Sodium 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:

Chlorine	(Cl)	14 atoms
Bromine	(Br)	10 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine, PDB code: 7op6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na928 b:33.3 occ:1.00 OE1 A:GLU112 2.7 29.9 1.0 O A:HOH1372 2.8 31.2 1.0 O A:HOH1036 2.8 28.5 1.0 O A:HOH1278 3.0 23.8 1.0 ND2 A:ASN403 3.5 27.7 1.0 CD A:GLU112 3.6 27.8 1.0 CG A:GLU112 3.7 26.1 1.0 CB A:GLU112 3.9 25.5 1.0 OH A:TYR443 4.0 24.2 1.0 CD A:ARG447 4.2 21.3 1.0 CG A:ASN403 4.3 25.8 1.0 CD A:ARG211 4.4 27.2 1.0 O A:HOH1083 4.4 39.1 1.0 NH1 A:ARG211 4.4 24.7 1.0 OD1 A:ASN403 4.5 21.5 1.0 OE2 A:GLU112 4.7 33.1 1.0 O A:HOH1189 4.7 35.5 1.0 NH1 A:ARG447 4.8 23.1 1.0 CA A:GLU112 4.8 25.5 1.0 O A:GLU112 4.9 24.3 1.0 NE A:ARG447 4.9 21.6 1.0 O A:HOH1369 4.9 41.3 1.0 BR A:BR902 5.0 39.7 0.5

Sodium binding site 2 out of 3 in the Bacteroides Thetaiotaomicron Mannosidase GH2 with Beta-Manno- Configured Cyclophellitol Aziridine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na929 b:47.2 occ:1.00 O A:HOH1246 2.7 39.7 1.0 OD1 A:ASP697 2.8 37.8 1.0 NE A:ARG633 3.4 30.4 1.0 CG A:ASP697 3.6 32.5 1.0 CG2 A:ILE695 3.7 31.9 1.0 CG A:PHE356 3.7 25.2 1.0 OD2 A:ASP697 3.8 40.8 1.0 CB A:ARG633 3.8 30.9 1.0 CG A:ARG633 3.9 30.9 1.0 NH2 A:ARG633 3.9 27.9 1.0 CB A:PHE356 4.0 27.1 1.0 NH1 A:ARG636 4.0 38.1 1.0 CD1 A:PHE356 4.0 26.5 1.0 CD2 A:PHE356 4.1 26.0 1.0 CZ A:ARG633 4.1 31.4 1.0 CA A:ARG633 4.2 29.5 1.0 O A:ARG633 4.2 27.2 1.0 CD A:ARG633 4.2 29.6 1.0 CD A:ARG636 4.4 34.5 1.0 CE1 A:PHE356 4.6 26.2 1.0 C A:ARG633 4.6 30.2 1.0 CE2 A:PHE356 4.7 25.3 1.0 O A:SER696 4.7 33.5 1.0 CB A:ARG636 4.9 31.8 1.0 CZ A:PHE356 4.9 25.8 1.0 CZ A:ARG636 5.0 37.5 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 B:Na931 b:55.8 occ:1.00 OE1 B:GLN768 3.0 48.5 1.0 O B:HOH1308 3.6 19.2 0.5 CA B:ALA770 3.6 40.9 1.0 CG B:GLN768 3.8 51.7 1.0 CD B:GLN768 3.8 50.2 1.0 N B:ALA770 3.8 42.6 1.0 O B:VAL769 3.9 44.7 1.0 C B:ALA770 3.9 38.0 1.0 C B:VAL769 3.9 47.0 1.0 N B:GLU771 4.0 37.4 1.0 CG B:GLU771 4.4 52.3 1.0 O B:GLN768 4.6 51.2 1.0 OE2 B:GLU771 4.6 66.0 1.0 O B:ALA770 4.6 34.5 1.0 C B:GLN768 4.8 51.5 1.0 CA B:VAL769 4.8 50.1 1.0 CD B:GLU771 4.8 62.5 1.0 N B:VAL769 4.8 48.9 1.0 CB B:GLU771 4.9 47.3 1.0 CB B:GLN768 5.0 50.8 1.0 CB B:ALA770 5.0 39.0 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