.5 CG A:HIS774 4.9 44.2 1.0 NH1 A:ARG626 5.0 33.0 0.5

Chlorine binding site 5 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl926 b:76.0 occ:1.00 O A:HOH1027 3.4 54.1 1.0 O A:ALA315 3.5 36.4 1.0 N A:GLY317 3.7 53.8 1.0 CA A:ALA256 3.8 32.7 1.0 N A:GLU257 3.9 34.1 1.0 C A:ALA256 3.9 28.9 1.0 N A:ALA256 4.1 31.0 1.0 CA A:CYS316 4.2 43.8 1.0 O A:PRO255 4.2 32.4 1.0 C A:PRO255 4.3 33.5 1.0 C A:ALA315 4.4 36.8 1.0 C A:CYS316 4.5 47.9 1.0 CB A:GLU257 4.5 37.5 1.0 CA A:GLY317 4.6 54.4 1.0 O A:ALA256 4.6 30.9 1.0 N A:CYS316 4.7 38.7 1.0 CA A:GLU257 4.8 33.7 1.0

Chlorine binding site 6 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl927 b:72.1 occ:1.00 O A:HOH1413 3.3 44.3 1.0 NE2 A:GLN577 3.8 52.8 1.0 CG A:GLN577 4.4 47.6 1.0 CD A:GLN577 4.5 50.8 1.0

Chlorine binding site 7 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl923 b:62.9 occ:1.00 N B:TYR509 3.2 28.4 1.0 O B:TYR509 3.6 27.3 1.0 CD1 B:PHE508 3.7 32.6 1.0 CA B:PHE508 3.7 29.7 1.0 C B:PHE508 4.0 31.3 1.0 CA B:TYR509 4.2 28.8 1.0 CG B:PHE508 4.3 32.1 1.0 CE1 B:PHE508 4.3 32.4 1.0 C B:TYR509 4.3 27.9 1.0 CB B:TYR509 4.4 28.6 1.0 CB B:PHE508 4.4 32.6 1.0 O B:HOH1293 4.4 45.0 1.0 O B:HOH1401 4.5 47.4 1.0 O B:HOH1374 4.5 56.7 1.0 O B:ARG507 4.5 29.8 1.0 O B:HOH1096 4.6 32.9 1.0 N B:PHE508 4.8 30.6 1.0

Chlorine binding site 8 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl924 b:67.7 occ:1.00 N B:MET76 3.3 42.3 1.0 CA B:GLY75 3.8 40.8 1.0 CB B:MET76 4.0 46.0 1.0 OD1 B:ASN77 4.1 39.1 1.0 C B:GLY75 4.1 42.5 1.0 CA B:MET76 4.2 43.8 1.0 CG B:MET76 4.2 51.3 1.0 CD2 B:TYR74 4.6 50.1 1.0 C B:MET76 4.7 40.7 1.0 O B:TYR74 4.7 39.6 1.0 CE2 B:TYR74 4.7 50.3 1.0 N B:ASN77 4.8 37.2 1.0 N B:GLY75 4.8 42.8 1.0 CG B:ASN77 4.9 39.3 1.0

Chlorine binding site 9 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl925 b:46.8 occ:1.00 N B:THR477 3.5 48.5 1.0 CG2 B:THR477 3.7 42.0 1.0 CD1 B:PHE476 3.8 45.1 1.0 CA B:PHE476 3.8 46.9 1.0 CG2 B:VAL480 3.8 41.7 1.0 CB B:VAL480 4.1 40.2 1.0 CB B:PHE476 4.1 47.4 1.0 OG1 B:THR477 4.1 43.7 1.0 C B:PHE476 4.2 46.7 1.0 CB B:PHE172 4.2 37.6 1.0 CG1 B:VAL480 4.2 41.2 1.0 CB B:THR477 4.3 46.0 1.0 CG B:PHE476 4.5 43.3 1.0 CA B:THR477 4.5 47.6 1.0 CE1 B:PHE476 4.8 44.4 1.0 O B:LYS475 4.8 41.8 1.0 O B:GLY171 4.9 50.2 1.0 CG B:PHE172 4.9 38.6 1.0 O B:HOH1268 5.0 37.0 1.0

Chlorine binding site 10 out of 14 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl926 b:49.7 occ:1.00 O B:HOH1384 2.7 45.4 1.0 N B:ILE578 3.2 37.1 1.0 CA B:GLN577 3.6 38.2 1.0 O B:HOH1337 3.7 48.5 1.0 CB B:GLN577 3.8 41.3 1.0 CG1 B:ILE578 3.8 45.3 1.0 C B:GLN577 3.9 39.3 1.0 CB B:ILE578 4.2 44.8 1.0 CA B:ILE578 4.3 43.5 1.0 CD1 B:ILE578 4.3 47.6 1.0 CD1 B:PHE610 4.4 33.5 1.0 CG B:GLN577 4.6 38.0 1.0 O B:HOH1180 4.7 44.5 1.0 CB B:PHE610 4.7 32.2 1.0 O B:TYR576 4.8 40.1 1.0 N B:GLN577 4.9 41.1 1.0 CA B:PHE610 5.0 32.9 1.0

N.G.S.Mcgregor, C.L.Kuo, T.J.M.Beenakker, C.S.Wong, W.A.Offen, Z.Armstrong, B.I.Florea, J.D.C.Codee, H.S.Overkleeft, J.M.F.G.Aerts, G.J.Davies. Synthesis of Broad-Specificity Activity-Based Probes For Exo -Beta-Mannosidases. Org.Biomol.Chem. V. 20 877 2022.
ISSN: ESSN 1477-0539
PubMed: 35015006
DOI: 10.1039/D1OB02287C