Sodium in PDB 8sy0: X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9

The structure of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9, PDB code: 8sy0 was solved by J.O.Mcknight, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.67 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.34, 128.608, 58.934, 90, 111.24, 90
R / Rfree (%)	18 / 23.1

The structure of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9 (pdb code 8sy0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9, PDB code: 8sy0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:35.2 occ:1.00 O A:GLU257 2.3 40.4 1.0 O A:HOH606 2.4 27.8 1.0 O A:VAL259 2.4 30.4 1.0 O A:HOH632 2.7 32.3 1.0 C A:GLU257 3.3 34.2 1.0 C A:VAL259 3.6 24.1 1.0 O A:HOH627 3.7 40.4 1.0 CA A:GLU257 3.9 38.5 1.0 O A:LEU256 4.1 22.5 1.0 CA A:VAL260 4.3 21.9 1.0 N A:VAL259 4.3 28.9 1.0 N A:LYS258 4.4 32.5 1.0 N A:VAL260 4.4 22.6 1.0 C A:LYS258 4.4 33.7 1.0 N A:ALA261 4.5 20.7 1.0 CA A:VAL259 4.6 24.4 1.0 O A:LYS258 4.6 43.3 1.0 CA A:LYS258 4.7 33.4 1.0 CB A:GLU257 4.9 47.1 1.0 N A:GLU257 4.9 32.3 1.0 C A:LEU256 4.9 26.2 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27 in Complex with Its Product Udp-2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid at pH 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:39.0 occ:1.00 O B:VAL170 2.7 19.8 1.0 O B:HOH522 2.8 21.9 1.0 NZ B:LYS353 2.9 38.8 1.0 OD1 B:ASP347 3.0 41.8 1.0 N B:ALA350 3.3 27.2 1.0 N B:ASP347 3.3 26.5 1.0 O B:HOH602 3.4 42.1 1.0 CA B:GLY346 3.4 27.0 1.0 CA B:ALA350 3.6 24.6 1.0 C B:VAL170 3.7 20.4 1.0 CB B:ALA350 3.7 25.6 1.0 C B:GLY346 3.9 28.8 1.0 C B:ARG349 3.9 31.8 1.0 N B:ARG349 3.9 25.9 1.0 CG B:ASP347 4.0 42.6 1.0 CA B:GLY171 4.0 19.3 1.0 O B:TYR345 4.1 23.7 1.0 N B:GLY348 4.1 25.8 1.0 N B:GLY171 4.3 20.6 1.0 CE B:LYS353 4.3 37.1 1.0 CA B:ASP347 4.4 31.2 1.0 CA B:ARG349 4.4 32.8 1.0 N B:GLY346 4.5 26.5 1.0 O B:ARG349 4.5 28.6 1.0 C B:TYR345 4.7 24.2 1.0 C B:ASP347 4.7 29.4 1.0 C B:GLY171 4.8 18.9 1.0 CB B:ASP347 4.8 35.2 1.0 CD B:LYS353 4.8 34.2 1.0 OD1 B:ASP176 4.8 18.4 1.0 OD2 B:ASP347 4.9 48.5 1.0 C B:GLY348 4.9 25.2 1.0 CA B:VAL170 4.9 22.3 1.0 CA B:GLY348 5.0 26.1 1.0 CB B:ARG349 5.0 39.5 1.0 N B:ASP172 5.0 19.8 1.0

J.B.Thoden, J.O.Mcknight, C.W.Kroft, J.D.T.Jast, H.M.Holden. Structural Analysis of A Bacterial Udp-Sugar 2-Epimerase Reveals the Active Site Architecture Before and After Catalysis. J.Biol.Chem. 05200 2023.
ISSN: ESSN 1083-351X
PubMed: 37660908
DOI: 10.1016/J.JBC.2023.105200