Sodium in PDB 8sxw: X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Mutation, Apo Structure at pH 6

The structure of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Mutation, Apo Structure at pH 6, PDB code: 8sxw was solved by C.W.Kroft, 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)	41.72 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.327, 85.34, 86.535, 108.23, 110.06, 97.1
R / Rfree (%)	17.9 / 22.4

The structure of X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Mutation, Apo Structure at pH 6 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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, D98N Mutation, Apo Structure at pH 6 (pdb code 8sxw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Mutation, Apo Structure at pH 6, PDB code: 8sxw:

Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Udp- 2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Mutation, Apo Structure at pH 6


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, D98N Mutation, Apo Structure at pH 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:25.4 occ:1.00 O B:HOH559 2.4 30.4 1.0 CA B:ILE342 3.9 33.6 1.0 OE2 B:GLU341 4.0 39.3 1.0 O B:GLU341 4.0 41.7 1.0 N B:ASP343 4.5 27.0 1.0 C B:GLU341 4.5 32.5 1.0 C B:ILE342 4.5 34.4 1.0 N B:ILE342 4.5 34.5 1.0 OD1 B:ASP343 4.7 31.7 1.0 CG B:GLU341 4.7 35.1 1.0 O B:HOH514 4.7 37.2 1.0 CD B:GLU341 4.8 34.1 1.0 CG1 B:ILE342 4.8 38.0 1.0 CB B:ILE342 4.9 38.1 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