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Calcium in PDB 7c7d: Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3

Enzymatic activity of Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3

All present enzymatic activity of Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3:
3.2.1.59;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3, PDB code: 7c7d was solved by T.Itoh, N.Panti, Y.Toyotake, J.Hayashi, W.Suyotha, S.Yano, M.Wakayama, T.Hibi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.21 / 1.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.508, 91.329, 164.447, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 15.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3 (pdb code 7c7d). 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 the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3, PDB code: 7c7d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7c7d

Go back to Calcium Binding Sites List in 7c7d
Calcium binding site 1 out of 2 in the Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3


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 the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:11.8
occ:1.00
 OD1 A:ASP191 2.3 12.6 1.0
OE2 A:GLU63 2.3 12.9 1.0
O A:GLN91 2.4 12.0 1.0
O A:SER88 2.4 11.5 1.0
OE1 A:GLU65 2.5 13.5 1.0
OE2 A:GLU65 2.5 13.6 1.0
O A:ASP191 2.6 12.7 1.0
CD A:GLU65 2.8 13.3 1.0
CD A:GLU63 3.4 14.0 1.0
C A:ASP191 3.5 11.9 1.0
C A:SER88 3.5 11.7 1.0
CG A:ASP191 3.5 11.6 1.0
C A:GLN91 3.5 11.6 1.0
CA A:ASP191 3.9 11.8 1.0
CB A:SER88 4.0 12.2 1.0
CA A:SER88 4.1 11.3 1.0
CB A:GLU63 4.2 13.3 1.0
N A:SER88 4.2 11.0 1.0
OE1 A:GLU63 4.2 16.0 1.0
CB A:ASP191 4.3 11.8 1.0
CG A:GLU63 4.3 13.2 1.0
N A:ALA92 4.4 13.3 1.0
CG A:GLU65 4.4 14.6 1.0
CA A:ALA92 4.4 13.6 1.0
N A:GLN91 4.4 11.9 1.0
OD2 A:ASP191 4.4 12.3 1.0
CA A:GLN91 4.4 12.8 1.0
N A:ALA64 4.5 13.6 1.0
N A:VAL192 4.5 12.6 1.0
CB A:ALA87 4.5 12.2 1.0
N A:GLY89 4.5 10.8 1.0
CA A:GLU63 4.6 13.7 1.0
CB A:VAL192 4.6 12.8 1.0
C A:ALA87 4.7 11.2 1.0
CB A:GLN91 4.8 13.9 1.0
OG A:SER88 4.8 12.8 1.0
CA A:GLY89 4.8 13.1 1.0
CB A:ALA92 4.9 13.4 1.0
O A:HOH939 4.9 20.8 1.0
CA A:VAL192 4.9 12.7 1.0
C A:GLU63 5.0 13.8 1.0

Calcium binding site 2 out of 2 in 7c7d

Go back to Calcium Binding Sites List in 7c7d
Calcium binding site 2 out of 2 in the Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3


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 the Catalytic Unit of Thermostable GH87 Alpha-1, 3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:12.2
occ:1.00
 OD1 B:ASP191 2.3 13.0 1.0
OE2 B:GLU63 2.3 13.2 1.0
O B:GLN91 2.4 13.2 1.0
O B:SER88 2.4 12.4 1.0
OE1 B:GLU65 2.5 14.1 1.0
OE2 B:GLU65 2.5 14.5 1.0
O B:ASP191 2.6 12.7 1.0
CD B:GLU65 2.8 13.8 1.0
CD B:GLU63 3.4 14.4 1.0
C B:ASP191 3.5 11.8 1.0
C B:SER88 3.5 11.5 1.0
CG B:ASP191 3.5 12.2 1.0
C B:GLN91 3.5 12.7 1.0
CA B:ASP191 3.9 12.1 1.0
CB B:SER88 4.1 12.9 1.0
CA B:SER88 4.1 12.3 1.0
CB B:GLU63 4.1 13.9 1.0
N B:SER88 4.2 12.1 1.0
OE1 B:GLU63 4.2 16.1 1.0
CG B:GLU63 4.3 13.6 1.0
CB B:ASP191 4.3 12.6 1.0
N B:ALA92 4.4 14.1 1.0
CG B:GLU65 4.4 15.4 1.0
CA B:ALA92 4.4 13.7 1.0
N B:GLN91 4.4 12.9 1.0
OD2 B:ASP191 4.4 12.7 1.0
CA B:GLN91 4.5 13.4 1.0
CB B:ALA87 4.5 12.8 1.0
N B:ALA64 4.5 13.0 1.0
N B:VAL192 4.5 12.3 1.0
N B:GLY89 4.6 12.6 1.0
CA B:GLU63 4.6 13.5 1.0
CB B:VAL192 4.6 12.8 1.0
C B:ALA87 4.7 11.2 1.0
OG B:SER88 4.8 13.2 1.0
CB B:GLN91 4.8 16.0 1.0
CB B:ALA92 4.8 15.3 1.0
CA B:GLY89 4.8 13.4 1.0
O B:HOH978 4.9 29.7 1.0
CA B:VAL192 4.9 12.4 1.0
C B:GLU63 5.0 13.2 1.0

Reference:

T.Itoh, N.Panti, J.Hayashi, Y.Toyotake, D.Matsui, S.Yano, M.Wakayama, T.Hibi. Crystal Structure of the Catalytic Unit of Thermostable GH87 Alpha-1,3-Glucanase From Streptomyces Thermodiastaticus Strain HF3-3. Biochem.Biophys.Res.Commun. 2020.
ISSN: ESSN 1090-2104
PubMed: 33041007
DOI: 10.1016/J.BBRC.2020.09.133
Page generated: Thu Jul 18 23:28:54 2024

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