Chlorine 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:

Sodium

(Na)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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, 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:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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, 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 Chlorine with other atoms in the Cl 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 A:Cl403 b:24.4 occ:1.00 O A:HOH561 2.7 14.7 1.0 O A:HOH534 3.0 19.4 1.0 NH2 A:ARG12 3.0 20.5 1.0 O A:HOH564 3.3 15.2 1.0 ND1 A:HIS208 3.5 13.6 1.0 CB A:THR206 3.5 16.4 1.0 CB A:HIS240 3.6 17.8 1.0 O A:HOH547 3.6 14.6 1.0 CD2 A:HIS240 4.1 17.0 1.0 OG1 A:THR206 4.1 14.8 1.0 CG A:HIS208 4.1 14.8 1.0 CZ A:ARG12 4.1 19.2 1.0 CB A:HIS208 4.2 15.5 1.0 CG2 A:THR206 4.2 16.0 1.0 N A:HIS240 4.2 18.7 1.0 CG A:HIS240 4.2 17.7 1.0 CA A:HIS240 4.3 18.3 1.0 CE1 A:HIS208 4.3 14.1 1.0 N A:ILE207 4.4 16.6 1.0 O A:PRO238 4.4 21.4 1.0 CA A:THR206 4.4 16.9 1.0 NH1 A:ARG12 4.4 19.5 1.0 C5 A:MJL401 4.5 18.2 1.0 O A:ILE207 4.6 16.5 1.0 O2A A:MJL401 4.6 17.8 1.0 C A:THR206 4.6 17.7 1.0 C A:ILE207 4.7 16.0 1.0 O1A A:MJL401 4.9 19.4 1.0 N A:HIS208 4.9 16.5 1.0 C6 A:MJL401 5.0 18.8 1.0

Chlorine 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, 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 Chlorine with other atoms in the Cl 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, 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:Cl403 b:21.0 occ:1.00 O B:HOH578 2.9 11.3 1.0 O B:HOH534 3.0 8.2 1.0 NH2 B:ARG12 3.2 17.4 1.0 O B:HOH585 3.5 16.6 1.0 CB B:HIS240 3.6 16.5 1.0 CB B:THR206 3.6 19.8 1.0 ND1 B:HIS208 3.6 18.5 1.0 O B:HOH529 3.6 27.6 1.0 ND1 B:HIS240 3.9 16.2 1.0 OG1 B:THR206 4.1 20.3 1.0 CG B:HIS240 4.2 16.2 1.0 CG B:HIS208 4.2 17.7 1.0 CB B:HIS208 4.2 16.3 1.0 N B:ILE207 4.2 15.6 1.0 N B:HIS240 4.2 17.2 1.0 CZ B:ARG12 4.3 17.1 1.0 CA B:HIS240 4.3 17.3 1.0 CG2 B:THR206 4.4 19.0 1.0 O B:ILE207 4.4 14.5 1.0 CA B:THR206 4.4 17.5 1.0 CE1 B:HIS208 4.5 17.5 1.0 O B:PRO238 4.5 18.8 1.0 C B:ILE207 4.5 15.8 1.0 C B:THR206 4.6 16.3 1.0 C5 B:MJL401 4.6 15.5 1.0 NH1 B:ARG12 4.6 16.7 1.0 N B:HIS208 4.8 16.2 1.0 O2A B:MJL401 4.8 12.2 1.0 O1A B:MJL401 5.0 11.6 1.0 CA B:ILE207 5.0 16.1 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