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Zinc in PDB 6rry: Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol, PDB code: 6rry was solved by Z.Armstrong, D.Lahav, R.Johnson, C.L.Kuo, T.J.M.Beenakker, C.De Boer, C.S.Wong, E.R.Van Rijssel, M.Debets, P.P.Geurink, H.Ovaa, M.Van Derstelt, 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) 74.31 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.473, 90.366, 132.772, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol (pdb code 6rry). 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 in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol, PDB code: 6rry:

Zinc binding site 1 out of 1 in 6rry

Go back to Zinc Binding Sites List in 6rry
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol


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 in Complex with (2S,3R)-2-(Hydroxymethyl)- 1,2,3,6-Tetrahydro-3-Pyridinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1106

b:25.2
occ:1.00
 OD2 A:ASP204 1.9 24.3 1.0
OD1 A:ASP92 2.0 25.3 1.0
NE2 A:HIS90 2.0 22.1 1.0
NE2 A:HIS471 2.1 20.6 1.0
O1 A:KGE1102 2.1 31.0 1.0
CG A:ASP92 2.9 29.3 1.0
CG A:ASP204 3.0 24.2 1.0
CE1 A:HIS90 3.0 24.6 1.0
CD2 A:HIS471 3.0 21.8 1.0
CD2 A:HIS90 3.1 23.6 1.0
OD2 A:ASP92 3.1 28.1 1.0
CE1 A:HIS471 3.1 20.9 1.0
C1 A:KGE1102 3.2 39.6 1.0
CB A:ASP204 3.4 23.6 1.0
C2 A:KGE1102 4.0 38.0 1.0
N1 A:KGE1102 4.0 43.8 1.0
OD2 A:ASP472 4.1 25.3 1.0
ND1 A:HIS90 4.1 22.8 1.0
OD1 A:ASP204 4.1 23.6 1.0
CG A:HIS471 4.2 23.5 1.0
CG A:HIS90 4.2 25.2 1.0
ND1 A:HIS471 4.2 21.9 1.0
CB A:ASP92 4.3 26.8 1.0
CE1 A:HIS470 4.3 23.5 1.0
O A:HOH1333 4.4 25.7 1.0
C6 A:KGE1102 4.5 40.3 1.0
CA A:ASP204 4.8 23.8 1.0
CA A:ASP92 4.9 26.7 1.0
OH A:TYR269 4.9 26.4 1.0
NE2 A:HIS470 5.0 23.4 1.0

Reference:

Z.Armstrong, D.Lahav, R.Johnson, C.L.Kuo, T.J.M.Beenakker, C.De Boer, C.S.Wong, E.R.Van Rijssel, M.Debets, P.P.Geurink, H.Ovaa, 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.
Page generated: Tue Oct 29 06:45:42 2024

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