Calcium in PDB 6dht: Bacteroides Ovatus GH9 BACOVA_02649

All present enzymatic activity of Bacteroides Ovatus GH9 BACOVA_02649:
3.2.1.151;

The structure of Bacteroides Ovatus GH9 BACOVA_02649, PDB code: 6dht was solved by N.M.Koropatkin, M.H.Foley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.74 / 1.42
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.646, 50.406, 95.980, 90.00, 109.00, 90.00
R / Rfree (%)	16.8 / 19.7

The structure of Bacteroides Ovatus GH9 BACOVA_02649 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Bacteroides Ovatus GH9 BACOVA_02649 (pdb code 6dht). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bacteroides Ovatus GH9 BACOVA_02649, PDB code: 6dht:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bacteroides Ovatus GH9 BACOVA_02649


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacteroides Ovatus GH9 BACOVA_02649 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:19.5 occ:1.00 O A:GLY390 2.4 20.3 1.0 OD2 A:ASP349 2.4 21.2 1.0 O A:HIS351 2.4 24.8 1.0 OD1 A:ASP354 2.4 21.6 1.0 O A:HOH909 2.5 26.1 1.0 OE2 A:GLU355 2.5 19.0 1.0 OE1 A:GLU355 2.5 20.3 1.0 OD2 A:ASP354 2.6 20.1 1.0 CD A:GLU355 2.9 19.1 1.0 CG A:ASP354 2.9 21.2 1.0 CG A:ASP349 3.4 23.2 1.0 C A:GLY390 3.5 18.8 1.0 OD1 A:ASP349 3.6 23.3 1.0 C A:HIS351 3.7 22.9 1.0 HA A:ALA352 3.7 26.3 1.0 HA A:ASN391 3.7 24.8 1.0 HB2 A:HIS351 4.0 33.0 1.0 HA2 A:GLY390 4.1 24.2 1.0 H A:GLU355 4.1 21.5 1.0 H A:ASP354 4.2 24.2 1.0 CA A:GLY390 4.3 20.1 1.0 CG A:GLU355 4.4 17.0 1.0 N A:ASN391 4.4 19.1 1.0 O A:HOH840 4.4 21.6 1.0 CB A:ASP354 4.4 17.6 1.0 H A:THR392 4.4 19.1 1.0 CA A:ALA352 4.5 21.9 1.0 CA A:ASN391 4.5 20.7 1.0 O A:HOH923 4.5 33.4 1.0 N A:ALA352 4.5 23.6 1.0 HA3 A:GLY390 4.5 24.2 1.0 HB3 A:HIS351 4.6 33.0 1.0 CB A:HIS351 4.6 27.5 1.0 H A:HIS351 4.6 31.4 1.0 CA A:HIS351 4.7 23.8 1.0 HG22 A:THR280 4.7 22.7 1.0 HG3 A:GLU355 4.7 20.4 1.0 CB A:ASP349 4.7 25.4 1.0 N A:GLU355 4.8 17.9 1.0 HG21 A:THR280 4.8 22.7 1.0 HB3 A:ASP354 4.8 21.2 1.0 HB2 A:ASP354 4.8 21.2 1.0 HG2 A:GLU355 4.8 20.4 1.0 HB3 A:ASP349 4.8 30.4 1.0 N A:ASP354 4.9 20.2 1.0 O A:HOH738 4.9 19.1 1.0 O A:HOH1150 4.9 40.9 1.0 C A:ALA352 5.0 21.0 1.0 HB2 A:GLU355 5.0 22.3 1.0 HB2 A:ASP349 5.0 30.4 1.0

Calcium binding site 2 out of 2 in the Bacteroides Ovatus GH9 BACOVA_02649


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacteroides Ovatus GH9 BACOVA_02649 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:17.8 occ:1.00 O A:THR225 2.3 17.1 1.0 OD2 A:ASP230 2.3 15.2 1.0 OD1 A:ASP227 2.4 16.0 1.0 O A:GLU220 2.4 18.1 1.0 OD1 A:ASN223 2.4 18.8 1.0 O A:HOH999 2.4 22.2 1.0 HA A:ASP227 3.3 16.9 1.0 HA A:SER221 3.3 22.3 1.0 CG A:ASN223 3.3 22.1 1.0 H A:THR225 3.4 23.9 1.0 C A:GLU220 3.5 19.3 1.0 C A:THR225 3.5 16.5 1.0 CG A:ASP230 3.5 16.2 1.0 CG A:ASP227 3.6 17.0 1.0 HD21 A:ASN223 3.6 24.9 1.0 H A:ASN223 3.6 28.2 1.0 HB A:THR225 3.8 21.2 1.0 N A:ASP227 3.8 13.9 1.0 HB3 A:GLU220 3.8 23.2 1.0 ND2 A:ASN223 3.9 20.7 1.0 CA A:ASP227 3.9 14.1 1.0 H A:ASP227 4.0 16.7 1.0 CA A:SER221 4.0 18.6 1.0 C A:PRO226 4.0 14.9 1.0 OD1 A:ASP230 4.1 16.3 1.0 N A:THR225 4.1 19.9 1.0 N A:SER221 4.2 18.6 1.0 HB2 A:GLU220 4.2 23.2 1.0 HE3 A:LYS215 4.2 47.8 1.0 C A:SER221 4.2 21.5 1.0 CA A:THR225 4.2 18.0 1.0 N A:ASN223 4.3 23.5 1.0 CB A:GLU220 4.4 19.3 1.0 CB A:ASP227 4.4 13.8 1.0 O A:SER221 4.4 23.7 1.0 O A:PRO226 4.4 15.1 1.0 O A:ASN223 4.4 24.3 1.0 HA A:PRO226 4.4 18.8 1.0 HB2 A:ASP230 4.4 15.7 1.0 CB A:THR225 4.5 17.6 1.0 N A:PRO226 4.5 15.8 1.0 OD2 A:ASP227 4.5 18.5 1.0 CA A:GLU220 4.5 17.4 1.0 C A:ASN223 4.5 19.8 1.0 CA A:PRO226 4.5 15.7 1.0 CB A:ASN223 4.6 24.1 1.0 CB A:ASP230 4.6 13.1 1.0 CA A:ASN223 4.7 20.6 1.0 HD22 A:ASN223 4.7 24.9 1.0 O1 A:EDO607 4.7 46.5 1.0 N A:ASN222 4.7 20.7 1.0 HO1 A:EDO607 4.7 55.9 1.0 HD11 A:ILE218 4.8 23.4 1.0 HA A:GLU220 4.9 20.9 1.0 H A:ASN222 4.9 24.8 1.0 HB3 A:ASN223 5.0 28.9 1.0 HG22 A:THR225 5.0 23.5 1.0 HB2 A:ASP227 5.0 16.6 1.0 HB3 A:ASP227 5.0 16.6 1.0

M.H.Foley, G.Dejean, G.R.Hemsworth, G.J.Davies, H.Brumer, N.M.Koropatkin. A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides Ovatus. J. Mol. Biol. V. 431 981 2019.
ISSN: ESSN 1089-8638
PubMed: 30668971
DOI: 10.1016/J.JMB.2019.01.008