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Calcium in PDB 7byv: Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose

Enzymatic activity of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose

All present enzymatic activity of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose:
3.2.1.145;

Protein crystallography data

The structure of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose, PDB code: 7byv was solved by K.Matsuyama, T.Ishida, N.Kishine, Z.Fujimoto, K.Igarashi, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.79 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.080, 50.412, 75.698, 90.00, 111.33, 90.00
R / Rfree (%) 16.6 / 24.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose (pdb code 7byv). 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 Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose, PDB code: 7byv:

Calcium binding site 1 out of 1 in 7byv

Go back to Calcium Binding Sites List in 7byv
Calcium binding site 1 out of 1 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose


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 Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208Q with Beta-1,3-Galactotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:18.9
occ:1.00
 O A:SER348 2.3 22.6 1.0
OE1 A:GLU329 2.3 24.1 1.0
OE1 A:GLU331 2.3 21.9 1.0
OD1 A:ASP443 2.4 27.5 1.0
O A:LYS351 2.4 25.4 1.0
O A:ASP443 2.6 22.2 1.0
OE2 A:GLU331 2.6 21.7 1.0
CD A:GLU331 2.8 20.0 1.0
CD A:GLU329 3.3 27.9 1.0
C A:SER348 3.4 25.7 1.0
C A:ASP443 3.5 24.6 1.0
C A:LYS351 3.5 23.7 1.0
CG A:ASP443 3.6 25.3 1.0
OE2 A:GLU329 3.9 24.8 1.0
CA A:ASP443 4.0 20.4 1.0
N A:SER348 4.1 26.9 1.0
CA A:SER348 4.1 24.9 1.0
N A:LYS351 4.3 22.7 1.0
CB A:SER348 4.3 19.1 1.0
CG A:GLU331 4.4 20.7 1.0
CG A:GLU329 4.4 24.6 1.0
CB A:ASP443 4.4 16.8 1.0
CA A:LYS351 4.4 24.5 1.0
N A:ALA352 4.5 21.6 1.0
OD2 A:ASP443 4.5 22.7 1.0
N A:GLY349 4.5 26.6 1.0
OG A:SER348 4.5 20.4 1.0
CA A:ALA352 4.5 19.6 1.0
N A:LYS444 4.6 22.0 1.0
CB A:GLU329 4.6 17.8 1.0
CB A:PHE347 4.6 27.4 1.0
N A:ALA330 4.6 22.0 1.0
CB A:LYS444 4.6 19.0 1.0
CA A:GLY349 4.7 23.9 1.0
C A:PHE347 4.7 26.6 1.0
CA A:GLU329 4.8 21.2 1.0
CB A:LYS351 4.9 21.7 1.0
N A:GLU331 4.9 20.0 1.0
CA A:LYS444 5.0 18.9 1.0

Reference:

K.Matsuyama, N.Kishine, Z.Fujimoto, N.Sunagawa, T.Kotake, Y.Tsumuraya, M.Samejima, K.Igarashi, S.Kaneko. Unique Active Site and Subsite Features in the Arabinogalactan-Degrading GH43 Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33093171
DOI: 10.1074/JBC.RA120.016149
Page generated: Wed Jul 9 21:04:40 2025

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