Bromine in PDB 7op7: Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine

The structure of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine, PDB code: 7op7 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)	67.66 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.761, 114.707, 98.639, 90, 112.89, 90
R / Rfree (%)	18.9 / 24.4

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

Chlorine

(Cl)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Bromine atom in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine (pdb code 7op7). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 13 binding sites of Bromine where determined in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine, PDB code: 7op7:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br912 b:41.2 occ:1.00 O A:HOH1139 3.2 27.0 1.0 NE2 A:GLN108 3.4 40.3 1.0 CB A:PRO140 3.8 41.5 1.0 N A:PRO140 3.9 33.8 1.0 CD A:PRO140 4.0 36.4 1.0 CA A:PRO140 4.0 33.2 1.0 ND2 A:ASN247 4.1 35.0 1.0 CB A:GLN108 4.1 36.0 1.0 CG2 A:THR138 4.2 33.6 1.0 CG A:PRO140 4.3 41.4 1.0 C A:LEU139 4.4 33.2 1.0 CD A:GLN108 4.5 40.4 1.0 O A:LEU139 4.6 31.3 1.0 OH A:TYR218 4.6 31.2 1.0 O A:HOH1046 4.7 30.8 1.0 CD1 A:ILE249 4.7 46.0 1.0 CG A:GLN108 4.7 43.0 1.0 O A:THR138 4.8 26.6 1.0 C A:THR138 4.9 30.4 1.0 N A:LEU139 5.0 29.7 1.0

Bromine binding site 2 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br913 b:35.7 occ:1.00 O A:HOH1298 3.2 39.4 1.0 O A:HOH1139 3.3 27.0 1.0 N A:ILE107 3.5 28.7 1.0 O A:ILE107 3.6 25.7 1.0 CB A:LYS142 3.6 27.8 1.0 N A:LYS142 3.7 24.8 1.0 CB A:PRO140 4.0 41.5 1.0 N A:VAL141 4.0 30.6 1.0 CG1 A:ILE249 4.1 41.6 1.0 CA A:GLY106 4.1 31.4 1.0 CA A:PRO140 4.1 33.2 1.0 CD1 A:ILE249 4.1 46.0 1.0 C A:PRO140 4.2 32.4 1.0 C A:ILE107 4.3 32.5 1.0 C A:GLY106 4.3 30.9 1.0 CA A:LYS142 4.3 30.2 1.0 CA A:ILE107 4.5 30.4 1.0 C A:VAL141 4.8 24.4 1.0 CG A:LYS142 4.9 29.0 1.0 OH A:TYR218 5.0 31.2 1.0 CD A:LYS142 5.0 27.4 1.0 O A:ASP105 5.0 26.4 1.0

Bromine binding site 3 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br914 b:48.4 occ:0.80 N A:ASP688 3.4 48.5 1.0 NE2 A:GLN685 3.5 47.8 1.0 N A:ASN687 3.6 55.2 1.0 CG A:GLN685 3.6 51.9 1.0 C A:GLN686 4.0 52.5 1.0 CA A:ASP688 4.0 54.1 1.0 CD A:GLN685 4.1 49.2 1.0 CA A:GLN686 4.2 47.2 1.0 O A:GLN685 4.3 42.0 1.0 C A:ASN687 4.4 50.8 1.0 CA A:ASN687 4.4 60.0 1.0 C A:GLN685 4.4 43.3 1.0 N A:GLN686 4.4 44.2 1.0 O A:GLN686 4.7 51.1 1.0 CB A:GLN685 4.9 48.2 1.0 N A:SER689 5.0 49.9 1.0

Bromine binding site 4 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br915 b:30.2 occ:1.00 N A:HIS284 3.2 29.1 1.0 O A:HOH1304 3.5 35.9 1.0 CA A:ASN283 3.8 32.4 1.0 O A:HIS284 3.9 34.2 1.0 C A:ASN283 4.0 30.7 1.0 CA A:HIS284 4.2 30.5 1.0 CB A:HIS284 4.3 32.9 1.0 CD2 A:HIS284 4.3 40.0 1.0 O A:ILE282 4.5 24.2 1.0 CB A:ASN283 4.5 31.2 1.0 C A:HIS284 4.6 34.1 1.0 OD1 A:ASN283 4.6 26.5 1.0 CG A:HIS284 4.7 39.8 1.0 N A:ASN283 4.9 27.6 1.0 CG A:ASN283 4.9 31.6 1.0

Bromine binding site 5 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br916 b:45.2 occ:1.00 O A:HOH1338 3.2 26.2 1.0 O A:HOH1024 3.7 50.1 1.0 CE2 A:TYR509 3.8 29.9 1.0 O A:PHE492 4.0 32.6 1.0 CA A:ARG493 4.0 30.4 1.0 CB A:HIS511 4.0 27.1 1.0 CG A:PRO497 4.0 24.7 1.0 CB A:PRO497 4.1 25.0 1.0 CD2 A:TYR509 4.1 27.5 1.0 O A:ARG493 4.4 28.3 1.0 CB A:ARG493 4.4 35.5 1.0 C A:ARG493 4.6 30.4 1.0 CG A:ARG493 4.7 38.8 1.0 N A:HIS511 4.7 25.0 1.0 CG A:HIS511 4.8 32.9 1.0 CD2 A:HIS511 4.8 36.4 1.0 CA A:HIS511 4.8 27.6 1.0 C A:PHE492 4.9 30.2 1.0 N A:ARG493 4.9 30.1 1.0 CD A:PRO497 5.0 22.6 1.0

Bromine binding site 6 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br917 b:58.6 occ:1.00 N A:THR477 3.4 40.7 1.0 CG2 A:VAL480 3.6 41.8 1.0 CA A:PHE476 3.6 53.8 1.0 CD1 A:PHE476 3.8 44.3 1.0 CG2 A:THR477 3.9 46.9 1.0 C A:PHE476 4.0 47.1 1.0 CB A:PHE476 4.0 47.6 1.0 CB A:VAL480 4.1 37.7 1.0 CB A:PHE172 4.1 36.8 1.0 OG1 A:THR477 4.2 44.8 1.0 CG1 A:VAL480 4.3 39.2 1.0 CG A:PHE476 4.4 52.3 1.0 CB A:THR477 4.4 46.0 1.0 CA A:THR477 4.5 42.7 1.0 O A:LYS475 4.6 57.1 1.0 CG A:PHE172 4.7 37.5 1.0 CE1 A:PHE476 4.9 54.7 1.0 N A:PHE476 4.9 52.9 1.0 O A:HOH1248 4.9 38.0 1.0 CD2 A:PHE172 5.0 32.5 1.0

Bromine binding site 7 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br918 b:49.1 occ:0.70 O A:HOH1076 3.2 29.7 1.0 O A:HOH1251 3.3 23.1 1.0 O A:HOH1229 3.5 30.3 1.0 CB A:ASN402 3.5 33.3 1.0 CD A:ARG211 3.9 26.4 1.0 CG A:ARG211 4.0 24.8 1.0 ND2 A:ASN402 4.0 41.8 1.0 O A:HOH1300 4.1 25.7 1.0 CD A:PRO212 4.1 24.1 1.0 NE A:ARG211 4.1 24.6 1.0 CG A:ASN402 4.3 37.1 1.0 O A:HOH1246 4.5 34.9 1.0 OE1 A:GLU112 4.5 26.4 1.0 CB A:ARG211 4.6 25.5 1.0 CA A:ASN402 4.7 29.1 1.0 CG A:PRO212 4.7 24.8 1.0 O A:HOH1218 4.9 22.1 1.0 CZ A:ARG211 5.0 25.7 1.0

Bromine binding site 8 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Br914 b:37.4 occ:1.00 O B:HOH1359 3.0 44.8 1.0 O B:HOH1182 3.2 31.0 1.0 O B:HOH1118 3.4 50.5 1.0 N B:ILE107 3.5 35.5 1.0 O B:ILE107 3.5 26.0 1.0 CB B:LYS142 3.6 32.8 1.0 N B:LYS142 3.8 27.3 1.0 CB B:PRO140 3.9 31.4 1.0 N B:VAL141 4.0 32.7 1.0 CA B:GLY106 4.0 35.5 1.0 CA B:PRO140 4.1 32.1 1.0 CG1 B:ILE249 4.2 43.6 1.0 CD1 B:ILE249 4.2 44.2 1.0 C B:GLY106 4.2 31.9 1.0 C B:ILE107 4.3 31.0 1.0 C B:PRO140 4.3 28.4 1.0 CA B:LYS142 4.4 32.5 1.0 CA B:ILE107 4.4 32.4 1.0 CD B:LYS142 4.8 35.2 1.0 O B:HOH1424 4.8 46.0 1.0 CG B:LYS142 4.8 38.0 1.0 C B:VAL141 4.9 28.5 1.0 O B:ASP105 5.0 32.4 1.0

Bromine binding site 9 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Br915 b:38.6 occ:0.80 O B:HOH1330 3.1 32.4 1.0 O B:HOH1339 3.1 20.5 0.5 CE2 B:TYR509 3.8 25.4 1.0 CG B:PRO497 3.9 26.8 1.0 CB B:HIS511 4.0 26.8 1.0 CD2 B:TYR509 4.1 26.7 1.0 O B:PHE492 4.1 27.9 1.0 CA B:ARG493 4.1 30.7 1.0 CB B:PRO497 4.1 27.3 1.0 O B:ARG493 4.4 32.5 1.0 CB B:ARG493 4.5 34.5 1.0 CG B:ARG493 4.5 42.4 1.0 N B:HIS511 4.6 28.2 1.0 C B:ARG493 4.7 30.5 1.0 CA B:HIS511 4.7 24.7 1.0 CG B:HIS511 4.8 26.9 1.0 CD B:PRO497 4.9 26.2 1.0 CD2 B:HIS511 5.0 34.1 1.0 C B:PHE492 5.0 28.6 1.0

Bromine binding site 10 out of 13 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured N-Alkyl Cyclophellitol Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Br916 b:57.0 occ:1.00 O B:HOH1182 3.4 31.0 1.0 NE2 B:GLN108 3.4 46.8 1.0 CG B:GLN108 3.7 42.9 1.0 CB B:PRO140 3.8 31.4 1.0 N B:PRO140 3.9 28.2 1.0 CD B:PRO140 4.0 29.0 1.0 CD B:GLN108 4.0 36.9 1.0 CA B:PRO140 4.1 32.1 1.0 CG2 B:THR138 4.1 36.9 1.0 CG B:PRO140 4.3 32.9 1.0 C B:LEU139 4.4 27.1 1.0 ND2 B:ASN247 4.5 49.7 1.0 O B:THR138 4.6 24.5 1.0 O B:HOH1040 4.9 36.7 1.0 O B:LEU139 4.9 27.4 1.0 C B:THR138 4.9 28.5 1.0 OH B:TYR218 4.9 31.1 1.0 CB B:GLN108 5.0 31.1 1.0 N B:LEU139 5.0 26.0 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