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

Protein crystallography data

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

Other elements in 6vhq:

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

Calcium Binding Sites:

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 6vhq

Go back to Calcium Binding Sites List in 6vhq
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 6vhq

Go back to Calcium Binding Sites List in 6vhq
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

Reference:

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.
Page generated: Sun Jan 24 09:35:13 2021

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