Bromine in PDB 6lzx: Structure of Phytolacca Americana UGT3 with 15-Crown-5

The structure of Structure of Phytolacca Americana UGT3 with 15-Crown-5, PDB code: 6lzx 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)	48.73 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.173, 103.298, 110.383, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26

The structure of Structure of Phytolacca Americana UGT3 with 15-Crown-5 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the Structure of Phytolacca Americana UGT3 with 15-Crown-5 (pdb code 6lzx). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of Phytolacca Americana UGT3 with 15-Crown-5, PDB code: 6lzx:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of Phytolacca Americana UGT3 with 15-Crown-5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Phytolacca Americana UGT3 with 15-Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br503 b:80.7 occ:1.00 CE A:LYS400 3.1 66.5 1.0 ND2 A:ASN403 3.4 52.1 1.0 CB A:ASN403 3.7 52.0 1.0 NZ A:LYS400 4.0 63.6 1.0 CG A:ASN403 4.1 55.8 1.0 CD A:LYS400 4.2 69.6 1.0 CD A:GLU399 4.2 62.5 1.0 CG A:PRO411 4.3 47.0 1.0 CG A:GLU399 4.3 56.3 1.0 OE1 A:GLU399 4.3 70.5 1.0 OE1 A:GLN404 4.4 78.1 1.0 CB A:PRO411 4.4 48.4 1.0 O A:GLU399 4.6 65.4 1.0 OE2 A:GLU399 4.6 63.5 1.0 CG A:GLN404 4.7 68.6 1.0 CD A:PRO411 4.8 49.0 1.0 CA A:LYS400 4.9 55.8 1.0 C A:GLU399 4.9 52.7 1.0 CD A:GLN404 5.0 76.0 1.0

Bromine binding site 2 out of 4 in the Structure of Phytolacca Americana UGT3 with 15-Crown-5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Phytolacca Americana UGT3 with 15-Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br504 b:65.7 occ:1.00 CB A:ASN230 3.6 57.5 1.0 CA A:GLU228 3.6 59.9 1.0 N A:ASN230 3.6 57.2 1.0 C A:GLU228 3.7 59.8 1.0 CD1 A:TYR231 3.8 45.5 1.0 CD A:PRO229 3.8 64.1 1.0 N A:PRO229 3.8 63.6 1.0 CE1 A:TYR231 3.9 48.0 1.0 CG A:PRO229 4.0 65.0 1.0 CG A:ASN230 4.1 55.0 1.0 CE1 A:HIS181 4.1 58.4 1.0 O A:GLU228 4.1 56.3 1.0 CA A:ASN230 4.2 57.1 1.0 ND2 A:ASN230 4.2 57.6 1.0 CB A:GLU228 4.3 64.3 1.0 CG2 A:ILE405 4.3 54.3 1.0 C A:PRO229 4.6 57.2 1.0 N A:TYR231 4.7 52.9 1.0 CA A:PRO229 4.7 61.2 1.0 NE2 A:HIS181 4.7 59.5 1.0 N A:GLU228 4.8 53.0 1.0 O A:LEU227 4.8 53.9 1.0 OD1 A:ASN230 4.9 60.7 1.0 C A:ASN230 4.9 55.2 1.0

Bromine binding site 3 out of 4 in the Structure of Phytolacca Americana UGT3 with 15-Crown-5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Phytolacca Americana UGT3 with 15-Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br501 b:0.2 occ:1.00 ND2 B:ASN403 3.3 37.4 1.0 CB B:ASN403 3.9 35.9 1.0 CD B:GLU399 3.9 60.1 1.0 OE1 B:GLU399 4.0 57.5 1.0 CG B:GLU399 4.0 53.3 1.0 CG B:ASN403 4.1 36.6 1.0 OE2 B:GLU399 4.3 67.1 1.0 CD B:LYS400 4.3 55.3 1.0 CB B:PRO411 4.3 43.8 1.0 CG B:PRO411 4.3 41.1 1.0 NZ B:LYS400 4.3 62.4 1.0 O B:GLU399 4.5 43.2 1.0 CE B:LYS400 4.7 58.2 1.0 C B:GLU399 4.9 43.0 1.0 CD B:PRO411 4.9 43.5 1.0 CA B:LYS400 5.0 47.8 1.0

Bromine binding site 4 out of 4 in the Structure of Phytolacca Americana UGT3 with 15-Crown-5


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Phytolacca Americana UGT3 with 15-Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br502 b:46.1 occ:1.00 ND2 B:ASN230 3.3 37.3 1.0 CB B:ASN230 3.6 41.9 1.0 CA B:GLU228 3.6 38.6 1.0 N B:ASN230 3.7 39.4 1.0 C B:GLU228 3.7 37.9 1.0 CD1 B:TYR231 3.7 35.8 1.0 CE1 B:TYR231 3.9 35.4 1.0 CD B:PRO229 3.9 38.4 1.0 N B:PRO229 4.0 39.9 1.0 CG B:ASN230 4.0 39.9 1.0 CG B:PRO229 4.0 39.8 1.0 O B:GLU228 4.1 38.3 1.0 CE1 B:HIS181 4.1 50.0 1.0 CG2 B:ILE405 4.1 40.9 1.0 CA B:ASN230 4.2 40.0 1.0 CB B:GLU228 4.3 41.7 1.0 N B:TYR231 4.6 43.7 1.0 C B:PRO229 4.7 37.9 1.0 N B:GLU228 4.8 38.4 1.0 NE2 B:HIS181 4.8 46.4 1.0 CA B:PRO229 4.8 38.0 1.0 O B:LEU227 4.8 44.5 1.0 C B:ASN230 4.9 42.5 1.0 ND1 B:HIS181 5.0 43.8 1.0

R.Maharjan, Y.Fukuda, T.Nakayama, T.Nakayama, H.Hamada, S.Ozaki, T.Inoue. Crown-Ether-Mediated Crystal Structures of the Glycosyltransferase PAGT3 From Phytolacca Americana. Acta Crystallogr.,Sect.D 2020.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798320005306