Calcium in PDB 1j0y: Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose

All present enzymatic activity of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose:
3.2.1.2;

The structure of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose, PDB code: 1j0y was solved by T.Oyama, H.Miyake, M.Kusunoki, Y.Nitta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.900, 112.900, 146.200, 90.00, 105.80, 90.00
R / Rfree (%)	17.9 / 23.6

The binding sites of Calcium atom in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose (pdb code 1j0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose, PDB code: 1j0y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:16.2 occ:1.00 OE1 A:GLU144 2.4 11.2 1.0 OD1 A:ASP60 2.4 17.3 1.0 OE2 A:GLU56 2.4 13.2 1.0 OE1 A:GLU141 2.5 11.5 1.0 OE1 A:GLN61 2.5 13.9 1.0 O A:HOH1697 2.6 18.1 1.0 CD A:GLU56 3.4 12.8 1.0 CD A:GLU144 3.5 10.8 1.0 CD A:GLU141 3.6 21.5 1.0 CG A:ASP60 3.6 10.8 1.0 CD A:GLN61 3.6 14.7 1.0 OE1 A:GLU56 3.6 16.2 1.0 N A:GLN61 3.8 17.5 1.0 CB A:GLU144 3.9 10.8 1.0 NZ A:LYS140 3.9 10.3 1.0 OE2 A:GLU141 4.0 22.2 1.0 CH2 A:TRP106 4.1 12.5 1.0 CG A:GLN61 4.2 10.3 1.0 OE2 A:GLU144 4.3 15.9 1.0 CG A:GLU144 4.3 7.4 1.0 CA A:ASP60 4.3 16.2 1.0 OD2 A:ASP60 4.3 16.8 1.0 CB A:ASP60 4.5 12.3 1.0 CZ A:PHE63 4.5 9.3 1.0 C A:ASP60 4.6 15.1 1.0 CA A:GLU141 4.6 14.0 1.0 NE2 A:GLN61 4.6 13.0 1.0 CA A:GLN61 4.6 14.4 1.0 O A:GLU141 4.7 13.7 1.0 CG A:GLU56 4.7 11.3 1.0 CZ2 A:TRP106 4.8 11.2 1.0 CG A:GLU141 4.8 10.1 1.0 CZ3 A:TRP106 4.9 11.8 1.0 CB A:GLU141 4.9 12.5 1.0

Calcium binding site 2 out of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:12.6 occ:1.00 OD1 B:ASP60 2.3 18.6 1.0 OE1 B:GLU144 2.4 13.9 1.0 OE2 B:GLU56 2.4 8.8 1.0 OE1 B:GLU141 2.4 11.7 1.0 OE1 B:GLN61 2.5 15.3 1.0 O B:HOH2695 2.5 10.7 1.0 CD B:GLU56 3.4 14.9 1.0 CD B:GLU144 3.5 15.3 1.0 CD B:GLU141 3.6 18.9 1.0 CD B:GLN61 3.6 11.0 1.0 CG B:ASP60 3.6 17.0 1.0 OE1 B:GLU56 3.6 16.3 1.0 CB B:GLU144 3.8 9.8 1.0 N B:GLN61 3.9 13.2 1.0 NZ B:LYS140 3.9 11.7 1.0 OE2 B:GLU141 4.1 19.2 1.0 CH2 B:TRP106 4.1 6.5 1.0 CG B:GLN61 4.2 8.9 1.0 CG B:GLU144 4.3 12.8 1.0 OD2 B:ASP60 4.3 15.2 1.0 OE2 B:GLU144 4.4 16.8 1.0 CA B:ASP60 4.5 12.5 1.0 CA B:GLU141 4.5 10.3 1.0 CA B:GLN61 4.6 13.0 1.0 CB B:ASP60 4.6 8.7 1.0 C B:ASP60 4.6 13.7 1.0 CZ B:PHE63 4.6 13.6 1.0 NE2 B:GLN61 4.7 8.8 1.0 O B:GLU141 4.8 15.4 1.0 CG B:GLU56 4.8 6.5 1.0 CG B:GLU141 4.8 12.8 1.0 CZ2 B:TRP106 4.8 12.3 1.0 CZ3 B:TRP106 4.8 13.8 1.0 CB B:GLU141 4.9 9.4 1.0 O B:HOH2637 5.0 15.6 1.0 CE2 B:PHE63 5.0 8.4 1.0

Calcium binding site 3 out of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:14.0 occ:1.00 OE1 C:GLU144 2.3 13.9 1.0 OD1 C:ASP60 2.4 14.7 1.0 OE2 C:GLU56 2.4 15.5 1.0 OE1 C:GLU141 2.5 16.1 1.0 OE1 C:GLN61 2.5 13.5 1.0 O C:HOH3701 2.5 12.9 1.0 CD C:GLU56 3.4 18.2 1.0 CD C:GLU144 3.5 14.9 1.0 CG C:ASP60 3.6 10.5 1.0 CD C:GLN61 3.6 11.3 1.0 CD C:GLU141 3.6 21.9 1.0 OE1 C:GLU56 3.6 21.2 1.0 CB C:GLU144 3.8 9.6 1.0 N C:GLN61 3.9 14.4 1.0 CH2 C:TRP106 4.0 9.4 1.0 NZ C:LYS140 4.0 12.0 1.0 OE2 C:GLU141 4.2 19.7 1.0 CG C:GLN61 4.2 9.7 1.0 CG C:GLU144 4.2 5.8 1.0 OE2 C:GLU144 4.3 11.5 1.0 OD2 C:ASP60 4.3 12.8 1.0 CA C:GLU141 4.4 11.0 1.0 CZ C:PHE63 4.5 8.5 1.0 CA C:ASP60 4.5 13.1 1.0 O C:GLU141 4.6 8.8 1.0 CA C:GLN61 4.6 12.0 1.0 CB C:ASP60 4.6 14.2 1.0 C C:ASP60 4.7 12.6 1.0 CB C:GLU141 4.7 11.6 1.0 NE2 C:GLN61 4.7 11.4 1.0 CG C:GLU141 4.7 14.8 1.0 CZ2 C:TRP106 4.7 11.8 1.0 CG C:GLU56 4.8 7.9 1.0 CZ3 C:TRP106 4.9 11.2 1.0

Calcium binding site 4 out of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:17.9 occ:1.00 OE2 D:GLU56 2.4 11.3 1.0 OE1 D:GLU144 2.4 13.8 1.0 OD1 D:ASP60 2.4 19.3 1.0 OE1 D:GLN61 2.5 15.2 1.0 OE1 D:GLU141 2.5 18.4 1.0 CD D:GLU56 3.3 11.2 1.0 OE1 D:GLU56 3.4 16.2 1.0 CD D:GLU144 3.5 11.4 1.0 CD D:GLN61 3.6 15.7 1.0 CD D:GLU141 3.6 20.5 1.0 CG D:ASP60 3.6 10.8 1.0 N D:GLN61 3.8 16.3 1.0 CB D:GLU144 3.9 12.6 1.0 OE2 D:GLU141 4.2 19.8 1.0 CH2 D:TRP106 4.2 7.0 1.0 CG D:GLN61 4.2 8.8 1.0 NZ D:LYS140 4.3 15.6 1.0 CG D:GLU144 4.3 8.0 1.0 CA D:ASP60 4.4 13.0 1.0 OE2 D:GLU144 4.4 15.4 1.0 OD2 D:ASP60 4.4 19.3 1.0 CA D:GLU141 4.5 11.4 1.0 CA D:GLN61 4.5 15.6 1.0 C D:ASP60 4.5 17.1 1.0 CB D:ASP60 4.6 13.0 1.0 CZ D:PHE63 4.6 11.1 1.0 NE2 D:GLN61 4.7 9.4 1.0 O D:GLU141 4.7 15.0 1.0 CG D:GLU56 4.7 12.7 1.0 CZ2 D:TRP106 4.8 13.3 1.0 CB D:GLU141 4.8 9.9 1.0 CG D:GLU141 4.8 13.7 1.0 CE2 D:PHE63 5.0 9.4 1.0 CB D:GLN61 5.0 15.1 1.0

T.Oyama, H.Miyake, M.Kusunoki, Y.Nitta. Crystal Structures of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents J.Biochem.(Tokyo) V. 133 467 2003.
ISSN: ISSN 0021-924X
PubMed: 12761294
DOI: 10.1093/JB/MVG061