Calcium in PDB 6quc: Truncated Beta-Galactosidase III From Bifidobacterium Bifidum

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

The structure of Truncated Beta-Galactosidase III From Bifidobacterium Bifidum, PDB code: 6quc 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)	46.10 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.500, 119.683, 144.602, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

The binding sites of Calcium atom in the Truncated Beta-Galactosidase III From Bifidobacterium Bifidum (pdb code 6quc). 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, PDB code: 6quc:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2101 b:65.8 occ:1.00 O A:VAL678 2.2 59.4 1.0 O A:HOH2244 2.4 52.0 1.0 O A:ASN675 2.4 53.2 1.0 OD2 A:ASP707 2.4 56.2 1.0 O A:HOH2291 2.5 52.7 1.0 CG A:ASP707 3.3 56.8 1.0 C A:VAL678 3.5 58.6 1.0 C A:ASN675 3.6 51.6 1.0 CB A:ASP707 3.8 56.0 1.0 CA A:ASP676 4.1 53.6 1.0 OD1 A:ASP707 4.2 57.7 1.0 N A:VAL678 4.2 57.0 1.0 N A:ASP676 4.3 50.9 1.0 ND1 A:HIS679 4.3 67.9 1.0 N A:HIS679 4.3 59.4 1.0 CA A:HIS679 4.3 59.7 1.0 C A:ASP676 4.4 54.9 1.0 CA A:VAL678 4.4 57.6 1.0 O A:GLN671 4.5 48.3 1.0 CG1 A:VAL678 4.6 56.0 1.0 O A:SER672 4.7 51.8 1.0 CA A:ASN675 4.7 49.3 1.0 O A:ASP676 4.8 56.6 1.0 OD1 A:ASP676 4.9 57.0 1.0 N A:ASP677 4.9 54.9 1.0 N A:ASN675 5.0 47.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2102 b:50.3 occ:1.00 OD1 A:ASN426 2.3 46.0 1.0 OE2 A:GLU113 2.4 50.9 1.0 O A:THR638 2.4 55.9 1.0 O A:HOH2350 2.4 48.0 1.0 OE1 A:GLU111 2.4 48.7 1.0 O A:ASN424 2.5 46.8 1.0 CG A:ASN426 3.3 45.3 1.0 CD A:GLU111 3.4 50.0 1.0 C A:THR638 3.5 54.1 1.0 CD A:GLU113 3.6 49.6 1.0 OE2 A:GLU111 3.6 51.4 1.0 C A:ASN424 3.7 46.9 1.0 ND2 A:ASN426 3.9 45.0 1.0 CA A:THR638 3.9 53.1 1.0 C A:GLY425 4.1 44.4 1.0 N A:ASN426 4.2 44.1 1.0 CB A:ASN424 4.2 46.9 1.0 CB A:PRO194 4.2 44.3 1.0 CB A:THR638 4.3 54.3 1.0 O A:GLY425 4.4 45.0 1.0 OE1 A:GLU113 4.4 50.1 1.0 CG A:GLU113 4.4 47.7 1.0 CA A:ASN426 4.5 44.5 1.0 CB A:ASN426 4.5 44.0 1.0 CA A:GLY425 4.6 45.9 1.0 N A:GLY425 4.6 46.7 1.0 N A:GLY639 4.6 53.3 1.0 CA A:ASN424 4.6 45.9 1.0 CG A:PRO194 4.7 47.0 1.0 CG A:GLU111 4.7 49.0 1.0 CA A:GLY639 5.0 53.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2101 b:61.1 occ:1.00 O B:VAL678 2.2 52.2 1.0 O B:HOH2230 2.4 45.2 1.0 O B:ASN675 2.4 49.8 1.0 OD2 B:ASP707 2.4 50.3 1.0 O B:HOH2517 2.4 43.3 1.0 O B:HOH2597 2.5 49.5 1.0 CG B:ASP707 3.2 49.7 1.0 C B:VAL678 3.4 50.9 1.0 C B:ASN675 3.6 48.0 1.0 CB B:ASP707 3.7 48.1 1.0 OD1 B:ASP707 4.1 50.1 1.0 CA B:ASP676 4.1 50.2 1.0 CA B:HIS679 4.2 50.7 1.0 ND1 B:HIS679 4.3 53.8 1.0 N B:HIS679 4.3 51.1 1.0 N B:VAL678 4.3 50.5 1.0 O B:GLN671 4.3 43.1 1.0 N B:ASP676 4.3 47.0 1.0 CA B:VAL678 4.4 50.4 1.0 C B:ASP676 4.5 50.6 1.0 O B:SER672 4.7 46.8 1.0 CA B:ASN675 4.7 44.3 1.0 OG1 B:THR680 4.8 45.4 1.0 O B:ASP676 4.8 50.2 1.0 N B:THR680 4.8 49.0 1.0 CG1 B:VAL678 4.9 50.7 1.0 N B:ASN675 4.9 42.9 1.0 OD1 B:ASP676 4.9 57.1 1.0 CB B:ASN675 4.9 44.0 1.0 C B:HIS679 5.0 49.5 1.0 N B:ASP677 5.0 51.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2102 b:41.5 occ:1.00 OD1 B:ASN426 2.3 32.7 1.0 O B:THR638 2.3 40.3 1.0 OE2 B:GLU113 2.3 42.4 1.0 OE1 B:GLU111 2.4 38.4 1.0 O B:HOH2215 2.4 35.4 1.0 O B:ASN424 2.4 34.1 1.0 CD B:GLU111 3.2 38.4 1.0 CG B:ASN426 3.3 33.3 1.0 OE2 B:GLU111 3.4 40.1 1.0 C B:THR638 3.4 39.6 1.0 CD B:GLU113 3.5 41.0 1.0 C B:ASN424 3.6 35.1 1.0 ND2 B:ASN426 3.8 31.6 1.0 CA B:THR638 4.0 40.4 1.0 O B:HOH2347 4.0 36.1 1.0 CB B:ASN424 4.1 35.2 1.0 C B:GLY425 4.2 34.5 1.0 N B:ASN426 4.2 34.7 1.0 OE1 B:GLU113 4.3 41.4 1.0 CB B:PRO194 4.3 35.5 1.0 CB B:THR638 4.4 41.6 1.0 CG B:GLU113 4.4 38.3 1.0 O B:GLY425 4.5 35.3 1.0 CB B:ASN426 4.5 34.1 1.0 N B:GLY639 4.5 39.4 1.0 CA B:ASN424 4.5 35.3 1.0 CA B:ASN426 4.5 34.5 1.0 N B:GLY425 4.6 34.2 1.0 CA B:GLY425 4.6 34.3 1.0 CG B:GLU111 4.6 35.4 1.0 CG B:PRO194 4.8 36.4 1.0 CA B:GLY639 4.8 38.8 1.0 CB B:GLU111 5.0 34.0 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.