Fluorine in PDB 7vej: Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE

The structure of Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE, PDB code: 7vej was solved by R.Maharjan, Y.Fukuda, T.Nakayama, T.Nakayama, H.Hamada, S.Ozaki, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.77 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.866, 103.067, 108.893, 90, 90, 90
R / Rfree (%)	20.5 / 23.8

The structure of Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE (pdb code 7vej). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE, PDB code: 7vej:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE


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 Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:22.9 occ:1.00 F1 A:U2F604 0.0 22.9 1.0 C2 A:U2F604 1.4 24.9 1.0 C3 A:U2F604 2.3 22.7 1.0 C1 A:U2F604 2.4 23.4 1.0 O1 A:U2F604 2.7 25.8 1.0 O3 A:U2F604 2.7 24.0 1.0 NE2 A:GLN395 2.9 25.1 1.0 OG1 A:THR293 3.5 44.3 1.0 O1B A:U2F604 3.6 35.4 1.0 CE1 A:PHE392 3.6 27.8 1.0 O5 A:U2F604 3.7 21.5 1.0 C4 A:U2F604 3.7 24.8 1.0 CG2 A:THR293 3.7 39.4 1.0 PB A:U2F604 3.8 29.2 1.0 CZ A:PHE392 4.1 31.2 1.0 C5 A:U2F604 4.1 25.1 1.0 O A:HOH716 4.2 41.8 1.0 C17 A:KMP605 4.2 28.4 1.0 CB A:THR293 4.2 49.0 1.0 CD A:GLN395 4.2 26.0 1.0 NE2 A:HIS370 4.3 28.3 1.0 C18 A:KMP605 4.3 29.6 1.0 C16 A:KMP605 4.4 33.1 1.0 CB A:ALA393 4.4 21.3 1.0 O24 A:KMP605 4.5 37.8 1.0 CD1 A:PHE392 4.6 28.9 1.0 CD2 A:HIS370 4.6 31.2 1.0 C19 A:KMP605 4.7 34.8 1.0 O2B A:U2F604 4.7 26.8 1.0 C15 A:KMP605 4.7 29.4 1.0 O4 A:U2F604 4.8 23.9 1.0 C14 A:KMP605 4.8 26.8 1.0 CG A:GLN395 4.9 18.5 1.0 O3A A:U2F604 5.0 36.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE


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 Phytolacca Americana UGT3 with Kaempferol and Udp-2FLUOROGLUCOSE within 5.0Å range: probe atom residue distance (Å) B Occ B:F604 b:29.8 occ:1.00 F1 B:U2F604 0.0 29.8 1.0 C2 B:U2F604 1.4 29.2 1.0 C1 B:U2F604 2.3 28.4 1.0 C3 B:U2F604 2.4 24.3 1.0 O1 B:U2F604 2.6 30.2 1.0 O3 B:U2F604 2.8 23.2 1.0 NE2 B:GLN395 3.1 25.2 1.0 OG1 B:THR293 3.6 54.6 1.0 O5 B:U2F604 3.7 31.3 1.0 C4 B:U2F604 3.7 24.9 1.0 PB B:U2F604 3.8 35.4 1.0 CE1 B:PHE392 3.8 38.2 1.0 O2B B:U2F604 4.0 38.4 1.0 C19 B:KMP605 4.0 35.2 1.0 CZ B:PHE392 4.1 48.4 1.0 CG2 B:THR293 4.2 58.8 1.0 C5 B:U2F604 4.2 27.8 1.0 NE2 B:HIS370 4.2 30.6 1.0 C18 B:KMP605 4.3 34.4 1.0 O1B B:U2F604 4.3 38.3 1.0 C14 B:KMP605 4.4 33.0 1.0 CB B:ALA393 4.4 23.8 1.0 O B:HOH879 4.4 47.6 1.0 CD B:GLN395 4.4 26.7 1.0 CB B:THR293 4.4 53.9 1.0 CD2 B:HIS370 4.5 30.0 1.0 CD1 B:PHE392 4.8 29.6 1.0 C11 B:KMP605 4.8 39.6 1.0 O4 B:U2F604 4.8 24.4 1.0 C17 B:KMP605 4.8 54.5 1.0 C15 B:KMP605 4.9 46.3 1.0 C10 B:KMP605 4.9 34.9 1.0

R.Maharjan, Y.Fukuda, T.Nakayama, T.Nakayama, H.Hamada, S.I.Ozaki, T.Inoue. Structural Basis For Substrate Recognition in the Phytolacca Americana Glycosyltransferase PAGT3. Acta Crystallogr D Struct V. 78 379 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35234151
DOI: 10.1107/S2059798322000869