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Calcium in PDB 5z5i: Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose

Enzymatic activity of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose

All present enzymatic activity of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose:
3.2.1.37;

Protein crystallography data

The structure of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose, PDB code: 5z5i was solved by A.Rohman, N.Van Oosterwijk, N.N.T.Puspaningsih, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.816, 59.816, 277.870, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose (pdb code 5z5i). 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 Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose, PDB code: 5z5i:

Calcium binding site 1 out of 1 in 5z5i

Go back to Calcium Binding Sites List in 5z5i
Calcium binding site 1 out of 1 in the Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08 in Complex with L-Arabinose and D-Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:13.3
occ:1.00
 O A:HOH736 2.3 18.8 1.0
O A:SER344 2.3 11.7 1.0
O A:ASP316 2.4 13.0 1.0
O A:ASP503 2.4 11.1 1.0
OD1 A:ASP503 2.4 14.0 1.0
O A:HOH1061 2.4 18.9 1.0
O A:HOH787 2.5 19.9 1.0
C A:ASP503 3.5 10.9 1.0
C A:ASP316 3.5 14.2 1.0
CG A:ASP503 3.5 12.8 1.0
C A:SER344 3.5 12.3 1.0
CA A:ASP503 4.0 11.3 1.0
CB A:ASP316 4.1 16.4 1.0
CA A:ASP316 4.1 14.7 1.0
CB A:SER344 4.1 12.2 0.5
CB A:SER344 4.1 13.6 0.5
OG A:SER344 4.2 11.1 0.5
CA A:SER344 4.3 12.3 0.5
CA A:SER344 4.3 12.9 0.5
CB A:ASP503 4.3 12.1 1.0
OD2 A:ASP503 4.3 13.0 1.0
O A:HOH830 4.4 24.7 1.0
OD1 A:ASN318 4.4 22.5 1.0
N A:TRP345 4.5 12.0 1.0
N A:PHE317 4.6 14.1 1.0
N A:TRP504 4.6 10.7 1.0
CA A:TRP345 4.7 12.4 1.0
CB A:PHE317 4.8 14.5 1.0
CD1 A:TRP345 4.9 13.3 1.0
CB A:TRP504 4.9 10.7 1.0
CG A:ASP316 4.9 18.5 1.0
C A:PHE317 4.9 16.3 1.0
O A:HOH1188 5.0 16.4 1.0
CA A:PHE317 5.0 15.1 1.0
CA A:TRP504 5.0 10.9 1.0

Reference:

A.Rohman, N.Van Oosterwijk, N.N.T.Puspaningsih, B.W.Dijkstra. Structural Basis of Product Inhibition By Arabinose and Xylose of the Thermostable GH43 Beta-1,4-Xylosidase From Geobacillus Thermoleovorans It-08. Plos One V. 13 96358 2018.
ISSN: ESSN 1932-6203
PubMed: 29698436
DOI: 10.1371/JOURNAL.PONE.0196358
Page generated: Wed Jul 9 12:09:48 2025

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