Calcium in PDB 6vhq: Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides

The structure of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides, PDB code: 6vhq was solved by A.Diaz-Vilchis, E.Raga-Carbajal, S.Rojas-Trejo, C.Olvera, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.21 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.313, 78.665, 78.732, 90, 93.94, 90
R / Rfree (%)	16.7 / 23.5

The structure of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides also contains other interesting chemical elements:

Bromine

(Br)

9 atoms

The binding sites of Calcium atom in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides (pdb code 6vhq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides, PDB code: 6vhq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.9 occ:1.00 OE1 A:GLN272 2.3 13.0 1.0 O A:LEU308 2.3 13.9 1.0 OD1 A:ASP241 2.3 17.4 1.0 OD1 A:ASN310 2.4 14.5 1.0 O A:HOH718 2.4 15.6 1.0 OD2 A:ASP339 2.6 16.7 1.0 OD1 A:ASP339 2.6 17.7 1.0 CG A:ASP339 2.9 23.5 1.0 CG A:ASP241 3.4 15.4 1.0 CG A:ASN310 3.5 17.7 1.0 CD A:GLN272 3.5 18.1 1.0 C A:LEU308 3.5 16.6 1.0 OD2 A:ASP241 3.7 19.8 1.0 N A:ASN310 4.0 19.6 1.0 ND2 A:ASN264 4.2 11.8 1.0 ND2 A:ASN310 4.3 14.8 1.0 NE2 A:GLN272 4.3 12.8 1.0 CA A:LEU308 4.3 18.7 1.0 CB A:GLN272 4.4 14.1 1.0 O A:ASN242 4.4 19.9 1.0 CB A:ASP339 4.4 16.4 1.0 CG A:GLN272 4.5 13.8 1.0 N A:ASN242 4.5 11.7 1.0 CB A:ASN310 4.5 12.2 1.0 N A:ALA309 4.5 17.1 1.0 CB A:LEU308 4.6 16.2 1.0 NE2 A:GLN226 4.6 15.9 1.0 CA A:ALA309 4.6 16.4 1.0 C A:ALA309 4.6 16.9 1.0 CG A:ASN264 4.6 15.8 1.0 CB A:ASP241 4.7 17.2 1.0 CA A:ASN310 4.7 16.6 1.0 OE1 A:GLN226 4.7 17.7 1.0 CB A:ASN264 4.9 12.2 1.0 C A:ASN242 4.9 16.7 1.0 CA A:ASP241 4.9 18.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:15.3 occ:1.00 OD1 B:ASP339 2.3 16.5 1.0 OD1 B:ASN310 2.4 9.8 1.0 OE1 B:GLN272 2.4 14.3 1.0 O B:LEU308 2.4 11.3 1.0 OD1 B:ASP241 2.4 12.4 1.0 O B:HOH711 2.4 13.9 1.0 OD2 B:ASP339 2.5 19.4 1.0 CG B:ASP339 2.7 16.2 1.0 CG B:ASP241 3.4 18.9 1.0 CG B:ASN310 3.5 12.1 1.0 CD B:GLN272 3.5 14.5 1.0 C B:LEU308 3.6 14.7 1.0 OD2 B:ASP241 3.7 15.5 1.0 N B:ASN310 3.9 13.3 1.0 ND2 B:ASN264 4.1 12.2 1.0 O B:ASN242 4.2 18.4 1.0 NE2 B:GLN272 4.2 9.6 1.0 ND2 B:ASN310 4.3 12.8 1.0 CB B:ASP339 4.3 15.9 1.0 CB B:GLN272 4.4 11.8 1.0 N B:ASN242 4.4 19.6 1.0 CA B:LEU308 4.4 16.3 1.0 N B:ALA309 4.5 7.9 1.0 CA B:ALA309 4.5 11.1 1.0 NE2 B:GLN226 4.6 12.2 1.0 C B:ALA309 4.6 14.2 1.0 CG B:GLN272 4.6 9.4 1.0 CB B:ASN310 4.6 10.3 1.0 CB B:LEU308 4.6 18.6 1.0 CG B:ASN264 4.7 14.2 1.0 CB B:ASP241 4.7 18.1 1.0 CA B:ASN310 4.7 11.8 1.0 O B:HOH708 4.8 15.3 1.0 OE1 B:GLN226 4.8 12.0 1.0 CB B:ASN264 4.8 12.1 1.0 C B:ASN242 4.8 22.2 1.0 CA B:ASP241 4.9 18.1 1.0

E.Raga-Carbajal, A.Diaz-Vilchis, S.Rojas-Trejo, E.Rudino-Pinera, C.Olvera. Crystal Structure of Bacillus Subtilis Levansucrase in Complex with Oligosaccharides To Be Published.