Zinc in PDB 6b9p: Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor

All present enzymatic activity of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor:
3.2.1.24;

The structure of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor, PDB code: 6b9p was solved by E.Howard, A.Cousido-Siah, M.Lepage, A.Bodlenner, A.Mitschler, A.Meli, F.Dericcardis, I.Izzo, A.Podjarny, P.Compain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.26 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.274, 119.761, 277.050, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.5

The binding sites of Zinc atom in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor (pdb code 6b9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor, PDB code: 6b9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:18.3 occ:1.00 NE2 A:HIS386 2.1 18.6 1.0 NE2 A:HIS23 2.1 18.1 1.0 OD1 A:ASP25 2.1 18.7 1.0 OD2 A:ASP145 2.1 22.1 1.0 O3A A:D0J1001 2.3 18.3 1.0 O2A A:D0J1001 2.3 19.2 1.0 C2A A:D0J1001 2.9 21.0 1.0 CE1 A:HIS23 3.0 20.6 1.0 CE1 A:HIS386 3.1 17.1 1.0 CD2 A:HIS386 3.1 18.9 1.0 CD2 A:HIS23 3.1 15.5 1.0 C3A A:D0J1001 3.1 18.0 1.0 CG A:ASP25 3.1 19.3 1.0 CG A:ASP145 3.1 21.4 1.0 OD2 A:ASP25 3.4 18.1 1.0 CB A:ASP145 3.5 20.0 1.0 OD2 A:ASP387 4.1 18.2 1.0 ND1 A:HIS23 4.2 17.2 1.0 ND1 A:HIS386 4.2 19.5 1.0 CG A:HIS386 4.2 19.2 1.0 CG A:HIS23 4.2 18.6 1.0 OD1 A:ASP145 4.2 18.9 1.0 C4A A:D0J1001 4.3 20.5 1.0 C1A A:D0J1001 4.4 20.4 1.0 CB A:ASP25 4.5 16.3 1.0 OH A:TYR210 4.6 18.6 1.0 CE1 A:HIS385 4.6 19.0 1.0 CA A:ASP25 4.9 14.2 1.0

Zinc binding site 2 out of 2 in the Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Gh 38 Jack Bean Alpha-Mannosidase in Complex with A 36- Valent Iminosugar Cluster Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:20.9 occ:1.00 OD2 B:ASP145 2.0 20.5 1.0 NE2 B:HIS386 2.1 21.8 1.0 OD1 B:ASP25 2.1 21.1 1.0 NE2 B:HIS23 2.1 21.8 1.0 O3A B:D0J1001 2.3 20.2 1.0 O2A B:D0J1001 2.3 22.3 1.0 C2A B:D0J1001 2.9 19.6 1.0 CD2 B:HIS386 3.0 21.8 1.0 CG B:ASP145 3.0 19.6 1.0 CG B:ASP25 3.1 23.5 1.0 CD2 B:HIS23 3.1 21.7 1.0 C3A B:D0J1001 3.1 21.2 1.0 CE1 B:HIS23 3.1 23.9 1.0 CE1 B:HIS386 3.1 17.5 1.0 OD2 B:ASP25 3.3 22.4 1.0 CB B:ASP145 3.5 20.9 1.0 OD1 B:ASP145 4.1 17.9 1.0 OD2 B:ASP387 4.1 20.8 1.0 CG B:HIS386 4.2 21.2 1.0 ND1 B:HIS386 4.2 19.8 1.0 ND1 B:HIS23 4.2 19.7 1.0 CG B:HIS23 4.2 21.2 1.0 C4A B:D0J1001 4.2 23.6 1.0 C1A B:D0J1001 4.4 21.8 1.0 CB B:ASP25 4.4 19.9 1.0 CE1 B:HIS385 4.5 20.3 1.0 OH B:TYR210 4.7 22.0 1.0 CA B:ASP25 4.9 19.5 1.0 O B:HOH1253 5.0 20.8 1.0

E.Howard, A.Cousido-Siah, M.L.Lepage, J.P.Schneider, A.Bodlenner, A.Mitschler, A.Meli, I.Izzo, H.A.Alvarez, A.Podjarny, P.Compain. Structural Basis of Outstanding Multivalent Effects in Jack Bean Alpha-Mannosidase Inhibition. Angew. Chem. Int. Ed. Engl. V. 57 8002 2018.
ISSN: ESSN 1521-3773
PubMed: 29722924
DOI: 10.1002/ANIE.201801202