Zinc in PDB 3bud: Golgi Mannosidase II D204A Catalytic Nucleophile Mutant with An Empty Active Site

All present enzymatic activity of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant with An Empty Active Site:
3.2.1.114;

The structure of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant with An Empty Active Site, PDB code: 3bud 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)	19.98 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.903, 109.478, 138.501, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.2

The binding sites of Zinc atom in the Golgi Mannosidase II D204A Catalytic Nucleophile Mutant with An Empty Active Site (pdb code 3bud). 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 D204A Catalytic Nucleophile Mutant with An Empty Active Site, PDB code: 3bud:

Zinc binding site 1 out of 1 in the Golgi Mannosidase II D204A Catalytic Nucleophile Mutant 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 Mannosidase II D204A Catalytic Nucleophile Mutant with An Empty Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1048 b:14.3 occ:1.00 OD1 A:ASP92 2.0 13.2 1.0 NE2 A:HIS90 2.1 8.6 1.0 NE2 A:HIS471 2.1 10.6 1.0 O A:HOH1052 2.2 16.7 1.0 O A:HOH1053 2.4 15.6 1.0 CG A:ASP92 2.8 12.1 1.0 CD2 A:HIS90 2.9 7.9 1.0 OD2 A:ASP92 3.0 14.7 1.0 CD2 A:HIS471 3.1 11.0 1.0 CE1 A:HIS90 3.1 8.9 1.0 CE1 A:HIS471 3.1 10.1 1.0 O A:HOH1054 3.8 26.1 1.0 CB A:ALA204 3.8 10.5 1.0 OD2 A:ASP472 3.9 10.1 1.0 CG A:HIS90 4.1 8.9 1.0 ND1 A:HIS90 4.2 11.6 1.0 CB A:ASP92 4.2 10.3 1.0 CG A:HIS471 4.2 9.2 1.0 ND1 A:HIS471 4.2 8.4 1.0 CE1 A:HIS470 4.3 9.9 1.0 O A:HOH1056 4.4 24.8 1.0 O A:HOH1375 4.5 10.2 1.0 OH A:TYR269 4.6 12.7 1.0 CA A:ASP92 4.8 11.6 1.0 NE2 A:HIS470 4.9 9.4 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