Chlorine in PDB 8syd: 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 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 Variant in the Presence of Udp-2,3-Diacetamido-2,3-Dideoxy-Glucuronic Acid and Udp-N-Acetylglucosamine at pH 6, PDB code: 8syd 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)	40.12 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.272, 128.436, 58.135, 90, 114.06, 90
R / Rfree (%)	17.2 / 22.9

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 6 (pdb code 8syd). 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 6, PDB code: 8syd:
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 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:10.3 occ:1.00 O A:HOH571 3.0 12.0 1.0 NH2 A:ARG12 3.0 9.6 1.0 O A:HOH530 3.2 8.3 1.0 O A:HOH602 3.3 6.5 1.0 CB A:HIS240 3.6 9.0 1.0 CB A:THR206 3.6 7.5 1.0 ND1 A:HIS208 3.6 10.6 1.0 O A:HOH552 3.7 8.0 1.0 CZ A:ARG12 4.1 9.5 1.0 N A:HIS240 4.1 8.8 1.0 CD2 A:HIS240 4.1 8.4 1.0 CB A:HIS208 4.2 10.5 1.0 CG A:HIS208 4.2 10.4 1.0 CG2 A:THR206 4.2 7.6 1.0 CA A:HIS240 4.2 9.1 1.0 CG A:HIS240 4.2 8.8 1.0 OG1 A:THR206 4.2 6.9 1.0 N A:ILE207 4.3 8.5 1.0 O A:PRO238 4.3 10.8 1.0 NH1 A:ARG12 4.3 9.8 1.0 O A:ILE207 4.3 8.4 1.0 C5 A:MJL401 4.5 8.0 1.0 CA A:THR206 4.5 7.7 1.0 CE1 A:HIS208 4.5 11.0 1.0 C A:ILE207 4.7 9.1 1.0 C A:THR206 4.7 8.2 1.0 O1A A:MJL401 4.7 7.8 1.0 O2A A:MJL401 4.9 7.5 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 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:11.4 occ:1.00 NH2 B:ARG12 3.0 7.1 1.0 O B:HOH551 3.1 4.9 1.0 O B:HOH556 3.1 12.4 1.0 O B:HOH567 3.2 4.6 1.0 CB B:HIS240 3.6 8.6 1.0 CB B:THR206 3.6 11.0 1.0 ND1 B:HIS208 3.6 9.5 1.0 CD2 B:HIS240 3.8 8.0 1.0 O B:HOH562 3.8 12.8 1.0 CG B:HIS240 4.0 8.0 1.0 CZ B:ARG12 4.1 7.0 1.0 OG1 B:THR206 4.1 11.0 1.0 CG B:HIS208 4.2 9.5 1.0 CG2 B:THR206 4.2 11.0 1.0 CB B:HIS208 4.3 8.9 1.0 C5 B:MJL401 4.3 7.3 1.0 N B:HIS240 4.3 9.8 1.0 CA B:HIS240 4.4 9.4 1.0 NH1 B:ARG12 4.4 7.1 1.0 N B:ILE207 4.4 9.3 1.0 CE1 B:HIS208 4.5 9.8 1.0 CA B:THR206 4.5 9.9 1.0 O B:ILE207 4.6 7.6 1.0 O B:PRO238 4.6 10.5 1.0 C B:ILE207 4.7 8.3 1.0 C B:THR206 4.7 9.4 1.0 O1A B:MJL401 4.8 6.1 1.0 C6 B:MJL401 4.9 7.4 1.0 O2A B:MJL401 4.9 6.1 1.0 N B:HIS208 4.9 8.2 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