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Sodium 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:

Bromine (Br) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Phytolacca Americana UGT3 with 18-Crown-6, PDB code: 6lzy:

Sodium binding site 1 out of 1 in 6lzy

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na607

b:34.7
occ:1.00
O A:GLU238 2.1 35.7 1.0
O B:GLU238 2.3 39.6 1.0
OAM B:O4B501 2.5 31.2 1.0
OAN B:O4B501 2.5 31.9 1.0
OAO B:O4B501 2.6 31.4 1.0
OAP B:O4B501 2.8 31.7 1.0
OAQ B:O4B501 2.8 30.7 1.0
OAR B:O4B501 3.0 29.8 1.0
C A:GLU238 3.3 38.6 1.0
CAA B:O4B501 3.4 33.0 1.0
CAB B:O4B501 3.4 31.2 1.0
C B:GLU238 3.5 32.8 1.0
CAI B:O4B501 3.5 30.2 1.0
CAH B:O4B501 3.5 29.6 1.0
CAG B:O4B501 3.5 31.3 1.0
CAC B:O4B501 3.5 31.7 1.0
CAE B:O4B501 3.6 32.1 1.0
CAD B:O4B501 3.6 31.9 1.0
CAL B:O4B501 3.7 29.6 1.0
CAF B:O4B501 3.7 31.1 1.0
CAJ B:O4B501 3.8 30.6 1.0
CAK B:O4B501 3.8 30.8 1.0
CA A:GLU238 4.2 38.1 1.0
N A:LEU239 4.3 35.1 1.0
CA A:LEU239 4.3 32.4 1.0
CA B:GLU238 4.3 34.5 1.0
N B:LEU239 4.5 29.1 1.0
CA B:LEU239 4.5 29.3 1.0
C A:LEU239 4.8 32.4 1.0
O B:LYS237 4.8 38.2 1.0
C B:LEU239 4.9 29.8 1.0
O A:LYS237 4.9 39.1 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: Tue Dec 15 12:34:28 2020

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