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Zinc in PDB 3ejt: Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine

Enzymatic activity of Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine, PDB code: 3ejt was solved by D.A.Kuntz, K.Shea, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.372, 110.384, 139.924, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine (pdb code 3ejt). 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-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine, PDB code: 3ejt:

Zinc binding site 1 out of 1 in 3ejt

Go back to Zinc Binding Sites List in 3ejt
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine


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-Substituted Swainsonine Analog:(5R)-5-[2'-(4-Tert-Butylphenyl)Ethyl]-Swainsonine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1047

b:7.2
occ:1.00
NE2 A:HIS90 2.1 7.5 1.0
NE2 A:HIS471 2.1 6.0 1.0
O2 A:HN61050 2.1 7.8 1.0
OD2 A:ASP204 2.2 7.4 1.0
O1 A:HN61050 2.2 7.1 1.0
OD1 A:ASP92 2.3 8.0 1.0
CD2 A:HIS90 3.1 7.2 1.0
CE1 A:HIS471 3.1 6.4 1.0
C2 A:HN61050 3.1 7.9 1.0
CD2 A:HIS471 3.1 6.2 1.0
CE1 A:HIS90 3.1 7.3 1.0
C1 A:HN61050 3.2 7.6 1.0
CG A:ASP204 3.2 7.0 1.0
CG A:ASP92 3.2 7.7 1.0
OD2 A:ASP92 3.5 9.5 1.0
CB A:ASP204 3.5 7.6 1.0
C3 A:HN61050 4.0 9.1 1.0
N4 A:HN61050 4.0 7.8 1.0
C8A A:HN61050 4.1 7.9 1.0
OD2 A:ASP472 4.1 7.0 1.0
CG A:HIS90 4.2 6.8 1.0
ND1 A:HIS90 4.2 6.8 1.0
ND1 A:HIS471 4.2 6.3 1.0
CG A:HIS471 4.3 5.7 1.0
OD1 A:ASP204 4.3 8.1 1.0
CB A:ASP92 4.6 7.5 1.0
CE1 A:HIS470 4.6 7.6 1.0
C8 A:HN61050 4.6 7.6 1.0
O A:HOH2130 4.7 10.3 1.0
OH A:TYR269 4.7 11.1 1.0

Reference:

D.A.Kuntz, S.Nakayama, K.Shea, H.Hori, Y.Uto, H.Nagasawa, D.R.Rose. Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi Alpha-Mannosidase II. Chembiochem V. 11 673 2010.
ISSN: ISSN 1439-4227
PubMed: 20209559
DOI: 10.1002/CBIC.200900750
Page generated: Wed Dec 16 04:16:25 2020

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