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Fluorine in PDB 3vo0: Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid

Enzymatic activity of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid

All present enzymatic activity of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid:
3.2.1.31;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid, PDB code: 3vo0 was solved by M.Momma, Z.Fujimoto, M.Michikawa, H.Ichinose, S.Jongkees, M.Yoshida, Y.Kotake, P.Biely, Y.Tsumuraya, S.Withers, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.09 / 1.90
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.489, 101.489, 218.238, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid (pdb code 3vo0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid, PDB code: 3vo0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3vo0

Go back to Fluorine Binding Sites List in 3vo0
Fluorine binding site 1 out of 3 in the Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:22.0
occ:1.00
 F2 A:GUZ501 0.0 22.0 1.0
C2 A:GUZ501 1.4 16.6 1.0
C1 A:GUZ501 2.3 18.0 1.0
C3 A:GUZ501 2.4 18.4 1.0
OE1 A:GLU287 2.6 25.1 1.0
O3 A:GUZ501 2.8 17.7 1.0
CA A:GLY79 3.0 17.9 1.0
OE2 A:GLU287 3.1 21.4 1.0
ND2 A:ASN172 3.1 21.0 1.0
CD A:GLU287 3.1 20.1 1.0
N A:ASN80 3.2 18.4 1.0
C A:GLY79 3.4 18.9 1.0
OD1 A:ASN172 3.4 20.3 1.0
OD1 A:ASN80 3.5 18.2 1.0
O5 A:GUZ501 3.5 18.2 1.0
CG A:ASN172 3.6 22.0 1.0
C4 A:GUZ501 3.7 17.7 1.0
CG A:ASN80 4.0 17.1 1.0
C5 A:GUZ501 4.1 18.8 1.0
N A:GLY79 4.1 18.4 1.0
CD A:GLU173 4.2 22.9 1.0
OE2 A:GLU173 4.2 24.4 1.0
CA A:ASN80 4.3 18.3 1.0
OE1 A:GLU173 4.3 25.0 1.0
O A:GLY79 4.5 20.4 1.0
CG A:GLU287 4.5 19.3 1.0
CG A:GLU173 4.5 22.6 1.0
CB A:ASN80 4.6 17.5 1.0
ND2 A:ASN80 4.7 18.6 1.0
NH1 A:ARG76 4.7 19.6 1.0
O4 A:GUZ501 4.8 16.2 1.0
OE2 A:GLU45 4.8 19.2 1.0
CE1 A:HIS241 4.8 16.9 1.0
NE2 A:HIS327 4.9 12.7 1.0
NH2 A:ARG76 4.9 19.8 1.0
CB A:ASN172 5.0 24.0 1.0
CE1 A:HIS327 5.0 14.0 1.0
ND1 A:HIS241 5.0 20.2 1.0

Fluorine binding site 2 out of 3 in 3vo0

Go back to Fluorine Binding Sites List in 3vo0
Fluorine binding site 2 out of 3 in the Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.0
occ:1.00
 F2 A:GUF502 0.0 47.0 1.0
C2 A:GUF502 1.4 46.3 1.0
C3 A:GUF502 2.4 47.1 1.0
C1 A:GUF502 2.4 44.3 1.0
O3 A:GUF502 2.8 47.2 1.0
O1 A:DNF503 2.9 41.2 1.0
O5 A:GUF502 3.7 46.7 1.0
C4 A:GUF502 3.8 47.0 1.0
O A:ASN180 3.8 32.4 1.0
CA A:ASN180 3.9 33.2 1.0
C1 A:DNF503 4.0 38.2 1.0
C A:ASN180 4.2 33.1 1.0
C5 A:GUF502 4.2 47.1 1.0
O A:ARG179 4.3 34.7 1.0
O22 A:DNF503 4.3 39.4 1.0
CB A:ASN180 4.4 32.8 1.0
O A:HIS108 4.4 29.3 1.0
N2 A:DNF503 4.6 37.7 1.0
C2 A:DNF503 4.7 38.4 1.0
C6 A:DNF503 4.7 36.9 1.0
O4 A:GUF502 4.8 48.4 1.0

Fluorine binding site 3 out of 3 in 3vo0

Go back to Fluorine Binding Sites List in 3vo0
Fluorine binding site 3 out of 3 in the Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Beta-Glucuronidase From Acidobacterium Capsulatum Covalent-Bonded with 2-Deoxy-2-Fluoro-D-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:49.1
occ:1.00
 F2 A:GUF504 0.0 49.1 1.0
C2 A:GUF504 1.3 47.5 1.0
C3 A:GUF504 2.3 48.1 1.0
C1 A:GUF504 2.4 45.9 1.0
O3 A:GUF504 2.8 49.9 1.0
O1 A:DNF505 3.0 43.1 1.0
CG2 A:THR145 3.5 27.5 1.0
C4 A:GUF504 3.6 47.6 1.0
O5 A:GUF504 3.7 46.4 1.0
O A:LYS143 3.8 28.9 1.0
C5 A:GUF504 4.1 47.8 1.0
C1 A:DNF505 4.2 41.9 1.0
O22 A:DNF505 4.3 44.3 1.0
N2 A:DNF505 4.4 44.6 1.0
N A:THR145 4.6 28.6 1.0
O4 A:GUF504 4.7 47.2 1.0
C2 A:DNF505 4.8 42.2 1.0
C A:GLY144 4.8 29.4 1.0
CB A:THR145 4.9 28.8 1.0
O21 A:DNF505 4.9 47.6 1.0
CA A:GLY144 5.0 29.5 1.0

Reference:

M.Michikawa, H.Ichinose, M.Momma, P.Biely, S.Jongkees, M.Yoshida, T.Kotake, Y.Tsumuraya, S.G.Withers, Z.Fujimoto, S.Kaneko. Structural and Biochemical Characterization of Glycoside Hydrolase Family 79 Beta-Glucuronidase From Acidobacterium Capsulatum J.Biol.Chem. V. 287 14069 2012.
ISSN: ISSN 0021-9258
PubMed: 22367201
DOI: 10.1074/JBC.M112.346288
Page generated: Mon Jul 14 19:54:14 2025

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