Zinc in PDB 3bub: Golgi Alpha-Mannosidase II with An Empty Active Site

All present enzymatic activity of Golgi Alpha-Mannosidase II with An Empty Active Site:
3.2.1.114;

The structure of Golgi Alpha-Mannosidase II with An Empty Active Site, PDB code: 3bub was solved by D.A.Kuntz, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.765, 109.624, 138.649, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II with An Empty Active Site (pdb code 3bub). 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 Alpha-Mannosidase II with An Empty Active Site, PDB code: 3bub:

Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II with An Empty Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Golgi Alpha-Mannosidase II with An Empty Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1047 b:8.2 occ:1.00 NE2 A:HIS90 2.0 6.5 1.0 NE2 A:HIS471 2.0 5.3 1.0 OD2 A:ASP204 2.1 7.8 1.0 OD1 A:ASP92 2.2 9.1 1.0 O A:HOH1051 2.3 19.9 1.0 CE1 A:HIS90 3.0 6.0 1.0 CE1 A:HIS471 3.0 5.8 1.0 CD2 A:HIS471 3.0 8.0 1.0 CD2 A:HIS90 3.0 6.9 1.0 CG A:ASP204 3.1 8.0 1.0 CG A:ASP92 3.1 8.9 1.0 OD2 A:ASP92 3.3 14.3 1.0 O A:HOH1053 3.3 22.8 1.0 CB A:ASP204 3.4 6.7 1.0 O A:HOH1054 4.0 16.9 1.0 OD2 A:ASP472 4.1 8.9 1.0 ND1 A:HIS90 4.1 6.8 1.0 ND1 A:HIS471 4.1 6.5 1.0 CG A:HIS471 4.2 5.4 1.0 CG A:HIS90 4.2 5.3 1.0 OD1 A:ASP204 4.2 8.8 1.0 CE1 A:HIS470 4.4 6.9 1.0 O A:HOH2263 4.4 9.8 1.0 CB A:ASP92 4.4 7.0 1.0 O A:HOH1055 4.8 24.5 1.0 OH A:TYR269 4.8 10.8 1.0 O A:HOH2098 4.9 33.6 1.0 CA A:ASP92 4.9 6.9 1.0 CA A:ASP204 4.9 7.0 1.0

W.Zhong, D.A.Kuntz, B.Ember, H.Singh, K.W.Moremen, D.R.Rose, G.J.Boons. Probing the Substrate Specificity of Golgi Alpha-Mannosidase II By Use of Synthetic Oligosaccharides and A Catalytic Nucleophile Mutant. J.Am.Chem.Soc. V. 130 8975 2008.
ISSN: ISSN 0002-7863
PubMed: 18558690
DOI: 10.1021/JA711248Y