Calcium in PDB 7bys: Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A Apo Form

Enzymatic activity of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A Apo Form

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

Protein crystallography data

The structure of Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A Apo Form, PDB code: 7bys 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) 8.00 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.470, 66.262, 74.021, 72.03, 84.68, 82.15
R / Rfree (%) 15.5 / 18.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 7bys

Go back to Calcium Binding Sites List in 7bys
Calcium binding site 1 out of 2 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:10.4
occ:1.00
OE1 A:GLU329 2.3 13.5 1.0
OD1 A:ASP443 2.3 11.7 1.0
O A:LYS351 2.3 9.8 1.0
O A:SER348 2.4 11.8 1.0
OE1 A:GLU331 2.5 12.3 1.0
O A:ASP443 2.5 10.3 1.0
OE2 A:GLU331 2.6 13.6 1.0
CD A:GLU331 2.9 13.1 1.0
C A:ASP443 3.4 10.8 1.0
C A:SER348 3.5 11.5 1.0
CD A:GLU329 3.5 14.9 1.0
C A:LYS351 3.5 11.3 1.0
CG A:ASP443 3.5 10.7 1.0
CA A:ASP443 3.9 7.6 1.0
CA A:SER348 4.2 11.5 1.0
CB A:SER348 4.2 11.8 1.0
N A:SER348 4.2 10.6 1.0
CB A:GLU329 4.3 12.4 1.0
N A:LYS351 4.3 11.4 1.0
CB A:ASP443 4.3 8.6 1.0
OE2 A:GLU329 4.3 14.1 1.0
CG A:GLU329 4.4 12.9 1.0
CG A:GLU331 4.4 11.8 1.0
N A:ALA352 4.4 10.9 1.0
CA A:LYS351 4.4 11.1 1.0
OD2 A:ASP443 4.5 11.3 1.0
CA A:ALA352 4.5 10.2 1.0
N A:GLY349 4.5 9.8 1.0
N A:LYS444 4.5 10.0 1.0
CB A:PHE347 4.6 11.7 1.0
N A:ALA330 4.6 11.9 1.0
CA A:GLU329 4.7 11.9 1.0
CB A:LYS444 4.7 11.4 1.0
OG A:SER348 4.7 14.1 1.0
CA A:GLY349 4.7 11.3 1.0
CB A:LYS351 4.8 12.4 1.0
C A:PHE347 4.8 10.2 1.0
CA A:LYS444 5.0 11.1 1.0

Calcium binding site 2 out of 2 in 7bys

Go back to Calcium Binding Sites List in 7bys
Calcium binding site 2 out of 2 in the Crystal Structure of Exo-Beta-1,3-Galactanase From Phanerochaete Chrysosporium PC1,3GAL43A Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:12.0
occ:1.00
OE1 B:GLU329 2.3 13.2 1.0
OD1 B:ASP443 2.3 13.5 1.0
O B:LYS351 2.4 14.1 1.0
O B:SER348 2.4 12.7 1.0
OE1 B:GLU331 2.4 13.8 1.0
OE2 B:GLU331 2.5 15.2 1.0
O B:ASP443 2.6 11.6 1.0
CD B:GLU331 2.8 13.8 1.0
C B:ASP443 3.4 9.2 1.0
CD B:GLU329 3.5 12.8 1.0
C B:LYS351 3.5 15.5 1.0
C B:SER348 3.5 12.3 1.0
CG B:ASP443 3.5 13.3 1.0
CA B:ASP443 3.9 9.5 1.0
CB B:SER348 4.1 14.3 1.0
CA B:SER348 4.2 12.4 1.0
N B:SER348 4.3 12.0 1.0
CB B:GLU329 4.3 11.4 1.0
CB B:ASP443 4.3 10.2 1.0
OE2 B:GLU329 4.3 14.8 1.0
N B:LYS351 4.3 14.4 1.0
CG B:GLU329 4.4 11.9 1.0
CG B:GLU331 4.4 13.8 1.0
N B:ALA352 4.4 12.5 1.0
CA B:LYS351 4.4 13.0 1.0
OD2 B:ASP443 4.4 14.0 1.0
CA B:ALA352 4.5 11.6 1.0
N B:LYS444 4.5 11.3 1.0
N B:GLY349 4.5 12.0 1.0
CB B:PHE347 4.6 14.9 1.0
N B:ALA330 4.6 10.8 1.0
CB B:LYS444 4.7 9.9 1.0
CA B:GLU329 4.7 10.7 1.0
OG B:SER348 4.7 14.4 1.0
CB B:LYS351 4.8 15.4 1.0
CA B:GLY349 4.8 13.2 1.0
C B:PHE347 4.8 13.2 1.0
CA B:LYS444 4.9 8.2 1.0
O B:HOH701 5.0 26.1 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: Sat Dec 12 08:03:15 2020

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