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Calcium in PDB 5z5d: Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08

Enzymatic activity of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08

All present enzymatic activity of Crystal Structure of A Thermostable Glycoside Hydrolase Family 43 {Beta}-1,4-Xylosidase From Geobacillus Thermoleovorans It-08:
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, PDB code: 5z5d 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) 46.13 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.076, 62.076, 275.789, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.6

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 (pdb code 5z5d). 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, PDB code: 5z5d:

Calcium binding site 1 out of 1 in 5z5d

Go back to Calcium Binding Sites List in 5z5d
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:15.3
occ:1.00
 OD1 A:ASP503 2.2 14.0 1.0
O A:SER344 2.3 16.1 1.0
O A:HOH960 2.3 20.1 1.0
O A:ASP503 2.4 10.2 1.0
O A:ASP316 2.4 14.0 1.0
O A:HOH712 2.5 30.6 1.0
O A:HOH842 2.6 23.6 1.0
C A:ASP503 3.4 11.3 1.0
CG A:ASP503 3.4 13.4 1.0
C A:SER344 3.5 17.2 1.0
C A:ASP316 3.5 15.1 1.0
CA A:ASP503 3.9 11.5 1.0
CB A:SER344 4.0 23.3 1.0
CA A:ASP316 4.0 16.7 1.0
CB A:ASP316 4.2 19.0 1.0
CA A:SER344 4.2 19.5 1.0
CB A:ASP503 4.3 12.1 1.0
OD2 A:ASP503 4.3 13.8 1.0
OD1 A:ASN318 4.4 31.1 1.0
N A:TRP345 4.5 15.4 1.0
O A:HOH734 4.5 36.9 1.0
N A:TRP504 4.6 10.5 1.0
N A:PHE317 4.6 14.8 1.0
OD1 A:ASP316 4.7 27.0 1.0
CA A:TRP345 4.7 14.8 1.0
CD1 A:TRP345 4.7 15.5 1.0
CB A:TRP504 4.8 10.5 1.0
CB A:PHE317 4.8 14.3 1.0
OG A:SER344 4.8 29.5 1.0
CA A:TRP504 4.9 10.4 1.0
CG A:ASP316 4.9 23.5 1.0
CG A:TRP345 4.9 15.1 1.0
NE1 A:TRP345 5.0 15.6 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: Mon Jul 15 15:42:57 2024

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