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Zinc in PDB 1qwn: Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride

Enzymatic activity of Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride

All present enzymatic activity of Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride, PDB code: 1qwn was solved by S.Numao, D.A.Kuntz, S.G.Withers, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.019, 110.019, 138.961, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.2

Other elements in 1qwn:

The structure of Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride (pdb code 1qwn). 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 Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride, PDB code: 1qwn:

Zinc binding site 1 out of 1 in 1qwn

Go back to Zinc Binding Sites List in 1qwn
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride


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 Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:6.5
occ:1.00
 OD1 A:ASP92 2.0 6.7 1.0
NE2 A:HIS471 2.1 5.2 1.0
NE2 A:HIS90 2.1 5.5 1.0
O3 A:GUL2003 2.1 6.6 1.0
O2 A:GUL2003 2.2 7.4 1.0
OD1 A:ASP204 2.6 6.2 1.0
CG A:ASP92 2.9 6.3 1.0
C2 A:GUL2003 2.9 7.0 1.0
CE1 A:HIS471 3.0 5.1 1.0
CD2 A:HIS90 3.1 5.2 1.0
CD2 A:HIS471 3.1 4.8 1.0
CE1 A:HIS90 3.1 5.4 1.0
C3 A:GUL2003 3.1 6.8 1.0
OD2 A:ASP92 3.2 7.9 1.0
C1 A:GUL2003 3.4 7.7 1.0
CG A:ASP204 3.6 6.2 1.0
CB A:ASP204 3.7 6.3 1.0
OD2 A:ASP472 4.0 5.7 1.0
C4 A:GUL2003 4.1 7.6 1.0
ND1 A:HIS471 4.2 5.3 1.0
ND1 A:HIS90 4.2 6.1 1.0
CG A:HIS90 4.2 5.6 1.0
CG A:HIS471 4.2 4.5 1.0
CE1 A:HIS470 4.3 5.6 1.0
CB A:ASP92 4.3 6.2 1.0
O A:HOH2097 4.5 7.8 1.0
O A:GUL2003 4.6 7.6 1.0
OD2 A:ASP204 4.7 6.8 1.0
CA A:ASP92 4.8 5.4 1.0
OH A:TYR269 4.9 8.8 1.0
NE2 A:HIS470 4.9 5.2 1.0

Reference:

S.Numao, D.A.Kuntz, S.G.Withers, D.R.Rose. Insights Into the Mechanism of Drosophila Melanogaster Golgi Alpha-Mannosidase II Through the Structural Analysis of Covalent Reaction Intermediates. J.Biol.Chem. V. 278 48074 2003.
ISSN: ISSN 0021-9258
PubMed: 12960159
DOI: 10.1074/JBC.M309249200
Page generated: Mon Jan 25 16:12:30 2021

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