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Zinc in PDB 3dx3: Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol, PDB code: 3dx3 was solved by D.A.Kuntz, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.52 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.062, 109.977, 138.660, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol (pdb code 3dx3). 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 Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol, PDB code: 3dx3:

Zinc binding site 1 out of 1 in 3dx3

Go back to Zinc Binding Sites List in 3dx3
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol


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 Mannostatin Analog (1R,2R, 3S,4R,5R)-5-Aminocyclopentane-1,2,3,4-Tetraol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1047

b:6.3
occ:1.00
 NE2 A:HIS90 2.1 6.7 1.0
OD2 A:ASP204 2.1 7.0 1.0
NE2 A:HIS471 2.1 5.0 1.0
OD1 A:ASP92 2.2 5.8 1.0
O2 A:YTB1050 2.2 7.6 1.0
O3 A:YTB1050 2.2 5.0 1.0
CD2 A:HIS90 3.0 7.3 1.0
CD2 A:HIS471 3.1 4.7 1.0
CE1 A:HIS90 3.1 6.5 1.0
CE1 A:HIS471 3.1 5.8 1.0
C2 A:YTB1050 3.1 7.3 1.0
CG A:ASP92 3.1 6.8 1.0
CG A:ASP204 3.2 6.5 1.0
C3 A:YTB1050 3.2 5.2 1.0
OD2 A:ASP92 3.4 8.4 1.0
CB A:ASP204 3.6 6.4 1.0
N1 A:YTB1050 3.9 11.0 1.0
C1 A:YTB1050 3.9 8.3 1.0
OD2 A:ASP472 4.1 5.8 1.0
C5 A:YTB1050 4.1 8.2 1.0
ND1 A:HIS90 4.2 6.1 1.0
CG A:HIS90 4.2 5.3 1.0
ND1 A:HIS471 4.2 5.8 1.0
OD1 A:ASP204 4.2 7.3 1.0
CG A:HIS471 4.2 3.7 1.0
C4 A:YTB1050 4.3 5.8 1.0
CE1 A:HIS470 4.5 6.0 1.0
CB A:ASP92 4.5 6.2 1.0
O A:HOH2327 4.6 9.1 1.0
OH A:TYR269 4.7 13.1 1.0
O4 A:YTB1050 4.9 7.1 1.0
CA A:ASP92 5.0 5.9 1.0

Reference:

D.A.Kuntz, W.Zhong, J.Guo, D.R.Rose, G.J.Boons. The Molecular Basis of Inhibition of Golgi Alpha-Mannosidase II By Mannostatin A. Chembiochem V. 10 268 2009.
ISSN: ISSN 1439-4227
PubMed: 19101978
DOI: 10.1002/CBIC.200800538
Page generated: Thu Oct 24 12:22:01 2024

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