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Calcium in PDB 7byx: Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose

Enzymatic activity of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose

All present enzymatic activity of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A 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 E208A with Beta-1,3-Galactotriose, PDB code: 7byx 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) 31.14 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.737, 156.737, 147.713, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose (pdb code 7byx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose, PDB code: 7byx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7byx

Go back to Calcium Binding Sites List in 7byx
Calcium binding site 1 out of 4 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A 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 E208A with Beta-1,3-Galactotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:18.2
occ:1.00
 OE2 A:GLU329 2.3 17.9 1.0
O A:LYS351 2.3 20.1 1.0
OD1 A:ASP443 2.3 22.5 1.0
O A:SER348 2.4 21.7 1.0
OE2 A:GLU331 2.5 26.8 1.0
OE1 A:GLU331 2.5 23.5 1.0
O A:ASP443 2.7 19.9 1.0
CD A:GLU331 2.8 26.6 1.0
C A:SER348 3.4 21.5 1.0
CD A:GLU329 3.5 19.3 1.0
C A:LYS351 3.5 24.2 1.0
C A:ASP443 3.5 17.7 1.0
CG A:ASP443 3.6 24.0 1.0
CA A:ASP443 4.0 18.7 1.0
CB A:SER348 4.1 22.2 1.0
CA A:SER348 4.1 22.9 1.0
N A:SER348 4.2 22.5 1.0
CB A:GLU329 4.3 25.3 1.0
OE1 A:GLU329 4.3 23.2 1.0
N A:LYS351 4.3 23.0 1.0
CG A:GLU331 4.4 23.1 1.0
CG A:GLU329 4.4 23.1 1.0
CB A:ASP443 4.4 19.5 1.0
N A:ALA352 4.4 20.8 1.0
CA A:LYS351 4.4 23.3 1.0
N A:GLY349 4.4 21.8 1.0
OD2 A:ASP443 4.4 26.9 1.0
CA A:ALA352 4.5 23.6 1.0
N A:LYS444 4.5 18.3 1.0
OG A:SER348 4.6 25.4 1.0
CB A:LYS444 4.6 20.1 1.0
CB A:PHE347 4.6 19.2 1.0
N A:ALA330 4.7 22.8 1.0
CA A:GLY349 4.7 20.1 1.0
CA A:GLU329 4.7 19.2 1.0
C A:PHE347 4.9 24.4 1.0
CB A:LYS351 4.9 18.5 1.0
O A:HOH695 4.9 33.3 1.0
CA A:LYS444 5.0 19.1 1.0

Calcium binding site 2 out of 4 in 7byx

Go back to Calcium Binding Sites List in 7byx
Calcium binding site 2 out of 4 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A 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 2 of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca508

b:20.6
occ:1.00
 O B:LYS351 2.2 22.4 1.0
OE1 B:GLU329 2.3 20.4 1.0
OD1 B:ASP443 2.3 22.0 1.0
O B:SER348 2.4 20.0 1.0
OE1 B:GLU331 2.6 24.9 1.0
O B:ASP443 2.7 20.5 1.0
OE2 B:GLU331 2.7 25.6 1.0
CD B:GLU331 3.0 31.2 1.0
C B:LYS351 3.4 25.7 1.0
C B:SER348 3.4 22.4 1.0
CD B:GLU329 3.5 23.5 1.0
CG B:ASP443 3.5 22.9 1.0
C B:ASP443 3.5 19.5 1.0
CA B:ASP443 4.0 20.4 1.0
CA B:SER348 4.1 19.0 1.0
N B:SER348 4.1 18.0 1.0
CB B:SER348 4.1 18.6 1.0
CB B:GLU329 4.2 22.9 1.0
N B:LYS351 4.2 23.1 1.0
N B:ALA352 4.3 22.8 1.0
OE2 B:GLU329 4.3 25.5 1.0
CA B:LYS351 4.3 27.2 1.0
CB B:ASP443 4.4 17.1 1.0
CG B:GLU329 4.4 20.8 1.0
OD2 B:ASP443 4.4 24.4 1.0
CA B:ALA352 4.4 26.0 1.0
N B:GLY349 4.5 21.7 1.0
N B:LYS444 4.5 18.8 1.0
CG B:GLU331 4.6 19.8 1.0
N B:ALA330 4.6 22.6 1.0
CB B:PHE347 4.7 23.1 1.0
OG B:SER348 4.7 19.8 1.0
CA B:GLU329 4.7 23.8 1.0
CB B:LYS444 4.7 20.9 1.0
CA B:GLY349 4.7 18.4 1.0
C B:PHE347 4.8 17.7 1.0
O B:HOH613 4.8 35.1 1.0
CB B:LYS351 4.9 27.4 1.0
C B:GLY349 5.0 22.9 1.0

Calcium binding site 3 out of 4 in 7byx

Go back to Calcium Binding Sites List in 7byx
Calcium binding site 3 out of 4 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A 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 3 of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca508

b:40.2
occ:1.00
 O C:LYS351 2.3 46.4 1.0
OE1 C:GLU329 2.3 43.8 1.0
O C:SER348 2.3 40.7 1.0
OD1 C:ASP443 2.3 45.1 1.0
OE2 C:GLU331 2.5 46.5 1.0
OE1 C:GLU331 2.6 49.0 1.0
O C:ASP443 2.7 44.9 1.0
CD C:GLU331 2.9 53.0 1.0
CD C:GLU329 3.4 45.6 1.0
C C:SER348 3.5 46.3 1.0
C C:LYS351 3.5 50.9 1.0
CG C:ASP443 3.5 45.1 1.0
C C:ASP443 3.6 41.1 1.0
CA C:ASP443 4.0 37.6 1.0
CA C:SER348 4.2 43.8 1.0
N C:SER348 4.2 37.7 1.0
OE2 C:GLU329 4.2 43.9 1.0
CG C:GLU329 4.2 48.5 1.0
CB C:SER348 4.2 36.3 1.0
CB C:GLU329 4.2 44.2 1.0
N C:LYS351 4.2 43.5 1.0
OD2 C:ASP443 4.3 41.1 1.0
CA C:LYS351 4.4 51.8 1.0
CB C:ASP443 4.4 45.1 1.0
N C:ALA352 4.4 50.1 1.0
CG C:GLU331 4.4 52.9 1.0
N C:GLY349 4.5 43.4 1.0
CA C:ALA352 4.5 51.4 1.0
OG C:SER348 4.5 40.3 1.0
N C:ALA330 4.6 48.3 1.0
CB C:LYS444 4.7 41.3 1.0
N C:LYS444 4.7 38.0 1.0
CB C:PHE347 4.7 47.2 1.0
CA C:GLU329 4.7 40.2 1.0
CA C:GLY349 4.7 40.7 1.0
CB C:LYS351 4.8 51.1 1.0
C C:PHE347 4.8 42.5 1.0
C C:GLY349 4.9 41.7 1.0

Calcium binding site 4 out of 4 in 7byx

Go back to Calcium Binding Sites List in 7byx
Calcium binding site 4 out of 4 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A 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 4 of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A E208A with Beta-1,3-Galactotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca507

b:42.0
occ:1.00
 OE1 D:GLU329 2.3 40.6 1.0
O D:SER348 2.3 45.5 1.0
O D:LYS351 2.3 50.2 1.0
OE2 D:GLU331 2.5 46.3 1.0
O D:ASP443 2.6 42.8 1.0
OE1 D:GLU331 2.6 46.5 1.0
OD1 D:ASP443 2.6 44.2 1.0
CD D:GLU331 2.9 46.6 1.0
C D:SER348 3.5 47.8 1.0
C D:LYS351 3.5 54.3 1.0
C D:ASP443 3.5 38.6 1.0
CD D:GLU329 3.5 41.5 1.0
CG D:ASP443 3.8 44.6 1.0
CA D:ASP443 4.0 43.0 1.0
CA D:SER348 4.2 42.6 1.0
CB D:SER348 4.2 34.6 1.0
N D:SER348 4.2 43.3 1.0
CB D:GLU329 4.3 41.2 1.0
N D:ALA352 4.4 58.3 1.0
OE2 D:GLU329 4.4 41.0 1.0
N D:LYS351 4.4 48.6 1.0
CA D:ALA352 4.4 57.8 1.0
CG D:GLU329 4.4 35.0 1.0
CG D:GLU331 4.5 46.8 1.0
CA D:LYS351 4.5 51.8 1.0
CB D:ASP443 4.5 42.1 1.0
N D:GLY349 4.5 50.1 1.0
N D:ALA330 4.5 48.1 1.0
N D:LYS444 4.6 37.0 1.0
CB D:PHE347 4.6 46.1 1.0
OD2 D:ASP443 4.7 45.8 1.0
CA D:GLY349 4.7 44.6 1.0
CA D:GLU329 4.7 40.6 1.0
CB D:LYS444 4.7 37.1 1.0
OG D:SER348 4.8 40.9 1.0
C D:PHE347 4.9 45.9 1.0
CB D:LYS351 4.9 50.8 1.0
CB D:ALA352 4.9 45.3 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 21:04:46 2025

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