Sodium in PDB 6mly: Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304

All present enzymatic activity of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304:
3.2.1.37;

The structure of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304, PDB code: 6mly was solved by N.M.Koropatkin, G.V.Pereira, I.Cann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	254.734, 93.310, 214.039, 90.00, 123.38, 90.00
R / Rfree (%)	22 / 26.9

The binding sites of Sodium atom in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304 (pdb code 6mly). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304, PDB code: 6mly:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:40.9 occ:1.00 O A:TYR726 2.3 67.9 1.0 O A:THR645 2.4 68.7 1.0 OD1 A:ASP728 2.5 71.5 1.0 OD1 A:ASP731 2.8 69.0 1.0 OD2 A:ASP731 2.9 68.2 1.0 CG A:ASP731 3.2 68.2 1.0 C A:TYR726 3.5 68.0 1.0 C A:THR645 3.6 68.2 1.0 CG A:ASP728 3.7 71.4 1.0 CB A:TYR726 4.2 68.1 1.0 CA A:TYR726 4.3 68.2 1.0 CB A:ASP728 4.3 70.3 1.0 N A:ASP728 4.3 68.7 1.0 CA A:THR645 4.4 67.4 1.0 N A:ILE727 4.4 67.7 1.0 C A:ILE727 4.5 68.2 1.0 N A:THR646 4.6 68.3 1.0 CG2 A:VAL649 4.6 72.6 1.0 CA A:ILE727 4.6 67.5 1.0 OD2 A:ASP728 4.7 72.5 1.0 CA A:THR646 4.7 69.1 1.0 CB A:ASP731 4.7 68.0 1.0 O A:ASN647 4.8 71.1 1.0 CB A:THR645 4.8 67.3 1.0 CA A:ASP728 4.9 69.4 1.0

Sodium binding site 2 out of 4 in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:60.4 occ:1.00 OD1 B:ASP728 2.4 55.8 1.0 O B:THR645 2.5 57.5 1.0 O B:TYR726 2.5 52.5 1.0 OD1 B:ASP731 3.1 58.6 1.0 OD2 B:ASP731 3.1 58.5 1.0 CG B:ASP731 3.5 57.2 1.0 CG B:ASP728 3.6 56.3 1.0 C B:TYR726 3.7 53.1 1.0 C B:THR645 3.7 56.6 1.0 CB B:TYR726 4.3 52.9 1.0 O B:ASN647 4.3 60.5 1.0 CB B:ASP728 4.4 55.7 1.0 CG2 B:VAL649 4.4 54.9 1.0 CA B:TYR726 4.4 53.0 1.0 OD2 B:ASP728 4.5 57.0 1.0 N B:ASP728 4.6 54.3 1.0 CA B:THR646 4.6 56.0 1.0 N B:THR646 4.6 56.1 1.0 CA B:THR645 4.7 54.5 1.0 N B:ILE727 4.7 53.2 1.0 C B:ILE727 4.7 53.8 1.0 N B:ASN647 4.9 55.3 1.0 CA B:ILE727 4.9 53.0 1.0

Sodium binding site 3 out of 4 in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na904 b:43.8 occ:1.00 O C:TYR726 2.2 58.4 1.0 O C:THR645 2.3 61.4 1.0 OD1 C:ASP728 2.3 62.0 1.0 OD2 C:ASP731 2.7 57.9 1.0 OD1 C:ASP731 3.0 60.0 1.0 CG C:ASP731 3.2 58.8 1.0 C C:TYR726 3.4 57.5 1.0 CG C:ASP728 3.5 62.0 1.0 C C:THR645 3.5 60.5 1.0 CB C:TYR726 3.9 57.3 1.0 CA C:TYR726 4.1 57.1 1.0 CB C:ASP728 4.3 60.8 1.0 N C:ASP728 4.4 58.9 1.0 OD2 C:ASP728 4.4 63.4 1.0 N C:ILE727 4.4 57.6 1.0 N C:THR646 4.4 60.4 1.0 CA C:THR646 4.5 61.2 1.0 CA C:THR645 4.5 59.5 1.0 C C:ILE727 4.6 58.5 1.0 CG2 C:VAL649 4.6 63.0 1.0 CA C:ILE727 4.7 58.1 1.0 CB C:ASP731 4.7 58.8 1.0 O C:ASN647 4.7 63.5 1.0 N C:ASN647 4.9 61.6 1.0

Sodium binding site 4 out of 4 in the Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bifunctional GH43-Ce Bacteroides Eggerthii, BACEGG_01304 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na906 b:37.4 occ:1.00 O D:THR645 2.3 54.8 1.0 OD1 D:ASP728 2.3 56.8 1.0 O D:TYR726 2.4 54.3 1.0 OD1 D:ASP731 2.9 57.1 1.0 OD2 D:ASP731 3.4 56.0 1.0 C D:THR645 3.5 54.3 1.0 CG D:ASP731 3.5 55.6 1.0 CG D:ASP728 3.6 56.5 1.0 C D:TYR726 3.6 53.4 1.0 CB D:TYR726 4.1 53.2 1.0 CA D:TYR726 4.2 53.0 1.0 N D:THR646 4.4 53.7 1.0 CB D:ASP728 4.4 55.6 1.0 CA D:THR645 4.4 53.7 1.0 CA D:THR646 4.5 53.8 1.0 OD2 D:ASP728 4.5 57.7 1.0 CG2 D:VAL649 4.5 54.1 1.0 O D:ASN647 4.6 56.8 1.0 N D:ASP728 4.7 54.7 1.0 N D:ILE727 4.7 53.4 1.0 C D:ILE727 4.7 54.1 1.0 N D:ASN647 4.8 53.9 1.0 CB D:THR645 4.9 54.0 1.0 CA D:ILE727 4.9 53.6 1.0 C D:THR646 4.9 54.2 1.0 O D:ILE727 5.0 55.0 1.0

G.V.Pereira, C.Dalessandro-Gabazza, J.Farris, D.Wefers, R.Mackie, N.M.Koropatkin, E.C.Gabazza, I.Cann. Complex Arabinoxylan Fermenting Bacteroidetes Release Dietary Antioxidants That Impact Host Immune Function To Be Published.