Calcium in PDB 1j12: Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg

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

The structure of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg, PDB code: 1j12 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 (%)	19.8 / 25.3

The binding sites of Calcium atom in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg (pdb code 1j12). 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 Alpha-Ebg, PDB code: 1j12:
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 Alpha-Ebg


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 Alpha-Ebg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:10.5 occ:1.00 OE1 A:GLU144 2.3 6.9 1.0 OE2 A:GLU56 2.4 13.0 1.0 OD1 A:ASP60 2.4 13.4 1.0 OE1 A:GLU141 2.6 11.4 1.0 O A:HOH752 2.6 10.6 1.0 OE1 A:GLN61 2.6 13.7 1.0 CD A:GLU56 3.4 11.8 1.0 CD A:GLU144 3.5 9.8 1.0 CD A:GLN61 3.6 16.5 1.0 CG A:ASP60 3.7 3.2 1.0 OE1 A:GLU56 3.7 16.4 1.0 CD A:GLU141 3.7 21.8 1.0 CB A:GLU144 3.9 8.3 1.0 N A:GLN61 3.9 13.5 1.0 NZ A:LYS140 4.0 6.8 1.0 CH2 A:TRP106 4.1 9.1 1.0 CG A:GLN61 4.2 5.9 1.0 OE2 A:GLU141 4.3 22.1 1.0 CG A:GLU144 4.3 2.5 1.0 OE2 A:GLU144 4.3 10.7 1.0 OD2 A:ASP60 4.4 9.4 1.0 CA A:ASP60 4.5 7.0 1.0 CA A:GLU141 4.5 7.0 1.0 CA A:GLN61 4.6 10.7 1.0 CZ A:PHE63 4.6 9.8 1.0 C A:ASP60 4.6 13.7 1.0 CB A:ASP60 4.6 6.7 1.0 O A:GLU141 4.6 15.0 1.0 NE2 A:GLN61 4.7 15.1 1.0 CZ2 A:TRP106 4.7 5.0 1.0 CG A:GLU56 4.8 7.9 1.0 CB A:GLU141 4.9 9.0 1.0 CG A:GLU141 4.9 12.1 1.0 CB A:GLN61 5.0 8.0 1.0

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


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 Alpha-Ebg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:11.9 occ:1.00 OE1 B:GLU144 2.4 13.0 1.0 OD1 B:ASP60 2.4 13.1 1.0 OE2 B:GLU56 2.4 8.7 1.0 O B:HOH773 2.5 12.9 1.0 OE1 B:GLU141 2.6 5.4 1.0 OE1 B:GLN61 2.6 22.1 1.0 CD B:GLU144 3.4 12.2 1.0 CD B:GLU56 3.5 14.9 1.0 CD B:GLN61 3.6 11.2 1.0 CG B:ASP60 3.7 10.0 1.0 CD B:GLU141 3.7 9.5 1.0 OE1 B:GLU56 3.7 13.6 1.0 CB B:GLU144 3.8 10.2 1.0 N B:GLN61 3.9 9.1 1.0 NZ B:LYS140 4.0 13.2 1.0 CH2 B:TRP106 4.1 7.3 1.0 OE2 B:GLU141 4.2 14.4 1.0 CG B:GLU144 4.2 9.7 1.0 OE2 B:GLU144 4.2 17.7 1.0 CG B:GLN61 4.2 8.9 1.0 OD2 B:ASP60 4.4 5.5 1.0 CA B:ASP60 4.5 11.2 1.0 CA B:GLU141 4.5 5.8 1.0 CZ B:PHE63 4.6 10.8 1.0 CA B:GLN61 4.6 12.4 1.0 C B:ASP60 4.6 13.0 1.0 CB B:ASP60 4.7 7.9 1.0 O B:GLU141 4.7 17.1 1.0 NE2 B:GLN61 4.7 10.5 1.0 CG B:GLU56 4.8 3.0 1.0 CZ2 B:TRP106 4.8 9.0 1.0 CG B:GLU141 4.8 7.0 1.0 CB B:GLU141 4.9 8.4 1.0 CE2 B:PHE63 4.9 7.1 1.0 CZ3 B:TRP106 5.0 8.2 1.0

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


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 Alpha-Ebg within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:14.9 occ:1.00 OD1 C:ASP60 2.4 11.9 1.0 OE1 C:GLU144 2.4 11.5 1.0 OE1 C:GLN61 2.6 17.8 1.0 OE2 C:GLU56 2.6 9.4 1.0 O C:HOH771 2.6 14.0 1.0 OE1 C:GLU141 2.6 13.2 1.0 CD C:GLU144 3.4 8.2 1.0 CD C:GLU56 3.6 9.8 1.0 CG C:ASP60 3.6 9.0 1.0 CD C:GLU141 3.6 17.0 1.0 CD C:GLN61 3.6 15.7 1.0 CB C:GLU144 3.8 10.3 1.0 OE1 C:GLU56 3.8 14.2 1.0 N C:GLN61 3.8 9.8 1.0 NZ C:LYS140 3.9 8.3 1.0 OE2 C:GLU141 4.1 12.7 1.0 CH2 C:TRP106 4.1 5.2 1.0 CG C:GLU144 4.2 3.2 1.0 OE2 C:GLU144 4.2 7.2 1.0 CG C:GLN61 4.2 5.5 1.0 OD2 C:ASP60 4.3 9.6 1.0 CA C:ASP60 4.5 6.5 1.0 CA C:GLU141 4.5 6.1 1.0 CA C:GLN61 4.6 9.4 1.0 CZ C:PHE63 4.6 9.2 1.0 C C:ASP60 4.6 13.4 1.0 CB C:ASP60 4.6 6.3 1.0 NE2 C:GLN61 4.7 12.7 1.0 O C:GLU141 4.7 11.8 1.0 CG C:GLU141 4.8 11.5 1.0 CB C:GLU141 4.8 13.9 1.0 CZ2 C:TRP106 4.8 4.4 1.0 CG C:GLU56 4.9 3.7 1.0 O C:HOH735 5.0 12.9 1.0 CZ3 C:TRP106 5.0 9.6 1.0

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


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 Alpha-Ebg within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:14.5 occ:1.00 OE1 D:GLU144 2.3 11.4 1.0 OE2 D:GLU56 2.4 13.7 1.0 OD1 D:ASP60 2.4 20.3 1.0 OE1 D:GLN61 2.5 17.8 1.0 OE1 D:GLU141 2.5 18.0 1.0 CD D:GLU56 3.3 13.3 1.0 CD D:GLU144 3.4 3.0 1.0 OE1 D:GLU56 3.6 15.0 1.0 CG D:ASP60 3.6 6.2 1.0 CD D:GLN61 3.6 11.7 1.0 CB D:GLU144 3.7 5.3 1.0 CD D:GLU141 3.7 15.7 1.0 N D:GLN61 3.8 12.0 1.0 CG D:GLU144 4.1 4.0 1.0 NZ D:LYS140 4.2 12.5 1.0 CG D:GLN61 4.2 9.5 1.0 OE2 D:GLU144 4.3 9.9 1.0 CH2 D:TRP106 4.4 10.8 1.0 CA D:GLU141 4.4 7.2 1.0 OD2 D:ASP60 4.4 10.3 1.0 OE2 D:GLU141 4.4 10.7 1.0 CZ D:PHE63 4.4 7.9 1.0 CA D:ASP60 4.4 6.8 1.0 CA D:GLN61 4.5 12.4 1.0 C D:ASP60 4.5 12.7 1.0 O D:GLU141 4.6 14.0 1.0 CB D:ASP60 4.6 5.1 1.0 NE2 D:GLN61 4.7 5.3 1.0 CG D:GLU56 4.7 7.5 1.0 CB D:GLU141 4.7 12.0 1.0 CG D:GLU141 4.8 16.3 1.0 CE2 D:PHE63 4.9 7.0 1.0 CZ2 D:TRP106 5.0 6.2 1.0 CB D:GLN61 5.0 10.9 1.0 C D:GLU141 5.0 14.4 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