Calcium in PDB 5bca: Beta-Amylase From Bacillus Cereus Var. Mycoides

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

The structure of Beta-Amylase From Bacillus Cereus Var. Mycoides, PDB code: 5bca was solved by T.Oyama, M.Kusunoki, Y.Kishimoto, Y.Takasaki, Y.Nitta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.20
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 (%)	18.6 / 24

The binding sites of Calcium atom in the Beta-Amylase From Bacillus Cereus Var. Mycoides (pdb code 5bca). 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, PDB code: 5bca:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:16.5 occ:1.00 OE1 A:GLU144 2.2 11.9 1.0 OE1 A:GLU141 2.3 15.4 1.0 OE2 A:GLU56 2.3 13.7 1.0 OD1 A:ASP60 2.4 17.1 1.0 O A:HOH602 2.5 10.4 1.0 OE1 A:GLN61 2.6 17.2 1.0 CD A:GLU144 3.3 13.4 1.0 CD A:GLU56 3.4 15.2 1.0 CD A:GLU141 3.4 16.0 1.0 CG A:ASP60 3.6 14.0 1.0 CD A:GLN61 3.7 18.6 1.0 N A:GLN61 3.8 18.0 1.0 OE1 A:GLU56 3.8 13.0 1.0 OE2 A:GLU141 3.9 18.9 1.0 CB A:GLU144 3.9 11.9 1.0 NZ A:LYS140 4.0 12.0 1.0 CG A:GLN61 4.1 18.6 1.0 OE2 A:GLU144 4.2 13.4 1.0 OD2 A:ASP60 4.2 18.6 1.0 CA A:ASP60 4.3 15.7 1.0 CG A:GLU144 4.3 13.4 1.0 CH2 A:TRP106 4.3 12.5 1.0 C A:ASP60 4.4 18.9 1.0 CA A:GLN61 4.5 17.8 1.0 CZ A:PHE63 4.6 15.2 1.0 CA A:GLU141 4.6 12.1 1.0 CB A:ASP60 4.6 14.0 1.0 O A:HOH778 4.7 26.9 1.0 O A:GLU141 4.7 12.9 1.0 CG A:GLU56 4.7 16.6 1.0 CG A:GLU141 4.8 13.9 1.0 NE2 A:GLN61 4.8 16.5 1.0 CB A:GLU141 4.9 12.3 1.0 CB A:GLN61 4.9 20.5 1.0 CZ2 A:TRP106 5.0 12.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:16.5 occ:1.00 OD1 B:ASP60 2.3 17.7 1.0 OE2 B:GLU56 2.4 11.7 1.0 OE1 B:GLU141 2.4 16.6 1.0 OE1 B:GLU144 2.4 15.7 1.0 OE1 B:GLN61 2.5 12.2 1.0 O B:HOH603 2.5 10.9 1.0 CD B:GLU56 3.4 10.7 1.0 CD B:GLU144 3.5 15.2 1.0 CD B:GLU141 3.6 17.4 1.0 CG B:ASP60 3.6 16.7 1.0 CD B:GLN61 3.6 12.7 1.0 OE1 B:GLU56 3.7 11.2 1.0 CB B:GLU144 3.7 11.7 1.0 N B:GLN61 3.9 15.1 1.0 NZ B:LYS140 4.0 16.9 1.0 CH2 B:TRP106 4.1 5.1 1.0 OE2 B:GLU141 4.1 16.6 1.0 CG B:GLU144 4.2 13.7 1.0 CG B:GLN61 4.2 12.3 1.0 OD2 B:ASP60 4.3 14.9 1.0 CA B:ASP60 4.4 14.2 1.0 CA B:GLU141 4.5 14.4 1.0 OE2 B:GLU144 4.5 16.0 1.0 CA B:GLN61 4.5 15.4 1.0 C B:ASP60 4.5 15.1 1.0 CZ B:PHE63 4.5 10.7 1.0 CB B:ASP60 4.6 13.4 1.0 NE2 B:GLN61 4.7 5.6 1.0 CG B:GLU141 4.7 17.0 1.0 CG B:GLU56 4.7 9.0 1.0 O B:GLU141 4.7 17.4 1.0 CB B:GLU141 4.8 15.1 1.0 CZ2 B:TRP106 4.9 9.2 1.0 CZ3 B:TRP106 4.9 7.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:16.3 occ:1.00 OE1 C:GLU144 2.2 13.2 1.0 OE2 C:GLU56 2.2 11.6 1.0 OD1 C:ASP60 2.4 17.4 1.0 O C:HOH604 2.4 6.7 1.0 OE1 C:GLU141 2.5 17.4 1.0 OE1 C:GLN61 2.6 16.2 1.0 CD C:GLU56 3.2 13.8 1.0 CD C:GLU144 3.3 16.4 1.0 OE1 C:GLU56 3.6 11.8 1.0 CD C:GLN61 3.6 17.2 1.0 CG C:ASP60 3.6 15.1 1.0 CD C:GLU141 3.6 15.7 1.0 N C:GLN61 3.7 14.6 1.0 NZ C:LYS140 3.8 11.5 1.0 CB C:GLU144 3.8 13.1 1.0 CG C:GLN61 4.0 14.6 1.0 CH2 C:TRP106 4.1 11.4 1.0 CG C:GLU144 4.1 13.3 1.0 OE2 C:GLU141 4.2 15.7 1.0 OE2 C:GLU144 4.2 16.5 1.0 OD2 C:ASP60 4.3 16.1 1.0 CA C:ASP60 4.4 12.8 1.0 CA C:GLN61 4.4 15.6 1.0 C C:ASP60 4.5 15.4 1.0 CG C:GLU56 4.6 12.7 1.0 CA C:GLU141 4.6 11.9 1.0 CZ C:PHE63 4.6 15.6 1.0 CB C:ASP60 4.6 13.6 1.0 CZ2 C:TRP106 4.6 8.8 1.0 CB C:GLU141 4.7 15.5 1.0 NE2 C:GLN61 4.8 16.0 1.0 CG C:GLU141 4.8 16.6 1.0 O C:GLU141 4.8 12.4 1.0 CB C:GLN61 4.9 11.6 1.0 CZ3 C:TRP106 5.0 13.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca604 b:18.9 occ:1.00 O D:HOH605 1.9 22.3 1.0 OD1 D:ASP60 2.1 16.8 1.0 OE1 D:GLN61 2.2 12.4 1.0 OE1 D:GLU144 2.2 18.1 1.0 OE2 D:GLU56 2.4 13.4 1.0 OE1 D:GLU141 2.5 20.6 1.0 CD D:GLN61 3.3 13.4 1.0 CD D:GLU56 3.3 12.4 1.0 CG D:ASP60 3.3 11.7 1.0 CD D:GLU144 3.4 16.5 1.0 OE1 D:GLU56 3.5 13.8 1.0 CD D:GLU141 3.7 18.7 1.0 CB D:GLU144 3.7 14.9 1.0 NZ D:LYS140 3.7 12.5 1.0 N D:GLN61 3.9 12.6 1.0 CG D:GLN61 3.9 15.2 1.0 OD2 D:ASP60 4.0 12.3 1.0 OE2 D:GLU141 4.0 19.6 1.0 CG D:GLU144 4.1 14.1 1.0 CA D:ASP60 4.3 13.6 1.0 OE2 D:GLU144 4.3 18.2 1.0 CB D:ASP60 4.4 11.8 1.0 NE2 D:GLN61 4.4 10.6 1.0 C D:ASP60 4.4 11.8 1.0 CA D:GLU141 4.4 18.5 1.0 CH2 D:TRP106 4.5 12.8 1.0 CA D:GLN61 4.6 15.7 1.0 O D:GLU141 4.6 21.0 1.0 CG D:GLU56 4.7 13.3 1.0 CZ D:PHE63 4.7 21.4 1.0 O D:HOH706 4.8 20.4 1.0 CB D:GLU141 4.8 16.9 1.0 CG D:GLU141 4.9 15.5 1.0 CB D:GLN61 4.9 17.0 1.0

T.Oyama, M.Kusunoki, Y.Kishimoto, Y.Takasaki, Y.Nitta. Crystal Structure of Beta-Amylase From Bacillus Cereus Var. Mycoides at 2.2 A Resolution. J.Biochem.(Tokyo) V. 125 1120 1999.
ISSN: ISSN 0021-924X
PubMed: 10348915