Calcium in PDB 6qub: Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose

All present enzymatic activity of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose:
3.2.1.23;

The structure of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose, PDB code: 6qub was solved by S.S.Thirup, J.A.Nielsen, J.L.Andersen, H.Alsarraf, M.Blaise, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.14 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	112.781, 54.592, 143.357, 90.00, 107.72, 90.00
R / Rfree (%)	16.9 / 21.5

The binding sites of Calcium atom in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose (pdb code 6qub). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose, PDB code: 6qub:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:27.2 occ:1.00 O A:VAL678 2.3 18.1 1.0 O A:ASN675 2.4 14.6 1.0 O A:HOH2940 2.5 23.9 1.0 O A:HOH2400 2.5 13.4 1.0 O A:HOH2714 2.6 13.7 1.0 OD2 A:ASP707 2.6 16.0 1.0 CG A:ASP707 3.4 16.3 1.0 C A:VAL678 3.5 18.8 1.0 C A:ASN675 3.5 16.8 1.0 CB A:ASP707 3.8 13.8 1.0 CA A:ASP676 4.0 18.8 1.0 CA A:HIS679 4.2 16.5 1.0 N A:ASP676 4.3 15.5 1.0 N A:VAL678 4.3 20.3 1.0 N A:HIS679 4.3 16.4 1.0 O A:HOH2102 4.3 28.9 1.0 OD1 A:ASP707 4.3 17.2 1.0 C A:ASP676 4.4 23.5 1.0 O A:GLN671 4.4 13.2 1.0 ND1 A:HIS679 4.4 21.3 1.0 CA A:VAL678 4.5 17.7 1.0 O A:HOH2969 4.6 27.1 1.0 CA A:ASN675 4.7 12.6 1.0 O A:HOH2961 4.7 24.1 1.0 O A:ASP676 4.8 23.7 1.0 CG1 A:VAL678 4.8 17.4 1.0 N A:ASP677 4.8 17.9 1.0 O A:SER672 4.8 14.6 1.0 CB A:ASN675 4.9 11.6 1.0 OD1 A:ASP676 4.9 30.9 1.0 N A:ASN675 4.9 11.0 1.0 C A:HIS679 5.0 21.5 1.0

Calcium binding site 2 out of 4 in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:32.1 occ:1.00 O A:HOH2611 2.3 24.6 1.0 O A:THR638 2.3 33.9 1.0 OD1 A:ASN426 2.3 16.5 1.0 OE2 A:GLU113 2.4 24.9 1.0 OE1 A:GLU111 2.7 31.3 1.0 O A:ASN424 2.8 20.7 1.0 CD A:GLU113 3.3 23.1 1.0 CG A:ASN426 3.4 16.7 1.0 C A:THR638 3.4 30.9 1.0 CD A:GLU111 3.6 26.6 1.0 OE1 A:GLU113 3.9 29.9 1.0 OE2 A:GLU111 3.9 27.7 1.0 CA A:THR638 3.9 33.2 1.0 ND2 A:ASN426 4.0 15.3 1.0 O A:HOH2782 4.0 32.7 1.0 C A:ASN424 4.0 15.5 1.0 CB A:THR638 4.1 30.9 1.0 CB A:PRO194 4.1 15.8 1.0 C A:GLY425 4.3 16.9 1.0 CG A:GLU113 4.3 18.3 1.0 N A:ASN426 4.3 14.1 1.0 O A:HOH2395 4.3 25.0 1.0 O A:GLY425 4.4 12.2 1.0 CB A:ASN424 4.5 18.5 1.0 CA A:ASN426 4.5 15.8 1.0 N A:GLY639 4.6 26.7 1.0 CB A:ASN426 4.6 14.1 1.0 CG A:PRO194 4.6 18.9 1.0 CA A:GLY425 4.7 20.2 1.0 N A:GLY425 4.9 19.0 1.0 CG A:GLU111 4.9 20.8 1.0 CA A:GLY639 4.9 24.9 1.0 CA A:ASN424 4.9 19.1 1.0 CG2 A:THR638 5.0 32.6 1.0

Calcium binding site 3 out of 4 in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:24.8 occ:1.00 O B:VAL678 2.3 15.9 1.0 O B:ASN675 2.4 12.3 1.0 O B:HOH2965 2.4 16.0 1.0 O B:HOH2860 2.4 17.2 1.0 OD2 B:ASP707 2.5 15.0 1.0 O B:HOH2249 2.6 13.2 1.0 CG B:ASP707 3.3 18.6 1.0 C B:ASN675 3.5 15.6 1.0 C B:VAL678 3.6 13.1 1.0 CB B:ASP707 3.8 15.2 1.0 CA B:ASP676 4.0 18.9 1.0 N B:ASP676 4.2 16.4 1.0 CA B:HIS679 4.3 16.5 1.0 OD1 B:ASP707 4.3 15.2 1.0 O B:HOH3166 4.3 33.8 1.0 N B:VAL678 4.3 19.3 1.0 C B:ASP676 4.4 17.6 1.0 ND1 B:HIS679 4.4 19.5 1.0 O B:HOH2992 4.4 24.7 1.0 N B:HIS679 4.4 16.1 1.0 O B:GLN671 4.5 14.8 1.0 O B:HOH2950 4.5 24.3 1.0 CA B:VAL678 4.6 18.3 1.0 CA B:ASN675 4.7 10.1 1.0 OD1 B:ASP676 4.7 22.5 1.0 O B:SER672 4.7 14.1 1.0 N B:ASP677 4.8 15.1 1.0 O B:ASP676 4.8 21.8 1.0 CG1 B:VAL678 4.8 17.9 1.0 CB B:ASN675 5.0 11.7 1.0 N B:ASN675 5.0 12.0 1.0

Calcium binding site 4 out of 4 in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:33.3 occ:1.00 OD1 B:ASN426 2.2 18.4 1.0 O B:HOH2789 2.3 27.2 1.0 O B:THR638 2.4 29.8 1.0 OE2 B:GLU113 2.4 27.0 1.0 OE1 B:GLU111 2.7 28.4 1.0 O B:ASN424 2.9 21.8 1.0 CG B:ASN426 3.3 18.9 1.0 CD B:GLU113 3.3 20.9 1.0 C B:THR638 3.5 33.2 1.0 CD B:GLU111 3.6 27.6 1.0 OE2 B:GLU111 3.8 28.9 1.0 ND2 B:ASN426 3.9 12.5 1.0 OE1 B:GLU113 3.9 27.7 1.0 O B:HOH2960 3.9 29.5 1.0 CA B:THR638 3.9 32.3 1.0 C B:ASN424 4.1 18.4 1.0 CB B:PRO194 4.1 17.8 1.0 CB B:THR638 4.1 34.1 1.0 C B:GLY425 4.2 19.8 1.0 N B:ASN426 4.3 13.0 1.0 O B:GLY425 4.4 16.2 1.0 CG B:GLU113 4.4 16.8 1.0 CA B:ASN426 4.5 16.2 1.0 CB B:ASN426 4.5 13.7 1.0 CB B:ASN424 4.5 13.6 1.0 CG B:PRO194 4.6 13.9 1.0 N B:GLY639 4.6 24.5 1.0 O B:HOH2311 4.7 22.4 1.0 CA B:GLY425 4.8 18.5 1.0 N B:GLY425 4.9 21.1 1.0 CA B:ASN424 5.0 16.1 1.0 CG B:GLU111 5.0 27.0 1.0 CG2 B:THR638 5.0 26.7 1.0

J.A.Nielsen, J.L.Andersen, H.Alsarraf, M.Blaise, S.S.Thirup, M.K.Larsen, J.F.Cramer. Truncated Beta-Galactosidase III From Bifidobacterium Bifidum To Be Published.