Zinc in PDB 3d4y: Golgi Mannosidase II Complex with Mannoimidazole

All present enzymatic activity of Golgi Mannosidase II Complex with Mannoimidazole:
3.2.1.114;

The structure of Golgi Mannosidase II Complex with Mannoimidazole, PDB code: 3d4y was solved by D.A.Kuntz, C.A.Tarling, S.G.Withers, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.634, 108.798, 137.035, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20.8

The binding sites of Zinc atom in the Golgi Mannosidase II Complex with Mannoimidazole (pdb code 3d4y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Golgi Mannosidase II Complex with Mannoimidazole, PDB code: 3d4y:

Zinc binding site 1 out of 1 in the Golgi Mannosidase II Complex with Mannoimidazole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Golgi Mannosidase II Complex with Mannoimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1047 b:20.7 occ:1.00 O2 A:MVL1049 2.1 29.2 1.0 NE2 A:HIS90 2.1 19.1 1.0 NE2 A:HIS471 2.1 17.2 1.0 OD2 A:ASP204 2.2 21.6 1.0 OD1 A:ASP92 2.2 20.6 1.0 O3 A:MVL1049 2.2 18.2 1.0 CD2 A:HIS471 3.0 17.6 1.0 CE1 A:HIS90 3.1 17.4 1.0 CG A:ASP92 3.1 19.9 1.0 CD2 A:HIS90 3.1 21.2 1.0 C2 A:MVL1049 3.1 23.6 1.0 C3 A:MVL1049 3.1 18.9 1.0 CE1 A:HIS471 3.1 19.1 1.0 CG A:ASP204 3.2 22.3 1.0 OD2 A:ASP92 3.3 23.1 1.0 CB A:ASP204 3.6 19.1 1.0 C4 A:MVL1049 4.0 18.8 1.0 OD2 A:ASP472 4.1 19.3 1.0 ND1 A:HIS90 4.2 19.3 1.0 CG A:HIS90 4.2 18.6 1.0 CG A:HIS471 4.2 17.1 1.0 ND1 A:HIS471 4.2 17.1 1.0 OD1 A:ASP204 4.3 24.0 1.0 C1 A:MVL1049 4.4 26.6 1.0 CE1 A:HIS470 4.4 18.6 1.0 CB A:ASP92 4.4 18.0 1.0 O A:HOH1846 4.6 21.0 1.0 OH A:TYR269 4.8 25.2 1.0 O4 A:MVL1049 4.8 19.3 1.0 CA A:ASP92 5.0 17.3 1.0

D.A.Kuntz, C.A.Tarling, S.G.Withers, D.R.Rose. Structural Analysis of Golgi Alpha-Mannosidase II Inhibitors Identified From A Focused Glycosidase Inhibitor Screen. Biochemistry V. 47 10058 2008.
ISSN: ISSN 0006-2960
PubMed: 18759458
DOI: 10.1021/BI8010785