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Fluorine in PDB 3ptq: The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside

Enzymatic activity of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside

All present enzymatic activity of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside:
3.2.1.21;

Protein crystallography data

The structure of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside, PDB code: 3ptq was solved by S.Sansenya, R.Opassiri, B.Kuaprasert, C.J.Chen, J.R.Ketudat Cairns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.112, 114.112, 184.541, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.1

Other elements in 3ptq:

The structure of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside (pdb code 3ptq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside, PDB code: 3ptq:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3ptq

Go back to Fluorine Binding Sites List in 3ptq
Fluorine binding site 1 out of 2 in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:60.2
occ:0.80
 F A:NFG1001 0.0 60.2 0.8
C2 A:NFG1001 1.4 60.8 0.8
C3 A:NFG1001 2.4 59.9 0.8
C1 A:NFG1001 2.4 61.7 0.8
OE1 A:GLU393 2.8 31.5 1.0
CD A:GLU179 3.0 26.4 1.0
OE2 A:GLU179 3.0 26.5 1.0
O3 A:NFG1001 3.0 59.3 0.8
OE2 A:GLU393 3.1 32.9 1.0
OE1 A:GLU179 3.1 29.3 1.0
O5 A:NFG1001 3.2 60.4 0.8
CD A:GLU393 3.3 30.1 1.0
ND2 A:ASN178 3.4 25.8 1.0
O1 A:NFG1001 3.6 65.4 0.8
C4 A:NFG1001 3.6 58.9 0.8
CG A:GLU179 3.7 26.0 1.0
C5 A:NFG1001 3.9 59.0 0.8
NE2 A:HIS133 3.9 23.2 1.0
OD1 A:ASN178 3.9 27.8 1.0
ND2 A:ASN320 4.0 28.7 1.0
CG A:ASN178 4.1 25.7 1.0
CZ2 A:TRP134 4.2 21.5 1.0
CH2 A:TRP134 4.4 20.5 1.0
CE1 A:HIS133 4.4 22.5 1.0
CB A:GLU179 4.6 25.1 1.0
C11 A:NFG1001 4.6 66.4 0.8
O4 A:NFG1001 4.8 57.9 0.8
OH A:TYR322 4.8 30.8 1.0
CG A:GLU393 4.8 29.5 1.0
C16 A:NFG1001 5.0 66.4 0.8

Fluorine binding site 2 out of 2 in 3ptq

Go back to Fluorine Binding Sites List in 3ptq
Fluorine binding site 2 out of 2 in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with Dinitrophenyl 2-Deoxy-2-Fluoro-Beta-D-Glucopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:56.1
occ:0.80
 F B:NFG1002 0.0 56.1 0.8
C2 B:NFG1002 1.4 58.0 0.8
C3 B:NFG1002 2.4 56.3 0.8
C1 B:NFG1002 2.4 59.9 0.8
OE2 B:GLU393 2.6 34.2 1.0
OE1 B:GLU393 2.8 33.2 1.0
ND2 B:ASN178 3.0 27.7 1.0
O3 B:NFG1002 3.1 54.8 0.8
CD B:GLU393 3.1 32.3 1.0
OE2 B:GLU179 3.1 28.2 1.0
CD B:GLU179 3.2 27.8 1.0
O5 B:NFG1002 3.2 58.2 0.8
O1 B:NFG1002 3.5 65.5 0.8
OE1 B:GLU179 3.5 32.2 1.0
C4 B:NFG1002 3.6 55.6 0.8
NE2 B:HIS133 3.7 23.2 1.0
CG B:GLU179 3.8 26.6 1.0
CG B:ASN178 3.8 27.2 1.0
OD1 B:ASN178 3.9 28.9 1.0
C5 B:NFG1002 3.9 56.1 0.8
ND2 B:ASN320 4.0 31.7 1.0
CE1 B:HIS133 4.0 23.6 1.0
CZ2 B:TRP134 4.3 22.3 1.0
CH2 B:TRP134 4.4 21.8 1.0
CG B:GLU393 4.5 30.2 1.0
C11 B:NFG1002 4.6 66.5 0.8
CB B:GLU179 4.7 25.9 1.0
CD2 B:HIS133 4.8 22.9 1.0
O4 B:NFG1002 4.9 54.2 0.8
C16 B:NFG1002 4.9 66.9 0.8
OH B:TYR322 5.0 32.9 1.0

Reference:

S.Sansenya, R.Opassiri, B.Kuaprasert, C.J.Chen, J.R.Ketudat Cairns. The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12, An Oligosaccharide and Tuberonic Acid Glucoside-Hydrolyzing Beta-Glucosidase with Significant Thioglucohydrolase Activity Arch.Biochem.Biophys. V. 510 62 2011.
ISSN: ISSN 0003-9861
PubMed: 21521631
DOI: 10.1016/J.ABB.2011.04.005
Page generated: Mon Jul 14 18:50:07 2025

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