Sodium in PDB 7b7h: The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate

The structure of The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate, PDB code: 7b7h was solved by S.Mazurkewich, J.Larsbrink, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.15 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.333, 47.298, 51.112, 61.95, 67.92, 88.27
R / Rfree (%)	18.3 / 22.2

The binding sites of Sodium atom in the The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate (pdb code 7b7h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate, PDB code: 7b7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na513 b:27.7 occ:1.00 OXT A:GLY530 2.3 40.8 1.0 O A:ASP253 2.4 29.8 1.0 O1 A:EDO524 2.4 29.6 1.0 O A:VAL256 2.4 26.7 1.0 O A:LEU250 2.5 28.0 1.0 C1 A:EDO524 3.3 25.5 1.0 O A:GLU251 3.4 36.9 1.0 C A:ASP253 3.4 34.1 1.0 C A:GLY530 3.5 42.8 1.0 C A:VAL256 3.6 28.7 1.0 C A:GLU251 3.6 31.7 1.0 C A:LEU250 3.6 25.2 1.0 N A:ASP253 3.8 30.8 1.0 CA A:GLU251 3.9 29.4 1.0 CG2 A:VAL256 4.0 33.1 1.0 N A:ALA258 4.1 28.3 1.0 CA A:ASP253 4.1 29.9 1.0 O A:GLY530 4.3 52.0 1.0 N A:VAL256 4.3 28.1 1.0 N A:GLU251 4.3 26.2 1.0 CA A:GLY530 4.3 38.1 1.0 N A:THR252 4.3 30.1 1.0 N A:PRO254 4.4 30.8 1.0 CA A:VAL256 4.4 24.4 1.0 C A:THR252 4.4 30.5 1.0 C2 A:EDO524 4.4 40.1 1.0 CA A:PRO254 4.5 33.1 1.0 N A:ASP257 4.5 28.4 1.0 CB A:ALA258 4.5 24.9 1.0 CB A:ASP253 4.7 29.0 1.0 CA A:ASP257 4.7 29.7 1.0 CD A:ARG132 4.8 39.9 1.0 CB A:VAL256 4.8 30.7 1.0 CA A:LEU250 4.8 21.0 1.0 CA A:THR252 4.8 30.4 1.0 C A:PRO254 4.8 31.9 1.0 C A:ASP257 4.9 27.5 1.0 CA A:ALA258 5.0 23.0 1.0

Sodium binding site 2 out of 2 in the The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Glucuronoyl Esterase OTCE15A R268A Variant From Opitutus Terrae in Complex with, and Covalently Linked to, D-Glucuronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na514 b:29.0 occ:1.00 O A:HIS303 2.3 28.6 1.0 O A:GLU305 2.3 28.6 1.0 O A:HOH679 2.3 22.7 1.0 O A:HOH691 2.3 28.7 1.0 O A:HOH630 2.4 29.3 1.0 C A:HIS303 3.4 25.8 1.0 C A:GLU305 3.4 26.2 1.0 N A:GLU305 3.9 26.5 1.0 N A:HIS303 3.9 27.9 1.0 CB A:ASP360 4.1 25.0 1.0 CA A:GLU305 4.2 28.1 1.0 C A:GLY304 4.2 30.1 1.0 CA A:HIS303 4.2 27.3 1.0 CB A:CYS293 4.4 27.6 1.0 OD2 A:ASP360 4.4 27.6 1.0 N A:GLY304 4.4 25.9 1.0 N A:THR306 4.4 25.3 1.0 O A:HOH619 4.5 30.3 1.0 CA A:GLY304 4.5 23.6 1.0 O A:TRP358 4.5 27.3 1.0 O A:LEU298 4.5 26.3 1.0 SG A:CYS293 4.7 29.8 1.0 CA A:THR306 4.7 28.6 1.0 CG A:ASP360 4.7 27.3 1.0 CB A:ALA297 4.7 22.0 1.0 O A:GLY304 4.8 28.1 1.0 CA A:CYS293 4.8 21.9 1.0 CB A:GLU305 4.8 25.2 1.0 C A:ILE302 4.9 35.7 1.0 CB A:HIS303 4.9 26.6 1.0 O A:HOH632 5.0 26.3 1.0

Z.Zong, S.Mazurkewich, C.S.Pereira, H.Fu, W.Cai, X.Shao, M.S.Skaf, J.Larsbrink, L.Lo Leggio. Mechanism and Biomass Association of Glucuronoyl Esterase: An Alpha / Beta Hydrolase with Potential in Biomass Conversion. Nat Commun V. 13 1449 2022.
ISSN: ESSN 2041-1723
PubMed: 35304453
DOI: 10.1038/S41467-022-28938-W