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Zinc in PDB 6rrj: Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide, PDB code: 6rrj 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) 75.46 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.354, 91.517, 132.748, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide (pdb code 6rrj). 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 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide, PDB code: 6rrj:

Zinc binding site 1 out of 1 in 6rrj

Go back to Zinc Binding Sites List in 6rrj
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide


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 5-(Adamantan-1YL-Methoxy)- Pentyl 2,5-Dideoxy-2,5-Imino-D-Talo-Hexonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1103

b:29.9
occ:1.00
 OD2 A:ASP204 1.9 28.3 1.0
OD1 A:ASP92 2.0 33.8 1.0
NE2 A:HIS471 2.1 31.5 1.0
NE2 A:HIS90 2.2 28.0 1.0
O4 A:KFE1101 2.3 29.6 1.0
O5 A:KFE1101 2.3 28.2 1.0
CG A:ASP92 3.0 31.9 1.0
CG A:ASP204 3.0 30.5 1.0
CD2 A:HIS471 3.1 29.3 1.0
C22 A:KFE1101 3.1 32.8 1.0
CD2 A:HIS90 3.1 29.4 1.0
C21 A:KFE1101 3.2 32.0 1.0
CE1 A:HIS471 3.2 28.1 1.0
CE1 A:HIS90 3.2 29.3 1.0
OD2 A:ASP92 3.3 34.1 1.0
CB A:ASP204 3.6 29.6 1.0
C18 A:KFE1101 3.7 31.9 1.0
N2 A:KFE1101 3.8 33.2 1.0
OD2 A:ASP472 4.0 28.9 1.0
OD1 A:ASP204 4.0 27.4 1.0
C19 A:KFE1101 4.1 31.9 1.0
CG A:HIS471 4.2 28.7 1.0
ND1 A:HIS471 4.2 29.8 1.0
CG A:HIS90 4.3 29.1 1.0
ND1 A:HIS90 4.3 26.0 1.0
CB A:ASP92 4.3 31.6 1.0
CE1 A:HIS470 4.5 27.4 1.0
C20 A:KFE1101 4.7 33.1 1.0
OH A:TYR269 4.8 30.4 1.0
O A:HOH1256 4.8 25.4 1.0
CA A:ASP92 4.9 30.8 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: Tue Oct 29 06:44:53 2024

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