Zinc in PDB 3cqj: Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+

All present enzymatic activity of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+:
5.1.3.22;

The structure of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+, PDB code: 3cqj was solved by R.Shi, A.Matte, M.Cygler, Montreal-Kingston Bacterial Structuralgenomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.04
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	104.208, 132.596, 81.798, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.3

The binding sites of Zinc atom in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ (pdb code 3cqj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+, PDB code: 3cqj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn285 b:36.0 occ:1.00 OE1 A:GLU251 2.0 34.9 1.0 OD2 A:ASP185 2.0 25.4 1.0 OE2 A:GLU155 2.1 31.5 1.0 ND1 A:HIS211 2.1 26.4 1.0 O A:HOH371 2.4 45.7 1.0 CD A:GLU251 3.1 35.7 1.0 CG A:ASP185 3.1 26.1 1.0 CE1 A:HIS211 3.1 27.3 1.0 CG A:HIS211 3.1 23.8 1.0 CD A:GLU155 3.3 31.1 1.0 CB A:HIS211 3.4 23.3 1.0 OE2 A:GLU251 3.4 39.4 1.0 CB A:ASP185 3.5 25.5 1.0 O A:HOH329 3.7 39.1 1.0 OE1 A:GLU155 4.0 35.6 1.0 NZ A:LYS213 4.1 30.4 1.0 OD1 A:ASP185 4.2 24.9 1.0 NE2 A:HIS211 4.2 25.8 1.0 CD2 A:HIS211 4.3 24.6 1.0 CG A:GLU155 4.4 30.5 1.0 CG A:GLU251 4.4 32.7 1.0 ND2 A:ASN188 4.4 23.9 1.0 O A:HOH317 4.4 42.8 1.0 NE2 A:GLN115 4.7 34.2 1.0 CB A:GLU251 4.7 30.1 1.0 CA A:ASP185 4.7 25.9 1.0 CD A:LYS213 4.8 28.9 1.0 CA A:HIS211 4.9 23.6 1.0 CE A:LYS213 5.0 28.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn286 b:53.0 occ:1.00 O A:HOH382 2.2 47.4 1.0 NE2 A:HIS206 2.4 35.6 1.0 O A:HOH364 2.5 45.7 1.0 CD2 A:HIS206 3.0 32.0 1.0 CE1 A:HIS206 3.6 34.3 1.0 CE1 A:HIS173 3.7 40.9 1.0 ND1 A:HIS173 4.1 39.2 1.0 CD2 A:LEU169 4.2 28.0 1.0 CG A:HIS206 4.2 30.2 1.0 O A:HOH334 4.4 46.1 1.0 ND1 A:HIS206 4.5 33.7 1.0 O A:HOH367 4.7 57.3 0.5 O A:HOH353 4.8 43.0 1.0 NE2 A:HIS173 5.0 39.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn285 b:42.2 occ:1.00 OD2 B:ASP185 2.0 32.9 1.0 OE2 B:GLU155 2.1 36.0 1.0 ND1 B:HIS211 2.1 32.6 1.0 OE2 B:GLU251 2.3 39.0 1.0 CG B:ASP185 3.0 32.0 1.0 CE1 B:HIS211 3.0 33.1 1.0 CG B:HIS211 3.2 30.6 1.0 CD B:GLU251 3.2 37.6 1.0 CD B:GLU155 3.2 36.3 1.0 OE1 B:GLU251 3.5 42.1 1.0 CB B:HIS211 3.5 29.9 1.0 CB B:ASP185 3.5 30.4 1.0 O B:HOH300 3.6 31.7 1.0 OE1 B:GLU155 3.9 39.0 1.0 O B:HOH362 4.1 44.8 1.0 OD1 B:ASP185 4.1 31.8 1.0 NE2 B:HIS211 4.2 31.2 1.0 CD2 B:HIS211 4.3 30.0 1.0 CG B:GLU155 4.4 34.5 1.0 ND2 B:ASN188 4.4 32.2 1.0 NZ B:LYS213 4.4 40.9 1.0 CG B:GLU251 4.6 37.0 1.0 CE B:LYS213 4.6 38.2 1.0 CA B:ASP185 4.7 30.7 1.0 NE2 B:GLN115 4.8 33.8 1.0 CB B:GLU251 4.9 35.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn286 b:56.8 occ:1.00 O B:HOH383 2.3 49.7 1.0 NE2 B:HIS206 2.4 35.9 1.0 O A:HOH337 2.7 47.7 1.0 CD2 B:HIS206 3.0 33.1 1.0 CE1 B:HIS206 3.5 36.4 1.0 CE1 B:HIS173 3.7 34.1 1.0 ND1 B:HIS173 4.1 33.3 1.0 CG B:HIS206 4.3 32.1 1.0 CD2 B:LEU169 4.4 29.2 1.0 ND1 B:HIS206 4.5 34.0 1.0 NE2 B:HIS173 4.7 34.0 1.0 O A:HOH370 4.9 46.0 1.0 O A:HOH367 5.0 57.3 0.5

R.Shi, M.Pineda, E.Ajamian, Q.Cui, A.Matte, M.Cygler. Structure of L-Xylulose-5-Phosphate 3-Epimerase (Ulae) From the Anaerobic L-Ascorbate Utilization Pathway of Escherichia Coli: Identification of A Novel Phosphate Binding Motif Within A Tim Barrel Fold. J.Bacteriol. V. 190 8137 2008.
ISSN: ISSN 0021-9193
PubMed: 18849419
DOI: 10.1128/JB.01049-08