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Sodium in PDB 7dfn: Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose

Enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose

All present enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose, PDB code: 7dfn was solved by Z.Fujimoto, N.Kishine, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.233, 134.233, 72.235, 90, 90, 120
R / Rfree (%) 16.5 / 20.9

Other elements in 7dfn:

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose also contains other interesting chemical elements:

Chlorine (Cl) 59 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose (pdb code 7dfn). 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 Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose, PDB code: 7dfn:

Sodium binding site 1 out of 1 in 7dfn

Go back to Sodium Binding Sites List in 7dfn
Sodium binding site 1 out of 1 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na418

b:32.2
occ:1.00
 O A:HOH574 2.2 28.0 1.0
O A:HOH587 2.3 26.6 1.0
O A:HOH623 2.4 34.9 1.0
O A:GLY162 2.4 18.8 1.0
O A:HOH594 2.5 26.2 1.0
O A:HOH627 3.6 31.0 1.0
C A:GLY162 3.6 17.8 1.0
CA A:MET163 4.1 17.4 1.0
O A:HOH537 4.1 28.5 1.0
OE1 A:GLN118 4.2 24.7 1.0
N A:MET163 4.3 17.4 1.0
CL A:CL404 4.3 33.6 1.0
O A:HOH641 4.5 14.6 1.0
O A:HOH635 4.6 30.0 1.0
N A:GLN164 4.6 17.3 1.0
CA A:GLY162 4.7 17.8 1.0
OH A:TYR136 4.8 14.7 1.0
C A:MET163 4.9 17.7 1.0
CG A:MET163 4.9 18.9 1.0
NE2 A:GLN118 5.0 28.2 1.0

Reference:

Z.Fujimoto, K.Naomi, K.Teramoto, S.Tsutsui, S.Kaneko. Structure-Based Substrate Specificity of GH11 Xylanase From Streptomyces Olivaceoviridis E-86 To Be Published.
Page generated: Tue Oct 8 16:34:34 2024

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