Fluorine in PDB 1qx1: Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F

All present enzymatic activity of Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F:
3.2.1.114;

The structure of Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F, PDB code: 1qx1 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)	29.23 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.046, 109.826, 138.907, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 18.9

The structure of Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F (pdb code 1qx1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F, PDB code: 1qx1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F


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 D341N Mutant Complex with 2-F-Mannosyl-F within 5.0Å range: probe atom residue distance (Å) B Occ A:F2003 b:14.0 occ:0.50 F2 A:FMF2003 0.0 14.0 0.5 F2 A:FMF2003 0.1 18.1 0.5 C2 A:FMF2003 1.3 14.3 0.5 C2 A:FMF2003 1.3 12.7 0.5 C1 A:FMF2003 2.3 14.6 0.5 C1 A:FMF2003 2.4 14.2 0.5 C3 A:FMF2003 2.4 14.1 0.5 C3 A:FMF2003 2.4 11.6 0.5 ZN A:ZN2004 2.6 12.9 1.0 O3 A:FMF2003 2.6 6.7 0.5 O3 A:FMF2003 2.7 21.9 0.5 OD1 A:ASP204 2.7 11.4 1.0 OD2 A:ASP92 2.8 16.7 1.0 CD2 A:HIS90 3.0 10.0 1.0 NE2 A:HIS90 3.1 9.8 1.0 O A:HOH2894 3.3 22.9 1.0 O A:FMF2003 3.5 13.0 0.5 O A:FMF2003 3.5 17.1 0.5 OD1 A:ASP92 3.6 13.0 1.0 CG A:ASP92 3.6 14.0 1.0 OH A:TYR269 3.7 12.9 1.0 OD1 A:ASN341 3.8 13.0 1.0 C4 A:FMF2003 3.8 13.6 0.5 C4 A:FMF2003 3.8 11.5 0.5 CG A:ASP204 3.9 9.9 1.0 O A:HOH2876 3.9 26.0 1.0 ND2 A:ASN341 4.0 17.5 1.0 C5 A:FMF2003 4.0 16.2 0.5 C5 A:FMF2003 4.0 16.3 0.5 CG A:ASN341 4.1 12.0 1.0 CZ3 A:TRP95 4.1 17.3 1.0 CE3 A:TRP95 4.3 15.1 1.0 CG A:HIS90 4.3 8.8 1.0 CE1 A:HIS90 4.3 8.3 1.0 OD2 A:ASP204 4.5 10.6 1.0 NE2 A:HIS471 4.5 6.7 1.0 CH2 A:TRP95 4.7 18.1 1.0 O4 A:FMF2003 4.8 11.8 0.5 CB A:ASP204 4.8 10.2 1.0 O4 A:FMF2003 4.8 11.6 0.5 OD2 A:ASP472 4.8 9.3 1.0 CB A:ASP92 5.0 11.5 1.0 ND1 A:HIS90 5.0 10.7 1.0 CZ A:TYR269 5.0 10.8 1.0

Fluorine binding site 2 out of 2 in the Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Golgi Alpha-Mannosidase II D341N Mutant Complex with 2-F-Mannosyl-F within 5.0Å range: probe atom residue distance (Å) B Occ A:F2003 b:18.1 occ:0.50 F2 A:FMF2003 0.0 18.1 0.5 F2 A:FMF2003 0.1 14.0 0.5 C2 A:FMF2003 1.4 14.3 0.5 C2 A:FMF2003 1.4 12.7 0.5 C1 A:FMF2003 2.4 14.6 0.5 C1 A:FMF2003 2.4 14.2 0.5 C3 A:FMF2003 2.4 14.1 0.5 C3 A:FMF2003 2.5 11.6 0.5 ZN A:ZN2004 2.5 12.9 1.0 O3 A:FMF2003 2.6 6.7 0.5 O3 A:FMF2003 2.6 21.9 0.5 OD1 A:ASP204 2.7 11.4 1.0 OD2 A:ASP92 2.8 16.7 1.0 CD2 A:HIS90 2.9 10.0 1.0 NE2 A:HIS90 3.0 9.8 1.0 O A:HOH2894 3.3 22.9 1.0 OD1 A:ASP92 3.5 13.0 1.0 O A:FMF2003 3.5 13.0 0.5 CG A:ASP92 3.5 14.0 1.0 O A:FMF2003 3.6 17.1 0.5 OH A:TYR269 3.7 12.9 1.0 OD1 A:ASN341 3.8 13.0 1.0 C4 A:FMF2003 3.8 13.6 0.5 C4 A:FMF2003 3.8 11.5 0.5 CG A:ASP204 3.9 9.9 1.0 O A:HOH2876 4.0 26.0 1.0 ND2 A:ASN341 4.0 17.5 1.0 C5 A:FMF2003 4.0 16.2 0.5 C5 A:FMF2003 4.1 16.3 0.5 CG A:ASN341 4.1 12.0 1.0 CZ3 A:TRP95 4.2 17.3 1.0 CG A:HIS90 4.3 8.8 1.0 CE1 A:HIS90 4.3 8.3 1.0 CE3 A:TRP95 4.3 15.1 1.0 NE2 A:HIS471 4.4 6.7 1.0 OD2 A:ASP204 4.5 10.6 1.0 CB A:ASP204 4.8 10.2 1.0 CH2 A:TRP95 4.8 18.1 1.0 OD2 A:ASP472 4.8 9.3 1.0 O4 A:FMF2003 4.8 11.8 0.5 O4 A:FMF2003 4.9 11.6 0.5 ND1 A:HIS90 4.9 10.7 1.0 CB A:ASP92 4.9 11.5 1.0 CZ A:TYR269 5.0 10.8 1.0

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