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Zinc in PDB 6rs0: Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol, PDB code: 6rs0 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) 75.25 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.984, 91.437, 132.460, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol (pdb code 6rs0). 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,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol, PDB code: 6rs0:

Zinc binding site 1 out of 1 in 6rs0

Go back to Zinc Binding Sites List in 6rs0
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with (2S,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol


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,3S,4R,5R)-1-(2- (Benzyloxy)Ethyl)-2-(Hydroxymethyl)Piperidine-3,4,5-Triol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:25.5
occ:1.00
 OD2 A:ASP204 2.0 22.8 1.0
OD1 A:ASP92 2.0 28.8 1.0
NE2 A:HIS90 2.1 24.2 1.0
NE2 A:HIS471 2.2 25.0 1.0
O3 A:KGB1104 2.2 29.1 1.0
O4 A:KGB1104 2.3 38.4 1.0
CG A:ASP92 3.0 29.8 1.0
CD2 A:HIS471 3.0 23.2 1.0
CG A:ASP204 3.0 22.4 1.0
CE1 A:HIS90 3.1 23.5 1.0
CD2 A:HIS90 3.1 23.3 1.0
C5 A:KGB1104 3.2 37.3 1.0
CE1 A:HIS471 3.2 22.8 1.0
C4 A:KGB1104 3.3 33.3 1.0
OD2 A:ASP92 3.3 28.7 1.0
CB A:ASP204 3.5 22.8 1.0
N1 A:KGB1104 4.0 32.0 1.0
OD2 A:ASP472 4.0 25.6 1.0
C6 A:KGB1104 4.1 36.4 1.0
OD1 A:ASP204 4.1 23.9 1.0
ND1 A:HIS90 4.2 22.9 1.0
CG A:HIS471 4.2 23.1 1.0
C2 A:KGB1104 4.2 36.0 1.0
CG A:HIS90 4.2 24.4 1.0
ND1 A:HIS471 4.3 22.3 1.0
C3 A:KGB1104 4.3 33.7 1.0
CB A:ASP92 4.3 27.2 1.0
CE1 A:HIS470 4.4 26.7 1.0
O A:HOH1275 4.7 24.1 1.0
OH A:TYR269 4.9 25.4 1.0
CA A:ASP204 5.0 23.1 1.0
CA A:ASP92 5.0 27.4 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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