Zinc in PDB 6b9o: Structure of Gh 38 Jack Bean Alpha-Mannosidase

All present enzymatic activity of Structure of Gh 38 Jack Bean Alpha-Mannosidase:
3.2.1.24;

The structure of Structure of Gh 38 Jack Bean Alpha-Mannosidase, PDB code: 6b9o 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)	49.55 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.305, 119.667, 277.689, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.6

The binding sites of Zinc atom in the Structure of Gh 38 Jack Bean Alpha-Mannosidase (pdb code 6b9o). 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, PDB code: 6b9o:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.4 occ:1.00 OD1 A:ASP25 2.0 17.6 1.0 NE2 A:HIS23 2.0 14.5 1.0 NE2 A:HIS386 2.1 16.6 1.0 OD2 A:ASP145 2.1 18.4 1.0 O A:HOH1295 2.3 18.5 1.0 CG A:ASP25 2.9 16.5 1.0 CE1 A:HIS23 3.0 14.6 1.0 CE1 A:HIS386 3.0 14.1 1.0 CD2 A:HIS386 3.1 17.1 1.0 CD2 A:HIS23 3.1 12.1 1.0 CG A:ASP145 3.1 19.9 1.0 OD2 A:ASP25 3.2 18.7 1.0 CB A:ASP145 3.4 12.7 1.0 ND1 A:HIS23 4.1 10.7 1.0 ND1 A:HIS386 4.1 16.0 1.0 OD2 A:ASP387 4.1 20.3 1.0 CG A:HIS386 4.2 13.7 1.0 CG A:HIS23 4.2 13.2 1.0 OD1 A:ASP145 4.3 17.1 1.0 CB A:ASP25 4.3 14.3 1.0 CE1 A:HIS385 4.4 18.5 1.0 OH A:TYR210 4.6 18.2 1.0 O A:HOH1258 4.8 18.7 1.0 CA A:ASP25 4.8 14.5 1.0 O A:HOH1857 4.8 29.4 1.0 CA A:ASP145 4.9 14.6 1.0 NE2 A:HIS385 5.0 17.0 1.0

Zinc binding site 2 out of 2 in the Structure of Gh 38 Jack Bean Alpha-Mannosidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:17.9 occ:1.00 OD1 B:ASP25 2.0 19.3 1.0 OD2 B:ASP145 2.0 17.9 1.0 NE2 B:HIS386 2.1 16.8 1.0 NE2 B:HIS23 2.1 16.0 1.0 O B:HOH1188 2.4 21.6 1.0 CG B:ASP25 3.0 17.3 1.0 CG B:ASP145 3.0 18.8 1.0 CD2 B:HIS23 3.0 14.4 1.0 CD2 B:HIS386 3.0 16.3 1.0 CE1 B:HIS386 3.1 14.2 1.0 CE1 B:HIS23 3.1 17.7 1.0 OD2 B:ASP25 3.3 20.1 1.0 O B:HOH1632 3.3 31.5 1.0 CB B:ASP145 3.3 13.5 1.0 OD2 B:ASP387 4.1 20.6 1.0 OD1 B:ASP145 4.2 17.1 1.0 ND1 B:HIS386 4.2 18.8 1.0 ND1 B:HIS23 4.2 15.5 1.0 CG B:HIS23 4.2 15.8 1.0 CG B:HIS386 4.2 17.3 1.0 CB B:ASP25 4.3 14.3 1.0 CE1 B:HIS385 4.4 16.7 1.0 OH B:TYR210 4.7 17.5 1.0 O B:HOH1247 4.8 17.8 1.0 CA B:ASP25 4.8 14.6 1.0 CA B:ASP145 4.8 15.6 1.0 O B:HOH1597 4.9 44.0 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