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Zinc in PDB 3ejp: Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog: (5R)-5-[2'-Oxo-2'-(Phenyl)Ethyl]-Swainsonine

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

All present enzymatic activity of Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog: (5R)-5-[2'-Oxo-2'-(Phenyl)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'-Oxo-2'-(Phenyl)Ethyl]-Swainsonine, PDB code: 3ejp 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) 29.22 / 1.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.025, 109.883, 138.959, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.2

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'-Oxo-2'-(Phenyl)Ethyl]-Swainsonine (pdb code 3ejp). 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'-Oxo-2'-(Phenyl)Ethyl]-Swainsonine, PDB code: 3ejp:

Zinc binding site 1 out of 1 in 3ejp

Go back to Zinc Binding Sites List in 3ejp
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II in Complex with 5-Substituted Swainsonine Analog: (5R)-5-[2'-Oxo-2'-(Phenyl)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'-Oxo-2'-(Phenyl)Ethyl]-Swainsonine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1047

b:8.4
occ:1.00
O2 A:HN21049 2.1 8.8 1.0
OD2 A:ASP204 2.1 7.7 1.0
NE2 A:HIS90 2.1 7.8 1.0
OD1 A:ASP92 2.1 9.0 1.0
O1 A:HN21049 2.1 8.2 1.0
NE2 A:HIS471 2.1 6.7 1.0
CD2 A:HIS90 3.0 8.0 1.0
C2 A:HN21049 3.1 8.3 1.0
CD2 A:HIS471 3.1 6.4 1.0
C1 A:HN21049 3.1 8.0 1.0
CG A:ASP204 3.1 7.5 1.0
CG A:ASP92 3.1 8.2 1.0
CE1 A:HIS90 3.1 8.4 1.0
CE1 A:HIS471 3.1 7.4 1.0
OD2 A:ASP92 3.5 10.3 1.0
CB A:ASP204 3.5 8.0 1.0
C3 A:HN21049 3.9 8.9 1.0
N4 A:HN21049 3.9 8.4 1.0
C8A A:HN21049 4.1 8.6 1.0
OD2 A:ASP472 4.1 7.5 1.0
CG A:HIS90 4.2 7.5 1.0
ND1 A:HIS90 4.2 8.3 1.0
ND1 A:HIS471 4.2 7.0 1.0
OD1 A:ASP204 4.2 8.3 1.0
CG A:HIS471 4.3 6.9 1.0
CB A:ASP92 4.5 8.2 1.0
CE1 A:HIS470 4.5 7.9 1.0
C8 A:HN21049 4.6 7.5 1.0
O A:HOH2280 4.6 10.9 1.0
OH A:TYR269 4.8 10.9 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 04:16:21 2020

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