Atomistry » Sodium » PDB 8k7x-8oyl » 8k7x
Atomistry »
  Sodium »
    PDB 8k7x-8oyl »
      8k7x »

Sodium in PDB 8k7x: Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris

Enzymatic activity of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris

All present enzymatic activity of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris:
3.2.1.185;

Protein crystallography data

The structure of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris, PDB code: 8k7x was solved by L.Pan, S.Maruyama, M.Miyake, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.76 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.592, 111.571, 153.01, 90, 90, 90
R / Rfree (%) 14.3 / 16.7

Other elements in 8k7x:

The structure of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris (pdb code 8k7x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris, PDB code: 8k7x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8k7x

Go back to Sodium Binding Sites List in 8k7x
Sodium binding site 1 out of 2 in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1303

b:32.6
occ:1.00
 OD2 A:ASP948 2.2 28.1 1.0
O A:HOH1865 2.2 33.9 1.0
O A:HOH2083 2.2 27.8 1.0
CG A:ASP948 3.3 23.2 1.0
OD1 A:ASP948 3.9 26.5 1.0
CB A:ASP948 4.4 17.3 1.0

Sodium binding site 2 out of 2 in 8k7x

Go back to Sodium Binding Sites List in 8k7x
Sodium binding site 2 out of 2 in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1223) in Complex with Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1304

b:34.7
occ:1.00
 O A:HOH1753 2.0 25.3 1.0
O A:HOH1457 2.2 15.8 1.0
O A:HOH2323 2.3 38.7 1.0
O A:HOH1429 2.4 31.2 1.0
O A:HOH1642 2.5 29.6 1.0
OD2 A:ASP925 3.9 13.6 1.0
OD1 A:ASP925 4.2 13.1 1.0
O A:ALA927 4.2 13.0 1.0
O A:ALA926 4.3 10.5 1.0
CG A:ASP925 4.4 13.7 1.0
CA A:ALA927 4.5 12.9 1.0
O A:HOH2308 4.6 48.4 1.0
C A:ALA927 4.7 12.1 1.0

Reference:

K.Fujita, H.Tsunomachi, P.Lixia, S.Maruyama, M.Miyake, A.Dakeshita, K.Kitahara, K.Tanaka, Y.Ito, A.Ishiwata, S.Fushinobu. Bifidobacterial GH146 Beta-L-Arabinofuranosidase For the Removal of Beta 1,3-L-Arabinofuranosides on Plant Glycans. Appl.Microbiol.Biotechnol. V. 108 199 2024.
ISSN: ESSN 1432-0614
PubMed: 38324037
DOI: 10.1007/S00253-024-13014-8
Page generated: Mon Aug 18 14:51:44 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy