Zinc in PDB 1r34: Golgi Alpha-Mannosidase II Complex with 5-Thio-D- Mannopyranosylamidinium Salt

All present enzymatic activity of Golgi Alpha-Mannosidase II Complex with 5-Thio-D- Mannopyranosylamidinium Salt:
3.2.1.114;

The structure of Golgi Alpha-Mannosidase II Complex with 5-Thio-D- Mannopyranosylamidinium Salt, PDB code: 1r34 was solved by D.A.Kuntz, W.Xin, L.M.Kavelekar, D.R.Rose, B.M.Pinto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.25 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.774, 109.568, 138.737, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.6

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II Complex with 5-Thio-D- Mannopyranosylamidinium Salt (pdb code 1r34). 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 Complex with 5-Thio-D- Mannopyranosylamidinium Salt, PDB code: 1r34:

Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II Complex with 5-Thio-D- Mannopyranosylamidinium Salt


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 Complex with 5-Thio-D- Mannopyranosylamidinium Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:12.2 occ:1.00 NE2 A:HIS90 2.1 5.3 1.0 OD1 A:ASP92 2.1 11.1 1.0 NE2 A:HIS471 2.2 6.2 1.0 OD1 A:ASP204 2.2 8.0 1.0 O3 A:LKS1102 2.3 15.6 1.0 O2 A:LKS1102 2.4 20.8 1.0 CD2 A:HIS90 3.0 4.7 1.0 CD2 A:HIS471 3.0 7.0 1.0 C2 A:LKS1102 3.0 23.4 1.0 CG A:ASP92 3.0 9.5 1.0 CE1 A:HIS90 3.2 5.6 1.0 OD2 A:ASP92 3.2 11.4 1.0 C3 A:LKS1102 3.2 19.1 1.0 CE1 A:HIS471 3.2 5.1 1.0 CG A:ASP204 3.3 11.9 1.0 CB A:ASP204 3.7 8.1 1.0 OD2 A:ASP472 4.0 7.6 1.0 C4 A:LKS1102 4.1 20.1 1.0 C1 A:LKS1102 4.1 24.1 1.0 CG A:HIS90 4.2 3.9 1.0 CG A:HIS471 4.2 7.0 1.0 ND1 A:HIS90 4.2 8.1 1.0 ND1 A:HIS471 4.3 6.1 1.0 CE1 A:HIS470 4.3 7.9 1.0 OD2 A:ASP204 4.3 12.7 1.0 O A:HOH1552 4.4 10.6 1.0 CB A:ASP92 4.4 6.9 1.0 OH A:TYR269 4.6 14.6 1.0 N1 A:LKS1102 4.8 28.8 1.0 NE2 A:HIS470 4.9 5.9 1.0 O4 A:LKS1102 4.9 15.9 1.0 CA A:ASP92 5.0 10.1 1.0 CG A:ASP472 5.0 6.5 1.0

L.M.Kavelekar, D.A.Kuntz, W.Xin, B.D.Johnston, B.Svensson, D.R.Rose, B.M.Pinto. 5-Thio-D-Glycopyranosylamines and Their Amidinium Salts As Potential Transition-State Mimics of Glycosyl Hydrolases: Synthesis, Enzyme Inhibitory Activities, X-Ray Crystallography, and Molecular Modeling Tetrahedron Asymmetry V. 16 1035 2005.
ISSN: ISSN 0957-4166
DOI: 10.1016/J.TETASY.2005.01.021