Sodium in PDB 8q6s: A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482

The structure of A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482, PDB code: 8q6s was solved by S.Mazurkewich, A.Seveso, S.Banerjee, L.Lo Leggio, J.Larsbrink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.64 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.382, 58.697, 89.539, 90, 103.95, 90
R / Rfree (%)	19.4 / 25.8

The binding sites of Sodium atom in the A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482 (pdb code 8q6s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482, PDB code: 8q6s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:43.3 occ:1.00 O A:GLU302 2.3 42.7 1.0 O A:HOH730 2.4 40.9 1.0 O A:HOH686 2.4 41.2 1.0 O A:PHE300 2.4 39.9 1.0 O A:HOH712 2.5 43.0 1.0 C A:PHE300 3.5 40.7 1.0 C A:GLU302 3.5 38.5 1.0 N A:PHE300 3.7 42.6 1.0 N A:GLU302 4.1 40.9 1.0 CA A:PHE300 4.2 46.0 1.0 CB A:ASP357 4.2 42.3 1.0 CB A:CYS290 4.3 37.3 1.0 CA A:GLU302 4.3 47.2 1.0 O A:HOH654 4.3 46.0 1.0 C A:GLY301 4.3 40.8 1.0 SG A:CYS290 4.5 44.0 1.0 C A:CYS299 4.5 45.9 1.0 OD2 A:ASP357 4.5 39.4 1.0 N A:GLY301 4.5 43.1 1.0 N A:THR303 4.5 40.6 1.0 CB A:PHE300 4.7 44.7 1.0 CA A:GLY301 4.7 45.3 1.0 CA A:CYS290 4.7 43.6 1.0 CB A:GLU302 4.7 41.3 1.0 CA A:THR303 4.8 39.0 1.0 O A:ILE295 4.8 43.4 1.0 CA A:CYS299 4.8 40.9 1.0 O A:TRP355 4.8 44.5 1.0 CG A:ASP357 4.9 44.1 1.0 N A:CYS299 4.9 39.3 1.0 O A:GLY301 4.9 43.8 1.0 O A:HOH608 4.9 38.9 1.0

Sodium binding site 2 out of 2 in the A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Carbohydrate Esterase Family 15 (CE15) Glucuronoyl Esterase From Phocaeicola Vulgatus Atcc 8482 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:32.6 occ:1.00 O B:GLU302 2.3 41.3 1.0 O B:PHE300 2.3 35.5 1.0 O B:HOH666 2.3 31.7 1.0 O B:HOH714 2.4 34.8 1.0 O B:HOH712 2.5 38.0 1.0 C B:GLU302 3.4 38.6 1.0 C B:PHE300 3.4 37.8 1.0 N B:PHE300 3.8 39.9 1.0 N B:GLU302 3.9 36.4 1.0 CB B:ASP357 4.1 34.7 1.0 O B:HOH696 4.1 41.3 1.0 CA B:PHE300 4.1 42.0 1.0 CA B:GLU302 4.2 40.6 1.0 OD2 B:ASP357 4.3 39.3 1.0 C B:GLY301 4.3 38.8 1.0 CB B:CYS290 4.3 43.2 1.0 N B:THR303 4.5 32.6 1.0 SG B:CYS290 4.5 38.5 1.0 C B:CYS299 4.5 39.1 1.0 O B:TRP355 4.5 40.6 1.0 N B:GLY301 4.5 34.0 1.0 CA B:THR303 4.6 36.6 1.0 CG B:ASP357 4.7 40.2 1.0 CA B:GLY301 4.7 37.7 1.0 CA B:CYS290 4.7 37.6 1.0 CB B:PHE300 4.7 38.2 1.0 CB B:GLU302 4.7 37.5 1.0 O B:ILE295 4.8 37.2 1.0 CA B:CYS299 4.8 41.9 1.0 N B:CYS299 4.8 32.1 1.0 O B:GLY301 4.9 36.5 1.0 O B:HOH644 5.0 38.2 1.0

A.Seveso, S.Mazurkewich, S.Banerjee, L.Lo Leggio, J.Larsbrink. Polysaccharide Utilization Loci From Bacteroidota Encode CE15 Enzymes with Possible Role in Cleaving Pectin-Lignin Bonds To Be Published.