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Fluorine in PDB 1uhv: Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase

Enzymatic activity of Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase

All present enzymatic activity of Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase:
3.2.1.37;

Protein crystallography data

The structure of Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase, PDB code: 1uhv was solved by J.K.Yang, H.J.Yoon, H.J.Ahn, B.Il Lee, J.D.Pedelacq, E.C.Liong, J.Berendzen, M.Laivenieks, C.Vieille, G.J.Zeikus, D.J.Vocadlo, S.G.Withers, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.33 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.326, 152.276, 159.684, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase (pdb code 1uhv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase, PDB code: 1uhv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1uhv

Go back to Fluorine Binding Sites List in 1uhv
Fluorine binding site 1 out of 4 in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase


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-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3277

b:39.4
occ:1.00
 F2 A:DFX3277 0.0 39.4 1.0
C2 A:DFX3277 1.4 36.9 1.0
C1 A:DFX3277 2.4 35.2 1.0
C3 A:DFX3277 2.4 35.9 1.0
O3 A:DFX3277 2.8 36.1 1.0
OE1 A:GLU277 2.9 31.3 1.0
ND2 A:ASN159 2.9 23.7 1.0
OE1 A:GLU160 3.1 34.9 1.0
OE2 A:GLU277 3.1 27.5 1.0
OD1 A:ASN159 3.4 29.2 1.0
NE2 A:HIS54 3.4 23.6 1.0
CD A:GLU160 3.4 31.6 1.0
CD A:GLU277 3.4 27.0 1.0
CG A:ASN159 3.5 28.0 1.0
CZ A:PHE166 3.6 47.4 1.0
O5 A:DFX3277 3.7 37.9 1.0
CE1 A:HIS54 3.7 21.1 1.0
CE2 A:PHE166 3.7 48.0 1.0
C4 A:DFX3277 3.8 35.1 1.0
OE2 A:GLU160 3.8 31.2 1.0
CG A:GLU160 4.1 30.2 1.0
C5 A:DFX3277 4.2 36.3 1.0
CE1 A:HIS228 4.4 31.4 1.0
ND1 A:HIS228 4.5 34.5 1.0
CE1 A:PHE166 4.5 48.2 1.0
CD2 A:HIS54 4.6 22.3 1.0
CD2 A:PHE166 4.7 47.4 1.0
NH1 A:ARG52 4.8 33.8 1.0
O4 A:DFX3277 4.9 32.3 1.0
CG A:GLU277 4.9 24.8 1.0
ND1 A:HIS54 5.0 21.1 1.0
CB A:ASN159 5.0 25.9 1.0

Fluorine binding site 2 out of 4 in 1uhv

Go back to Fluorine Binding Sites List in 1uhv
Fluorine binding site 2 out of 4 in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase


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-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3277

b:33.1
occ:1.00
 F2 B:DFX3277 0.0 33.1 1.0
C2 B:DFX3277 1.4 33.2 1.0
C1 B:DFX3277 2.4 34.5 1.0
C3 B:DFX3277 2.4 33.8 1.0
ND2 B:ASN159 2.7 22.6 1.0
O3 B:DFX3277 2.8 36.5 1.0
OE1 B:GLU277 2.9 33.4 1.0
OE2 B:GLU277 3.0 32.7 1.0
OD1 B:ASN159 3.3 24.8 1.0
NE2 B:HIS54 3.3 17.8 1.0
CD B:GLU277 3.4 31.1 1.0
CG B:ASN159 3.4 23.1 1.0
CE1 B:HIS54 3.4 18.8 1.0
OE1 B:GLU160 3.6 33.1 1.0
O5 B:DFX3277 3.7 33.3 1.0
CD B:GLU160 3.7 30.3 1.0
C4 B:DFX3277 3.8 33.5 1.0
OE2 B:GLU160 4.1 30.3 1.0
CE1 B:HIS228 4.1 28.2 1.0
CZ B:PHE166 4.2 34.0 1.0
CG B:GLU160 4.2 30.2 1.0
C5 B:DFX3277 4.2 33.6 1.0
ND1 B:HIS228 4.3 26.7 1.0
CE2 B:PHE166 4.3 32.9 1.0
CD2 B:HIS54 4.6 19.0 1.0
NH1 B:ARG52 4.7 18.5 1.0
ND1 B:HIS54 4.7 18.3 1.0
CB B:ASN159 4.8 23.0 1.0
CE1 B:PHE166 4.8 33.0 1.0
O4 B:DFX3277 4.9 32.6 1.0
CG B:GLU277 4.9 29.0 1.0
O B:HOH2218 4.9 46.4 1.0
CZ2 B:TRP315 4.9 19.0 1.0

Fluorine binding site 3 out of 4 in 1uhv

Go back to Fluorine Binding Sites List in 1uhv
Fluorine binding site 3 out of 4 in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase


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-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3277

b:31.6
occ:1.00
 F2 C:DFX3277 0.0 31.6 1.0
C2 C:DFX3277 1.4 31.2 1.0
C1 C:DFX3277 2.4 30.6 1.0
C3 C:DFX3277 2.4 30.6 1.0
O3 C:DFX3277 2.9 30.3 1.0
ND2 C:ASN159 2.9 22.9 1.0
OE1 C:GLU277 2.9 30.8 1.0
OE2 C:GLU277 2.9 29.1 1.0
NE2 C:HIS54 3.1 14.6 1.0
CD C:GLU277 3.3 29.3 1.0
CE1 C:HIS54 3.4 13.2 1.0
OD1 C:ASN159 3.5 26.0 1.0
CG C:ASN159 3.6 23.4 1.0
O5 C:DFX3277 3.7 29.9 1.0
C4 C:DFX3277 3.8 28.9 1.0
CD C:GLU160 3.9 24.9 1.0
OE1 C:GLU160 3.9 27.2 1.0
OE2 C:GLU160 4.0 26.4 1.0
CZ C:PHE166 4.1 22.1 1.0
C5 C:DFX3277 4.2 28.2 1.0
CE1 C:HIS228 4.3 23.1 1.0
CE2 C:PHE166 4.3 21.2 1.0
CD2 C:HIS54 4.4 15.2 1.0
ND1 C:HIS228 4.4 20.1 1.0
CG C:GLU160 4.5 23.5 1.0
ND1 C:HIS54 4.7 17.4 1.0
NH1 C:ARG52 4.7 22.5 1.0
CE1 C:PHE166 4.7 23.3 1.0
CZ2 C:TRP315 4.8 16.3 1.0
O C:HOH2219 4.8 44.6 1.0
CG C:GLU277 4.8 27.5 1.0
O4 C:DFX3277 4.9 30.1 1.0

Fluorine binding site 4 out of 4 in 1uhv

Go back to Fluorine Binding Sites List in 1uhv
Fluorine binding site 4 out of 4 in the Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3277

b:37.3
occ:1.00
 F2 D:DFX3277 0.0 37.3 1.0
C2 D:DFX3277 1.4 37.5 1.0
C1 D:DFX3277 2.4 37.5 1.0
C3 D:DFX3277 2.4 37.6 1.0
O3 D:DFX3277 2.8 37.7 1.0
OE1 D:GLU277 2.9 36.3 1.0
ND2 D:ASN159 2.9 26.7 1.0
OD1 D:ASN159 3.1 23.8 1.0
OE2 D:GLU277 3.1 34.1 1.0
NE2 D:HIS54 3.3 27.5 1.0
CE1 D:HIS54 3.3 26.1 1.0
CG D:ASN159 3.3 26.3 1.0
CD D:GLU277 3.4 33.5 1.0
OE1 D:GLU160 3.6 29.9 1.0
O5 D:DFX3277 3.7 39.1 1.0
C4 D:DFX3277 3.8 37.5 1.0
CD D:GLU160 3.8 29.4 1.0
CZ D:PHE166 4.1 30.4 1.0
CE1 D:HIS228 4.1 27.2 1.0
OE2 D:GLU160 4.1 29.1 1.0
C5 D:DFX3277 4.2 38.5 1.0
CE2 D:PHE166 4.3 30.2 1.0
CG D:GLU160 4.3 28.4 1.0
ND1 D:HIS228 4.3 28.6 1.0
CD2 D:HIS54 4.6 24.4 1.0
NH1 D:ARG52 4.6 26.7 1.0
ND1 D:HIS54 4.6 24.9 1.0
CZ2 D:TRP315 4.7 17.1 1.0
CE1 D:PHE166 4.7 31.6 1.0
O D:HOH2220 4.7 39.2 1.0
CB D:ASN159 4.8 24.8 1.0
O4 D:DFX3277 4.9 38.9 1.0
CH2 D:TRP315 4.9 17.8 1.0
CG D:GLU277 5.0 31.9 1.0

Reference:

J.K.Yang, H.J.Yoon, H.J.Ahn, B.I.Lee, J.D.Pedelacq, E.C.Liong, J.Berendzen, M.Laivenieks, C.Vieille, G.J.Zeikus, D.J.Vocadlo, S.G.Withers, S.W.Suh. Crystal Structure of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase. J.Mol.Biol. V. 335 155 2004.
ISSN: ISSN 0022-2836
PubMed: 14659747
DOI: 10.1016/J.JMB.2003.10.026
Page generated: Wed Jul 31 13:02:22 2024

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