Zinc in PDB 6rpc: Golgi Alpha-Mannosidase II

All present enzymatic activity of Golgi Alpha-Mannosidase II:
3.2.1.114;

The structure of Golgi Alpha-Mannosidase II, PDB code: 6rpc was solved by Z.Armstrong, D.Lahav, R.Johnson, C.L.Kuo, T.J.M.Beenakker, C.De Boer, C.S.Wong, M.Debets, M.Van Der Stelt, J.D.C.Codee, J.M.F.G.Aerts, L.Wu, H.S.Overkleeft, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.66 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.525, 90.939, 84.249, 90.00, 101.63, 90.00
R / Rfree (%)	16.3 / 19.6

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II (pdb code 6rpc). 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, PDB code: 6rpc:

Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1109 b:23.6 occ:1.00 O A:HOH1352 2.0 28.3 1.0 OD2 A:ASP204 2.1 20.5 1.0 NE2 A:HIS471 2.1 20.3 1.0 NE2 A:HIS90 2.1 22.2 1.0 OD1 A:ASP92 2.2 23.0 1.0 CE1 A:HIS471 3.1 20.9 1.0 CG A:ASP92 3.1 23.8 1.0 CD2 A:HIS90 3.1 23.5 1.0 CD2 A:HIS471 3.1 20.4 1.0 CG A:ASP204 3.1 22.6 1.0 CE1 A:HIS90 3.2 21.6 1.0 OD2 A:ASP92 3.4 26.3 1.0 CB A:ASP204 3.5 21.2 1.0 O A:HOH1201 3.9 32.2 1.0 O A:HOH1610 4.0 46.8 1.0 OD2 A:ASP472 4.1 22.3 1.0 ND1 A:HIS471 4.3 20.4 1.0 OD1 A:ASP204 4.3 22.4 1.0 ND1 A:HIS90 4.3 21.5 1.0 CG A:HIS471 4.3 18.9 1.0 CG A:HIS90 4.3 24.5 1.0 CE1 A:HIS470 4.4 21.3 1.0 O A:HOH1474 4.5 22.4 1.0 CB A:ASP92 4.5 23.3 1.0 O1 A:EDO1107 4.6 32.1 1.0 OH A:TYR269 4.8 22.8 1.0 O A:HOH1250 5.0 26.3 1.0 CA A:ASP204 5.0 20.1 1.0

Z.Armstrong, D.Lahav, R.Johnson, C.L.Kuo, T.J.M.Beenakker, C.De Boer, C.S.Wong, M.Debets, M.Van Der Stelt, J.D.C.Codee, J.M.F.G.Aerts, L.Wu, H.S.Overkleeft, G.J.Davies. Manno-Configured Epi-Cyclophellitol Aziridine Based Fluorescence Polarization Activity-Based Protein Profiling Identifies New Golgi A-Mannosidase Inhibitors To Be Published.