Zinc in PDB 6rrw: Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol, PDB code: 6rrw 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) 75.47 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.171, 91.671, 132.316, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol (pdb code 6rrw). 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 (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol, PDB code: 6rrw:

Zinc binding site 1 out of 1 in 6rrw

Go back to Zinc Binding Sites List in 6rrw
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol


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 (2R,3R,4R,5S)-1-(5-{[4-(3, 4-Dihydro-2H-1,5-Benzodioxepin-7-Yl)Benzyl]Oxy}Pentyl)-2- (Hydroxymethyl)-3,4,5-Piperidinetriol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:28.8
occ:1.00
OD2 A:ASP204 1.9 25.6 1.0
OD1 A:ASP92 2.1 29.9 1.0
NE2 A:HIS471 2.1 28.5 1.0
NE2 A:HIS90 2.1 30.9 1.0
O4 A:KG51101 2.4 39.6 1.0
O3 A:KG51101 2.4 36.7 1.0
CG A:ASP204 2.9 29.1 1.0
C5 A:KG51101 2.9 41.2 1.0
CD2 A:HIS471 3.0 28.5 1.0
CG A:ASP92 3.0 31.4 1.0
CE1 A:HIS90 3.1 28.9 1.0
CD2 A:HIS90 3.1 31.1 1.0
C4 A:KG51101 3.2 39.0 1.0
CE1 A:HIS471 3.2 28.2 1.0
OD2 A:ASP92 3.4 34.8 1.0
CB A:ASP204 3.5 28.9 1.0
OD2 A:ASP472 4.0 27.9 1.0
OD1 A:ASP204 4.0 23.8 1.0
CG A:HIS471 4.2 26.7 1.0
ND1 A:HIS90 4.2 28.2 1.0
ND1 A:HIS471 4.2 25.0 1.0
CG A:HIS90 4.2 27.4 1.0
C3 A:KG51101 4.3 38.2 1.0
CB A:ASP92 4.4 27.2 1.0
C6 A:KG51101 4.4 39.7 1.0
CE1 A:HIS470 4.4 28.2 1.0
O A:HOH1284 4.6 25.0 1.0
O A:HOH1226 4.8 37.0 1.0
OH A:TYR269 4.9 24.2 1.0
CA A:ASP92 4.9 26.5 1.0
CA A:ASP204 4.9 28.7 1.0
CG A:ASP472 5.0 28.8 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: Wed Dec 16 12:41:53 2020

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