Calcium in PDB 5i78: Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger

The structure of Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger, PDB code: 5i78 was solved by W.D.Liu, J.J.Yan, Y.J.Li, Y.Y.Zheng, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.273, 50.822, 75.310, 90.00, 95.08, 90.00
R / Rfree (%)	14.3 / 17.5

The binding sites of Calcium atom in the Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger (pdb code 5i78). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger, PDB code: 5i78:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger


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 Beta-1,4-Endoglucanase From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.0 occ:1.00 O B:ASP69 2.3 12.7 1.0 O A:HOH717 2.4 21.0 1.0 O A:LEU332 2.4 16.9 1.0 O B:HOH738 2.4 25.7 1.0 OD1 B:ASP69 2.4 15.0 1.0 OE1 A:GLU29 2.5 20.4 1.0 OXT A:LEU332 2.6 17.3 1.0 OE2 A:GLU29 2.6 22.7 1.0 C A:LEU332 2.8 18.1 1.0 CD A:GLU29 2.9 19.3 1.0 C B:ASP69 3.4 13.2 1.0 CG B:ASP69 3.5 13.7 1.0 CA B:ASP69 3.7 12.3 1.0 CA A:CA402 4.0 14.0 1.0 CB B:ASP69 4.2 12.0 1.0 O A:HOH639 4.2 17.7 1.0 O A:HOH505 4.2 17.2 1.0 CA A:LEU332 4.4 16.1 1.0 CG A:GLU29 4.4 18.7 1.0 O A:HOH736 4.5 22.0 1.0 OD2 B:ASP69 4.5 18.8 1.0 N B:LYS70 4.5 12.0 1.0 O A:HOH584 4.8 25.0 1.0 CA A:GLY71 4.9 14.5 1.0 O B:ILE68 4.9 10.1 1.0 O A:HOH567 4.9 30.6 1.0 CA B:LYS70 5.0 14.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger


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 A Beta-1,4-Endoglucanase From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:14.0 occ:1.00 O B:HOH692 2.3 28.1 1.0 O A:HOH736 2.3 22.0 1.0 O A:GLU329 2.4 15.0 1.0 OD1 B:ASP69 2.4 15.0 1.0 OXT A:LEU332 2.4 17.3 1.0 O A:HOH639 2.4 17.7 1.0 OD2 B:ASP69 2.6 18.8 1.0 CG B:ASP69 2.9 13.7 1.0 C A:GLU329 3.6 14.0 1.0 C A:LEU332 3.6 18.1 1.0 CA A:CA401 4.0 14.0 1.0 OE1 A:GLU29 4.1 20.4 1.0 O B:HOH738 4.2 25.7 1.0 N A:LEU332 4.2 14.1 1.0 C A:ALA330 4.3 16.7 1.0 O A:ALA330 4.3 17.2 1.0 CA A:LEU332 4.4 16.1 1.0 N A:ALA330 4.4 16.2 1.0 CB B:ASP69 4.4 12.0 1.0 CA A:ALA330 4.4 16.4 1.0 CA A:GLU329 4.4 18.5 1.0 O A:LEU332 4.5 16.9 1.0 CB A:GLU329 4.6 21.1 1.0 CB A:LEU332 4.6 18.7 1.0 N A:TYR331 4.9 15.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Beta-1,4-Endoglucanase From Aspergillus Niger


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 A Beta-1,4-Endoglucanase From Aspergillus Niger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.0 occ:1.00 O A:HOH620 2.2 23.4 1.0 O7 A:NAG405 2.3 24.4 1.0 O A:HOH734 2.4 24.6 1.0 C7 A:NAG405 3.5 26.0 1.0 O A:HOH748 3.7 2.4 1.0 O A:HOH702 4.2 19.2 1.0 O A:HOH562 4.2 21.8 1.0 O A:HOH604 4.2 27.7 1.0 O3 A:NAG405 4.3 26.8 1.0 C8 A:NAG405 4.3 27.1 1.0 N2 A:NAG405 4.4 24.1 1.0 C2 A:NAG405 4.6 23.4 1.0

J.Yan, W.Liu, Y.Li, H.L.Lai, Y.Zheng, J.W.Huang, C.C.Chen, Y.Chen, J.Jin, H.Li, R.T.Guo. Functional and Structural Analysis of Pichia Pastoris-Expressed Aspergillus Niger 1,4-Beta-Endoglucanase Biochem. Biophys. Res. V. 475 8 2016COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27154222
DOI: 10.1016/J.BBRC.2016.05.012