Fluorine in PDB 3ptm: The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside

All present enzymatic activity of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside:
3.2.1.21;

The structure of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside, PDB code: 3ptm 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)	25.86 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.046, 114.046, 184.149, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside (pdb code 3ptm). 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 2- Fluoroglucopyranoside, PDB code: 3ptm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside


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 2- Fluoroglucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:20.0 occ:1.00 F2 A:G2F1000 0.0 20.0 1.0 C2 A:G2F1000 1.4 19.7 1.0 C1 A:G2F1000 2.4 20.7 1.0 C3 A:G2F1000 2.4 19.4 1.0 OE1 A:GLU393 2.7 24.1 1.0 OE2 A:GLU393 2.8 25.2 1.0 O3 A:G2F1000 2.8 18.6 1.0 NE2 A:HIS133 2.8 18.3 1.0 ND2 A:ASN178 2.9 19.7 1.0 CD A:GLU393 3.0 24.8 1.0 CE1 A:HIS133 3.1 18.0 1.0 OD1 A:ASN178 3.6 19.8 1.0 CG A:ASN178 3.6 19.8 1.0 O5 A:G2F1000 3.6 19.5 1.0 C4 A:G2F1000 3.7 19.1 1.0 OE1 A:GLU179 3.7 23.2 1.0 CD A:GLU179 4.0 21.5 1.0 CD2 A:HIS133 4.1 18.4 1.0 C5 A:G2F1000 4.1 18.9 1.0 ND1 A:HIS133 4.3 17.5 1.0 CZ2 A:TRP134 4.4 19.0 1.0 OE2 A:GLU179 4.4 21.5 1.0 CH2 A:TRP134 4.5 18.7 1.0 CG A:GLU393 4.5 24.7 1.0 CG A:GLU179 4.6 20.9 1.0 OH A:TYR322 4.7 26.1 0.5 CZ3 A:TRP442 4.7 18.5 1.0 O4 A:G2F1000 4.8 19.6 1.0 CG A:HIS133 4.8 17.9 1.0 CH2 A:TRP442 4.8 18.6 1.0 ND2 A:ASN320 4.9 24.3 1.0 CE3 A:TRP442 5.0 18.3 1.0 NH1 A:ARG87 5.0 22.8 1.0 OE1 A:GLN29 5.0 16.4 1.0 CB A:ASN178 5.0 19.7 1.0

Fluorine binding site 2 out of 2 in the The Crystal Structure of Rice (Oryza Sativa L.) OS4BGLU12 with 2- Fluoroglucopyranoside


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 2- Fluoroglucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:24.9 occ:1.00 F2 B:G2F1001 0.0 24.9 1.0 C2 B:G2F1001 1.4 23.9 1.0 C1 B:G2F1001 2.4 24.3 1.0 C3 B:G2F1001 2.4 23.6 1.0 OE1 B:GLU393 2.6 25.8 1.0 OE2 B:GLU393 2.7 25.8 1.0 O3 B:G2F1001 2.8 23.4 1.0 ND2 B:ASN178 3.0 20.7 1.0 CD B:GLU393 3.0 25.4 1.0 NE2 B:HIS133 3.0 18.1 1.0 CE1 B:HIS133 3.2 18.5 1.0 O5 B:G2F1001 3.6 23.4 1.0 C4 B:G2F1001 3.7 23.4 1.0 CG B:ASN178 3.8 20.6 1.0 OD1 B:ASN178 3.8 20.3 1.0 OE1 B:GLU179 3.9 24.9 1.0 CD B:GLU179 4.0 23.2 1.0 C5 B:G2F1001 4.1 23.6 1.0 CD2 B:HIS133 4.3 18.1 1.0 OE2 B:GLU179 4.3 23.4 1.0 CH2 B:TRP134 4.3 19.0 1.0 CZ2 B:TRP134 4.4 19.2 1.0 ND1 B:HIS133 4.4 18.1 1.0 CG B:GLU393 4.5 24.7 1.0 OH B:TYR322 4.5 26.2 0.5 CG B:GLU179 4.7 22.0 1.0 CZ3 B:TRP442 4.7 19.6 1.0 O4 B:G2F1001 4.8 23.0 1.0 ND2 B:ASN320 4.8 25.6 1.0 CH2 B:TRP442 4.8 19.4 1.0 O2 B:GOL3968 4.9 57.6 1.0 CE3 B:TRP442 4.9 19.4 1.0 OE1 B:GLN29 4.9 18.3 1.0 C1 B:GOL3968 5.0 57.3 1.0 CG B:HIS133 5.0 18.4 1.0

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