Chlorine in PDB 8syh: 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 at pH 8

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 at pH 8, PDB code: 8syh was solved by J.D.T.Jast, 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)	40.59 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.788, 128.158, 58.475, 90, 112.54, 90
R / Rfree (%)	18.3 / 23.4

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 at pH 8 (pdb code 8syh). 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 at pH 8, PDB code: 8syh:
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 at pH 8


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 at pH 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:25.3 occ:1.00 O A:HOH553 2.9 18.3 1.0 O A:HOH583 2.9 12.8 1.0 NH2 A:ARG12 3.1 16.4 1.0 O A:HOH612 3.3 15.8 1.0 CD2 A:HIS208 3.4 14.8 1.0 CB A:HIS240 3.6 16.9 1.0 O A:HOH562 3.7 16.6 1.0 CB A:THR206 3.7 15.1 1.0 CG A:HIS208 3.9 15.6 1.0 CD2 A:HIS240 4.1 15.0 1.0 CZ A:ARG12 4.2 18.7 1.0 CB A:HIS208 4.2 16.3 1.0 NE2 A:HIS208 4.2 18.2 1.0 N A:HIS240 4.2 18.6 1.0 CG2 A:THR206 4.2 15.5 1.0 OG1 A:THR206 4.2 15.6 1.0 CG A:HIS240 4.3 15.7 1.0 CA A:HIS240 4.3 17.8 1.0 C5 A:MJL401 4.4 22.1 1.0 NH1 A:ARG12 4.4 18.2 1.0 O A:PRO238 4.5 20.9 1.0 N A:ILE207 4.5 16.2 1.0 O1A A:MJL401 4.6 16.2 1.0 O A:ILE207 4.6 15.3 1.0 CA A:THR206 4.6 16.1 1.0 C A:ILE207 4.7 15.0 1.0 C A:THR206 4.8 17.0 1.0 C6 A:MJL401 4.9 20.5 1.0 O2A A:MJL401 4.9 17.2 1.0 N A:HIS208 4.9 15.7 1.0 ND1 A:HIS208 5.0 18.7 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 at pH 8


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 at pH 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:23.3 occ:1.00 O B:HOH533 2.9 20.6 1.0 O B:HOH574 3.0 14.9 1.0 NH2 B:ARG12 3.1 19.2 1.0 ND1 B:HIS208 3.4 22.9 1.0 O B:HOH614 3.4 22.7 1.0 CB B:THR206 3.7 21.9 1.0 CB B:HIS240 3.7 24.1 1.0 O B:HOH532 3.7 29.7 1.0 CD2 B:HIS240 3.8 24.6 1.0 CG B:HIS208 3.9 23.6 1.0 CB B:HIS208 4.0 22.9 1.0 CG B:HIS240 4.1 24.4 1.0 OG1 B:THR206 4.1 21.7 1.0 CZ B:ARG12 4.2 21.2 1.0 CE1 B:HIS208 4.2 24.2 1.0 CG2 B:THR206 4.3 22.6 1.0 N B:HIS240 4.3 25.1 1.0 O B:ILE207 4.4 24.1 1.0 N B:ILE207 4.4 22.5 1.0 O B:PRO238 4.4 26.7 1.0 CA B:HIS240 4.4 27.9 1.0 NH1 B:ARG12 4.5 22.1 1.0 C5 B:MJL401 4.5 25.3 1.0 CA B:THR206 4.5 19.7 1.0 C B:ILE207 4.6 22.0 1.0 O1A B:MJL401 4.6 19.5 1.0 C B:THR206 4.8 19.4 1.0 O2A B:MJL401 4.9 18.8 1.0 CD2 B:HIS208 4.9 24.2 1.0 N B:HIS208 5.0 20.4 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