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Fluorine 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:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total only one binding site of Fluorine was determined in the Golgi Alpha-Mannosidase II Covalent Intermediate Complex with 5- Fluoro-Gulosyl-Fluoride, PDB code: 1qwn:

Fluorine binding site 1 out of 1 in 1qwn

Go back to Fluorine Binding Sites List in 1qwn
Fluorine 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 Fluorine with other atoms in the F 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:F2003

b:8.2
occ:1.00
F1 A:GUL2003 0.0 8.2 1.0
C5 A:GUL2003 1.3 7.2 1.0
O A:GUL2003 2.2 7.6 1.0
C4 A:GUL2003 2.3 7.6 1.0
C6 A:GUL2003 2.3 8.1 1.0
O6 A:GUL2003 2.8 9.2 1.0
O4 A:GUL2003 2.8 7.5 1.0
CE1 A:PHE206 3.2 6.9 1.0
NH2 A:ARG228 3.4 8.2 1.0
C1 A:GUL2003 3.5 7.7 1.0
CZ3 A:TRP415 3.5 6.9 1.0
CH2 A:TRP415 3.6 7.4 1.0
CE2 A:TYR727 3.7 6.8 1.0
CZ A:PHE206 3.7 6.5 1.0
C3 A:GUL2003 3.7 6.8 1.0
CD1 A:PHE206 3.9 6.2 1.0
OD1 A:ASP204 3.9 6.2 1.0
CZ A:ARG228 4.0 6.6 1.0
C2 A:GUL2003 4.1 7.0 1.0
OD2 A:ASP204 4.1 6.8 1.0
NE A:ARG228 4.2 7.4 1.0
OH A:TYR727 4.3 7.0 1.0
CZ A:TYR727 4.3 6.5 1.0
CG A:ASP204 4.3 6.2 1.0
CD2 A:TYR727 4.4 7.1 1.0
O1 A:TRS2004 4.5 11.2 1.0
O3 A:GUL2003 4.6 6.6 1.0
CE2 A:PHE206 4.8 5.9 1.0
O A:ASP204 4.8 7.2 1.0
CE3 A:TRP415 4.8 6.5 1.0
NH1 A:ARG228 4.9 7.6 1.0
CG A:PHE206 4.9 5.9 1.0
CZ2 A:TRP415 5.0 7.5 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: Sun Dec 13 11:32:15 2020

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