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Zinc in PDB 3ddf: Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One

Enzymatic activity of Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One

All present enzymatic activity of Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One:
3.2.1.114;

Protein crystallography data

The structure of Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One, PDB code: 3ddf was solved by D.A.Kuntz, D.R.Rose, D.Hoffman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.923, 109.993, 138.909, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 15.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One (pdb code 3ddf). 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 Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One, PDB code: 3ddf:

Zinc binding site 1 out of 1 in 3ddf

Go back to Zinc Binding Sites List in 3ddf
Zinc binding site 1 out of 1 in the Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Golgi Mannosidase II Complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)- 2-Hydroxy-1 Phenylethyl]Amino}Methyl) Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:8.4
occ:1.00
 NE2 A:HIS90 2.0 7.6 1.0
OD1 A:ASP204 2.0 7.9 1.0
NE2 A:HIS471 2.1 6.7 1.0
O3 A:GB64001 2.2 8.4 1.0
OD1 A:ASP92 2.2 8.8 1.0
O4 A:GB64001 2.3 8.8 1.0
CD2 A:HIS90 3.0 7.2 1.0
CG A:ASP204 3.0 6.8 1.0
CE1 A:HIS90 3.1 7.5 1.0
CD2 A:HIS471 3.1 6.6 1.0
CG A:ASP92 3.1 7.9 1.0
CE1 A:HIS471 3.1 6.5 1.0
C4 A:GB64001 3.1 8.6 1.0
C3 A:GB64001 3.2 7.9 1.0
OD2 A:ASP92 3.4 8.9 1.0
CB A:ASP204 3.5 7.4 1.0
C5 A:GB64001 3.9 9.2 1.0
OD2 A:ASP204 4.1 8.5 1.0
C2 A:GB64001 4.1 8.5 1.0
CG A:HIS90 4.2 7.0 1.0
ND1 A:HIS90 4.2 7.5 1.0
CG A:HIS471 4.2 6.4 1.0
ND1 A:HIS471 4.3 6.4 1.0
OD2 A:ASP472 4.3 7.8 1.0
N1 A:GB64001 4.4 9.5 1.0
CB A:ASP92 4.5 7.7 1.0
O A:HOH7498 4.5 10.5 1.0
OH A:TYR269 4.6 10.4 1.0
NE2 A:HIS470 4.6 9.0 1.0
O2 A:GB64001 5.0 9.4 1.0
CA A:ASP204 5.0 7.0 1.0

Reference:

H.Fiaux, D.A.Kuntz, D.Hoffman, R.C.Janzer, S.Gerber-Lemaire, D.R.Rose, L.Juillerat-Jeanneret. Functionalized Pyrrolidine Inhibitors of Human Type II Alpha-Mannosidases As Anti-Cancer Agents: Optimizing the Fit to the Active Site Bioorg.Med.Chem. V. 16 7337 2008.
ISSN: ISSN 0968-0896
PubMed: 18599296
DOI: 10.1016/J.BMC.2008.06.021
Page generated: Thu Oct 24 12:09:46 2024

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