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Calcium in PDB 8xy0: Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr

Enzymatic activity of Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr

All present enzymatic activity of Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr:
3.2.1.8;

Protein crystallography data

The structure of Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr, PDB code: 8xy0 was solved by T.Nakamura, T.Takita, K.Mizutani, B.Mikami, S.Nakamura, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.27 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.179, 41.783, 80.873, 90, 90.52, 90
R / Rfree (%) 17.1 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr (pdb code 8xy0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr, PDB code: 8xy0:

Calcium binding site 1 out of 1 in 8xy0

Go back to Calcium Binding Sites List in 8xy0
Calcium binding site 1 out of 1 in the Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.6
occ:1.00
 O A:ARG348 2.3 24.3 1.0
OD1 A:ASP289 2.5 25.3 1.0
O A:HOH666 2.5 20.1 1.0
OD1 A:ASP351 2.5 24.2 1.0
O A:HOH533 2.6 24.7 1.0
O A:HOH548 2.6 26.2 1.0
O A:HOH767 2.6 31.7 1.0
CG A:ASP289 3.4 30.1 1.0
C A:ARG348 3.4 25.5 1.0
CG A:ASP351 3.5 28.3 1.0
OD2 A:ASP351 3.9 33.2 1.0
OD2 A:ASP289 4.0 30.5 1.0
O A:HOH669 4.2 36.3 1.0
CA A:ARG348 4.3 18.6 1.0
O A:HOH578 4.3 19.9 1.0
CA A:ILE349 4.3 16.5 1.0
N A:ILE349 4.3 19.2 1.0
O A:ASP351 4.3 18.2 1.0
O A:HOH744 4.4 35.3 1.0
CB A:ASP289 4.4 22.5 1.0
CA A:ASP289 4.4 17.7 1.0
O A:ASP289 4.6 18.4 1.0
CB A:ARG348 4.8 20.1 1.0
C A:ILE349 4.9 20.6 1.0
CB A:ASP351 4.9 26.4 1.0
N A:ASP351 4.9 20.4 1.0
C A:ASP351 4.9 24.7 1.0
C A:ASP289 5.0 20.9 1.0

Reference:

T.Nakamura, T.Takita, K.Kuwata, K.Mizutani, B.Mikami, S.Nakamura, K.Yasukawa. Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr. Sci Rep V. 14 7767 2024.
ISSN: ESSN 2045-2322
PubMed: 38565938
DOI: 10.1038/S41598-024-57819-Z
Page generated: Thu Jul 10 08:30:04 2025

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