Calcium in PDB 5d9o: Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose

The structure of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose, PDB code: 5d9o was solved by M.Morar, P.J.Stogios, X.Xu, H.Cui, R.Di Leo, V.Yim, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.46 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.180, 85.058, 74.978, 90.00, 101.40, 90.00
R / Rfree (%)	15.3 / 18

The binding sites of Calcium atom in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose (pdb code 5d9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose, PDB code: 5d9o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose


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 PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:14.9 occ:1.00 O A:THR272 2.4 17.9 1.0 O A:HOH592 2.4 19.5 1.0 O A:HOH649 2.4 19.0 1.0 O A:HOH568 2.4 11.0 1.0 O A:HOH923 2.4 27.3 1.0 O A:HOH618 2.4 26.1 1.0 O A:HOH742 2.4 14.8 1.0 C A:THR272 3.5 18.4 1.0 CA A:THR272 4.2 17.9 1.0 O A:HOH878 4.4 23.9 1.0 O A:HOH704 4.4 9.5 1.0 O A:HOH859 4.4 27.9 1.0 O A:HOH868 4.4 46.8 1.0 O A:HIS317 4.6 9.7 1.0 N A:THR273 4.6 17.2 1.0 N A:THR272 4.7 18.9 1.0 O A:ILE274 4.8 10.8 1.0 OG A:SER268 4.8 9.7 1.0 CA A:THR273 4.9 19.4 1.0 O A:SER268 5.0 11.9 1.0 OE1 A:GLN14 5.0 11.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose


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 PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:11.5 occ:1.00 OD2 A:ASP86 2.4 11.0 1.0 O A:HOH815 2.4 12.3 1.0 OD1 A:ASP86 2.4 12.2 1.0 O A:HOH537 2.4 19.0 1.0 CG A:ASP86 2.7 9.4 1.0 O A:HOH795 4.1 17.9 1.0 CB A:ASP86 4.2 6.3 1.0 O A:GLU77 4.3 7.7 1.0 O A:HOH888 4.6 30.3 1.0 O A:HOH644 4.7 13.8 1.0 O A:HOH572 4.7 10.8 1.0 N A:GLY38 4.8 8.1 1.0 CA A:HIS78 4.8 6.3 1.0 C A:HIS78 4.8 8.0 1.0 CB A:THR37 4.9 10.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, E280A Mutant in Complex with Cellotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:13.6 occ:1.00 OE2 B:GLU216 2.4 13.1 1.0 OD1 B:ASN217 2.4 12.0 1.0 OE1 B:GLU216 2.4 13.2 1.0 O B:HOH848 2.4 19.8 1.0 O B:HOH739 2.4 15.4 1.0 O B:HOH780 2.4 21.8 1.0 CD B:GLU216 2.7 12.9 1.0 CG B:ASN217 3.5 9.0 1.0 CG B:GLU216 4.2 11.4 1.0 ND2 B:ASN217 4.3 10.0 1.0 O B:HOH721 4.3 24.6 1.0 O B:HOH832 4.3 18.1 1.0 O B:HOH879 4.4 16.9 1.0 O B:HOH891 4.4 26.7 1.0 CA B:ASN217 4.5 9.4 1.0 O B:HOH988 4.5 30.6 1.0 CB B:ASN217 4.6 8.9 1.0 ND2 B:ASN220 4.7 16.9 1.0 N B:ASN217 4.7 9.3 1.0 C B:GLU216 5.0 7.0 1.0

N.Mcgregor, M.Morar, T.H.Fenger, P.Stogios, N.Lenfant, V.Yin, X.Xu, E.Evdokimova, H.Cui, B.Henrissat, A.Savchenko, H.Brumer. Structure-Function Analysis of A Mixed-Linkage Beta-Glucanase/Xyloglucanase From Key Ruminal Bacteroidetes Prevotella Bryantii B14. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 26507654
DOI: 10.1074/JBC.M115.691659