Calcium in PDB 1j11: Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Epg

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

The structure of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Epg, PDB code: 1j11 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 / 2.00
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 (%)	20 / 24.6

The binding sites of Calcium atom in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Epg (pdb code 1j11). 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-Epg, PDB code: 1j11:
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-Epg


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-Epg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:7.6 occ:1.00 OE1 A:GLU144 2.4 3.8 1.0 OD1 A:ASP60 2.4 12.4 1.0 OE2 A:GLU56 2.4 8.9 1.0 OE1 A:GLN61 2.5 6.6 1.0 OE1 A:GLU141 2.5 11.8 1.0 O A:HOH724 2.6 4.4 1.0 CD A:GLU56 3.4 7.3 1.0 CD A:GLU144 3.5 5.9 1.0 CD A:GLN61 3.6 6.2 1.0 CG A:ASP60 3.6 7.3 1.0 CD A:GLU141 3.6 13.2 1.0 OE1 A:GLU56 3.7 5.2 1.0 CB A:GLU144 3.8 5.3 1.0 N A:GLN61 3.9 7.8 1.0 NZ A:LYS140 4.0 9.6 1.0 OE2 A:GLU141 4.1 15.7 1.0 CG A:GLU144 4.2 4.1 1.0 CH2 A:TRP106 4.3 6.4 1.0 CG A:GLN61 4.3 4.6 1.0 OE2 A:GLU144 4.3 6.8 1.0 OD2 A:ASP60 4.4 8.5 1.0 CA A:ASP60 4.4 7.2 1.0 CZ A:PHE63 4.5 6.6 1.0 CA A:GLU141 4.5 5.6 1.0 CB A:ASP60 4.6 7.0 1.0 NE2 A:GLN61 4.6 9.0 1.0 CA A:GLN61 4.6 5.7 1.0 C A:ASP60 4.6 7.4 1.0 O A:GLU141 4.7 10.3 1.0 CG A:GLU56 4.8 8.1 1.0 CG A:GLU141 4.8 5.4 1.0 CZ2 A:TRP106 4.8 4.5 1.0 CB A:GLU141 4.9 7.4 1.0 O A:HOH733 4.9 6.8 1.0 CE2 A:PHE63 5.0 6.7 1.0

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


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-Epg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:3.5 occ:1.00 OE1 B:GLU144 2.4 10.6 1.0 OE1 B:GLN61 2.4 8.1 1.0 OE1 B:GLU141 2.4 8.4 1.0 OE2 B:GLU56 2.5 8.0 1.0 OD1 B:ASP60 2.5 11.9 1.0 O B:HOH724 2.6 5.0 1.0 CD B:GLU56 3.4 9.8 1.0 CD B:GLU144 3.4 9.7 1.0 CD B:GLN61 3.6 5.1 1.0 CD B:GLU141 3.6 10.5 1.0 OE1 B:GLU56 3.7 9.5 1.0 CG B:ASP60 3.7 7.3 1.0 CB B:GLU144 3.8 5.8 1.0 N B:GLN61 3.8 7.3 1.0 NZ B:LYS140 3.9 11.7 1.0 CH2 B:TRP106 4.1 2.0 1.0 OE2 B:GLU141 4.2 9.2 1.0 CG B:GLN61 4.2 3.2 1.0 CG B:GLU144 4.2 6.0 1.0 OE2 B:GLU144 4.3 7.3 1.0 CA B:GLU141 4.4 2.0 1.0 OD2 B:ASP60 4.4 9.5 1.0 CA B:ASP60 4.5 2.8 1.0 CZ B:PHE63 4.5 5.8 1.0 CA B:GLN61 4.5 8.4 1.0 C B:ASP60 4.6 7.3 1.0 NE2 B:GLN61 4.6 2.9 1.0 O B:GLU141 4.7 4.4 1.0 CB B:ASP60 4.7 5.4 1.0 CB B:GLU141 4.8 5.7 1.0 CG B:GLU141 4.8 8.8 1.0 CG B:GLU56 4.8 4.8 1.0 CZ2 B:TRP106 4.9 2.0 1.0 CZ3 B:TRP106 4.9 2.0 1.0 CE2 B:PHE63 4.9 6.0 1.0 CB B:GLN61 5.0 6.4 1.0 O B:HOH794 5.0 17.9 1.0

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


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-Epg within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:6.2 occ:1.00 OE1 C:GLU144 2.4 5.7 1.0 OE1 C:GLN61 2.4 5.9 1.0 OD1 C:ASP60 2.4 8.4 1.0 O C:HOH734 2.5 7.0 1.0 OE1 C:GLU141 2.5 15.9 1.0 OE2 C:GLU56 2.5 2.5 1.0 CD C:GLU144 3.3 5.1 1.0 CD C:GLU141 3.5 11.0 1.0 CD C:GLU56 3.5 3.7 1.0 CD C:GLN61 3.6 8.1 1.0 CG C:ASP60 3.6 5.4 1.0 CB C:GLU144 3.7 4.0 1.0 OE1 C:GLU56 3.8 2.0 1.0 NZ C:LYS140 3.9 5.7 1.0 N C:GLN61 3.9 2.3 1.0 OE2 C:GLU141 3.9 8.9 1.0 OE2 C:GLU144 4.0 5.8 1.0 CG C:GLU144 4.1 5.3 1.0 CG C:GLN61 4.2 4.8 1.0 CH2 C:TRP106 4.3 2.0 1.0 OD2 C:ASP60 4.3 5.5 1.0 CA C:GLU141 4.4 2.0 1.0 CA C:ASP60 4.5 2.0 1.0 CA C:GLN61 4.6 3.1 1.0 O C:GLU141 4.6 4.5 1.0 NE2 C:GLN61 4.7 2.0 1.0 CZ C:PHE63 4.7 2.0 1.0 C C:ASP60 4.7 6.3 1.0 CB C:ASP60 4.7 3.2 1.0 CG C:GLU141 4.7 8.2 1.0 CB C:GLU141 4.8 6.3 1.0 O C:HOH730 4.9 3.5 1.0 CG C:GLU56 4.9 2.0 1.0 CZ2 C:TRP106 5.0 2.0 1.0

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


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-Epg within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:12.2 occ:1.00 OD1 D:ASP60 2.4 11.6 1.0 OE1 D:GLN61 2.4 5.0 1.0 OE1 D:GLU144 2.5 7.9 1.0 OE2 D:GLU56 2.5 8.8 1.0 O D:HOH726 2.5 15.4 1.0 OE1 D:GLU141 2.6 11.2 1.0 CD D:GLU56 3.4 9.8 1.0 CD D:GLU144 3.5 5.3 1.0 OE1 D:GLU56 3.6 13.4 1.0 CD D:GLN61 3.6 5.0 1.0 CG D:ASP60 3.6 7.3 1.0 CB D:GLU144 3.7 5.1 1.0 CD D:GLU141 3.8 8.3 1.0 N D:GLN61 3.8 6.8 1.0 NZ D:LYS140 4.1 11.6 1.0 CG D:GLU144 4.2 5.4 1.0 CG D:GLN61 4.3 4.4 1.0 OE2 D:GLU144 4.4 9.2 1.0 CA D:GLU141 4.4 5.8 1.0 OD2 D:ASP60 4.4 12.1 1.0 CH2 D:TRP106 4.4 7.2 1.0 CA D:ASP60 4.4 5.6 1.0 CZ D:PHE63 4.4 5.0 1.0 OE2 D:GLU141 4.5 12.8 1.0 O D:GLU141 4.5 6.1 1.0 CA D:GLN61 4.6 6.2 1.0 C D:ASP60 4.6 10.8 1.0 CB D:ASP60 4.6 8.5 1.0 NE2 D:GLN61 4.6 3.1 1.0 CB D:GLU141 4.7 6.0 1.0 CG D:GLU56 4.8 8.5 1.0 CG D:GLU141 4.9 7.3 1.0 C D:GLU141 5.0 6.4 1.0 CE2 D:PHE63 5.0 5.6 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