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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: Wed Oct 9 12:43:07 2024

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