Calcium in PDB 5nbp: Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product

The structure of Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product, PDB code: 5nbp was solved by G.R.Hemsworth, K.Tamura, G.Dejean, T.E.Rogers, N.A.Pudlo, K.Urs, N.Jain, E.C.Martens, H.Brumer, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.57 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.342, 60.149, 49.673, 90.00, 93.75, 90.00
R / Rfree (%)	17.5 / 21.3

The binding sites of Calcium atom in the Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product (pdb code 5nbp). 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 Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product, PDB code: 5nbp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.7 occ:1.00 O A:SER80 2.2 18.9 1.0 O A:HOH490 2.3 19.0 1.0 OD1 A:ASP266 2.3 17.4 1.0 O A:ASP266 2.4 11.7 1.0 O A:ASP40 2.4 16.3 1.0 O1 A:EDO302 2.4 19.9 1.0 O2 A:EDO302 2.5 25.5 1.0 C2 A:EDO302 3.3 28.6 1.0 C1 A:EDO302 3.4 27.6 1.0 C A:ASP266 3.4 15.8 1.0 C A:SER80 3.4 18.1 1.0 C A:ASP40 3.5 14.8 1.0 CG A:ASP266 3.5 16.2 1.0 N A:SER80 3.9 19.3 1.0 CA A:ASP266 4.0 15.0 1.0 CA A:ASP40 4.0 16.7 1.0 CB A:ASP40 4.1 18.5 1.0 CA A:SER80 4.2 20.3 1.0 O A:HOH405 4.3 17.5 1.0 CB A:ASP266 4.3 15.9 1.0 OD2 A:ASP266 4.3 16.8 1.0 CB A:SER80 4.5 22.7 1.0 N A:VAL81 4.5 17.0 1.0 O A:HOH537 4.5 25.5 1.0 N A:TRP267 4.5 15.8 1.0 N A:PHE41 4.6 14.7 1.0 OD1 A:ASP40 4.7 23.1 1.0 CB A:PHE41 4.7 15.8 1.0 CA A:VAL81 4.7 15.5 1.0 C A:PHE41 4.8 17.3 1.0 O A:PHE41 4.8 17.5 1.0 CB A:TRP267 4.8 17.1 1.0 OD1 A:ASN42 4.8 19.1 1.0 CG A:ASP40 4.9 21.4 1.0 CA A:PHE41 4.9 15.7 1.0 CG1 A:VAL81 4.9 15.5 1.0 CA A:TRP267 4.9 16.4 1.0 C A:LYS79 5.0 20.5 1.0 CD1 A:TRP267 5.0 18.0 1.0

Calcium binding site 2 out of 2 in the Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacteroides Ovatus Mixed Linkage Glucan Pul (Mlgul) GH16 in Complex with G4G4G3G Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:16.5 occ:1.00 O B:SER80 2.2 15.7 1.0 O B:HOH420 2.3 15.9 1.0 O B:ASP40 2.3 19.2 1.0 OD1 B:ASP266 2.3 15.4 1.0 O B:ASP266 2.4 13.9 1.0 O2 B:EDO302 2.4 20.1 1.0 O1 B:EDO302 2.5 22.1 1.0 C B:ASP266 3.4 16.3 1.0 C B:SER80 3.4 17.9 1.0 CG B:ASP266 3.5 16.9 1.0 C B:ASP40 3.5 18.0 1.0 C1 B:EDO302 3.5 25.0 1.0 C2 B:EDO302 3.5 26.4 1.0 CA B:ASP266 4.0 16.2 1.0 N B:SER80 4.1 20.9 1.0 CA B:ASP40 4.1 18.8 1.0 CB B:ASP40 4.2 20.6 1.0 CA B:SER80 4.2 18.7 1.0 O B:HOH425 4.2 20.0 1.0 OD2 B:ASP266 4.3 18.9 1.0 CB B:ASP266 4.3 16.1 1.0 O B:HOH517 4.4 34.3 1.0 CB B:SER80 4.5 20.6 1.0 N B:VAL81 4.5 15.9 1.0 N B:TRP267 4.5 16.5 1.0 N B:PHE41 4.6 15.6 1.0 OD1 B:ASP40 4.6 24.9 1.0 O B:PHE41 4.6 19.2 1.0 CB B:PHE41 4.7 17.6 1.0 CA B:VAL81 4.7 17.2 1.0 C B:PHE41 4.7 18.3 1.0 CB B:TRP267 4.8 16.7 1.0 CG1 B:VAL81 4.8 17.7 1.0 OD1 B:ASN42 4.9 20.5 1.0 CA B:PHE41 4.9 16.9 1.0 CG B:ASP40 4.9 24.7 1.0 CA B:TRP267 4.9 17.1 1.0 CD1 B:TRP267 5.0 17.6 1.0

K.Tamura, G.R.Hemsworth, G.Dejean, T.E.Rogers, N.A.Pudlo, K.Urs, N.Jain, G.J.Davies, E.C.Martens, H.Brumer. Molecular Mechanism By Which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides. Cell Rep V. 21 417 2017.
ISSN: ESSN 2211-1247
PubMed: 29020628
DOI: 10.1016/J.CELREP.2017.09.049