Sodium in PDB 8syb: X-Ray Crystal Structure of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid-2-Epimerase From Thermus Thermophilus Strain HB27, D98N Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine 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, D98N Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 9, PDB code: 8syb 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)	44.79 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.842, 128.195, 58.525, 90, 113.63, 90
R / Rfree (%)	19.1 / 25.3

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 Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 9 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 Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 9 (pdb code 8syb). 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 Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 9, PDB code: 8syb:

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 Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine 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, D98N Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:28.2 occ:1.00 O B:VAL31 2.2 25.8 1.0 O B:ARG26 2.6 31.2 1.0 O B:LEU25 2.8 26.8 1.0 O B:SER28 2.9 37.5 1.0 O B:HOH591 2.9 18.9 1.0 C B:ARG26 3.2 31.0 1.0 C B:VAL31 3.4 25.5 1.0 CA B:ARG26 3.4 32.0 1.0 C B:LEU25 3.7 26.1 1.0 N B:ARG26 4.0 29.4 1.0 C B:SER28 4.1 38.8 1.0 N B:SER28 4.2 37.8 1.0 CB B:VAL31 4.3 27.1 1.0 CA B:VAL31 4.3 26.1 1.0 N B:ARG32 4.3 24.9 1.0 N B:ALA27 4.3 29.4 1.0 CA B:ARG32 4.4 24.9 0.5 CG1 B:VAL31 4.4 29.7 1.0 CA B:ARG32 4.4 24.9 0.5 N B:VAL31 4.7 29.3 1.0 CA B:SER28 4.7 36.8 1.0 CB B:ARG26 4.7 37.4 1.0 C B:ALA27 4.8 35.2 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