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Bromine in PDB 6lzy: Structure of Phytolacca Americana UGT3 with 18-Crown-6

Protein crystallography data

The structure of Structure of Phytolacca Americana UGT3 with 18-Crown-6, PDB code: 6lzy 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) 49.22 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.732, 103.864, 111.638, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.9

Other elements in 6lzy:

The structure of Structure of Phytolacca Americana UGT3 with 18-Crown-6 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of Phytolacca Americana UGT3 with 18-Crown-6 (pdb code 6lzy). 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 18-Crown-6, PDB code: 6lzy:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 6lzy

Go back to Bromine Binding Sites List in 6lzy
Bromine binding site 1 out of 4 in the Structure of Phytolacca Americana UGT3 with 18-Crown-6


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 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br601

b:34.2
occ:1.00
ND2 A:ASN230 3.1 32.7 1.0
N A:ASN230 3.6 34.3 1.0
CB A:ASN230 3.6 31.1 1.0
C A:GLU228 3.7 31.4 1.0
CD A:PRO229 3.7 43.1 1.0
N A:PRO229 3.7 37.1 1.0
CA A:GLU228 3.8 34.0 1.0
CG A:ASN230 3.8 31.1 1.0
CD2 A:TYR231 3.8 33.1 1.0
CE2 A:TYR231 3.9 33.2 1.0
CE1 A:HIS181 3.9 33.4 1.0
CG2 A:ILE405 4.0 34.9 1.0
CA A:ASN230 4.2 31.7 1.0
CG A:PRO229 4.2 42.5 1.0
O A:GLU228 4.3 34.3 1.0
CB A:GLU228 4.4 34.4 1.0
C A:PRO229 4.5 35.8 1.0
CA A:PRO229 4.6 36.9 1.0
N A:TYR231 4.6 32.4 1.0
NE2 A:HIS181 4.7 31.9 1.0
ND1 A:HIS181 4.8 34.0 1.0
O A:LEU227 4.9 32.5 1.0
C A:ASN230 4.9 33.7 1.0
N A:GLU228 4.9 32.8 1.0
OD1 A:ASN230 5.0 28.9 1.0

Bromine binding site 2 out of 4 in 6lzy

Go back to Bromine Binding Sites List in 6lzy
Bromine binding site 2 out of 4 in the Structure of Phytolacca Americana UGT3 with 18-Crown-6


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 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br602

b:45.4
occ:1.00
NE2 A:GLN404 3.2 49.7 1.0
ND2 A:ASN403 3.4 27.5 1.0
CB A:ASN403 3.7 26.4 1.0
CE A:LYS400 3.9 34.6 1.0
O A:HOH742 4.0 35.8 1.0
CG A:ASN403 4.1 28.4 1.0
NZ A:LYS400 4.1 36.9 1.0
CG A:GLU399 4.2 33.2 1.0
CG A:PRO411 4.2 28.5 1.0
CD A:LYS400 4.2 33.7 1.0
CD A:GLU399 4.3 36.3 1.0
CD A:GLN404 4.3 48.8 1.0
CB A:PRO411 4.4 30.4 1.0
OE1 A:GLU399 4.5 34.8 1.0
O A:GLU399 4.5 24.2 1.0
CG A:GLN404 4.6 38.1 1.0
CD A:PRO411 4.6 31.1 1.0
O A:HOH707 4.8 39.1 1.0
OE2 A:GLU399 4.9 41.4 1.0
C A:GLU399 5.0 29.0 1.0
CA A:LYS400 5.0 28.7 1.0

Bromine binding site 3 out of 4 in 6lzy

Go back to Bromine Binding Sites List in 6lzy
Bromine binding site 3 out of 4 in the Structure of Phytolacca Americana UGT3 with 18-Crown-6


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 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:28.6
occ:1.00
ND2 B:ASN230 3.1 24.8 1.0
N B:ASN230 3.6 24.9 1.0
C B:GLU228 3.7 25.2 1.0
CA B:GLU228 3.7 23.9 1.0
CB B:ASN230 3.7 27.2 1.0
N B:PRO229 3.7 25.4 1.0
CD2 B:TYR231 3.8 22.7 1.0
CD B:PRO229 3.8 24.7 1.0
CG B:ASN230 3.8 25.6 1.0
CE2 B:TYR231 3.9 25.5 1.0
CE1 B:HIS181 3.9 34.6 1.0
CG2 B:ILE405 4.0 29.7 1.0
CG B:PRO229 4.2 23.8 1.0
CA B:ASN230 4.2 25.7 1.0
O B:GLU228 4.3 27.7 1.0
CB B:GLU228 4.4 27.3 1.0
C B:PRO229 4.5 25.5 1.0
CA B:PRO229 4.6 24.2 1.0
N B:TYR231 4.7 28.1 1.0
NE2 B:HIS181 4.8 36.7 1.0
O B:LEU227 4.8 21.9 1.0
ND1 B:HIS181 4.8 31.1 1.0
N B:GLU228 4.8 24.1 1.0
C B:ASN230 4.9 26.2 1.0
CB B:PRO229 5.0 25.7 1.0
OD1 B:ASN230 5.0 26.9 1.0

Bromine binding site 4 out of 4 in 6lzy

Go back to Bromine Binding Sites List in 6lzy
Bromine binding site 4 out of 4 in the Structure of Phytolacca Americana UGT3 with 18-Crown-6


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 18-Crown-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br512

b:0.0
occ:1.00
ND2 B:ASN403 3.3 24.6 1.0
CB B:ASN403 3.5 24.7 1.0
OE1 B:GLN404 3.7 41.2 1.0
CG B:ASN403 3.9 27.6 1.0
CG B:GLU399 4.0 33.8 1.0
O B:HOH630 4.1 37.1 1.0
CD B:GLU399 4.1 33.9 1.0
CG B:PRO411 4.2 26.2 1.0
CB B:PRO411 4.3 24.5 1.0
OE2 B:GLU399 4.3 35.9 1.0
CD B:GLN404 4.4 49.2 1.0
CG B:GLN404 4.5 45.0 1.0
O B:GLU399 4.5 27.3 1.0
OE1 B:GLU399 4.5 29.2 1.0
CE B:LYS400 4.6 41.6 1.0
CD B:PRO411 4.6 25.8 1.0
NZ B:LYS400 4.6 42.9 1.0
CD B:LYS400 4.8 38.3 1.0
CA B:ASN403 4.9 26.8 1.0
C B:GLU399 4.9 31.1 1.0
O B:HOH624 5.0 36.4 1.0

Reference:

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
Page generated: Sat Dec 12 02:34:48 2020

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