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

Enzymatic activity of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate

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

Protein crystallography data

The structure of Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate, PDB code: 3cqk 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) 44.24 / 2.33
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.028, 132.550, 82.079, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate (pdb code 3cqk). 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+ and Sulfate, PDB code: 3cqk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3cqk

Go back to Zinc Binding Sites List in 3cqk
Zinc binding site 1 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate


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+ and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn285

b:33.2
occ:1.00
 ND1 A:HIS211 2.0 24.9 1.0
OE1 A:GLU251 2.0 34.2 1.0
OE2 A:GLU155 2.1 27.0 1.0
OD2 A:ASP185 2.1 19.3 1.0
CE1 A:HIS211 3.0 23.8 1.0
CD A:GLU251 3.0 33.5 1.0
CG A:HIS211 3.1 21.4 1.0
CG A:ASP185 3.2 21.9 1.0
OE2 A:GLU251 3.3 36.1 1.0
CD A:GLU155 3.3 29.3 1.0
CB A:HIS211 3.4 20.2 1.0
CB A:ASP185 3.6 22.3 1.0
NZ A:LYS213 3.9 22.8 1.0
OE1 A:GLU155 4.0 33.9 1.0
NE2 A:HIS211 4.1 24.1 1.0
CD2 A:HIS211 4.2 23.3 1.0
OD1 A:ASP185 4.3 24.4 1.0
CG A:GLU251 4.3 30.3 1.0
CG A:GLU155 4.4 28.3 1.0
ND2 A:ASN188 4.4 24.7 1.0
NE2 A:GLN115 4.6 29.4 1.0
CE A:LYS213 4.6 23.6 1.0
CB A:GLU251 4.7 27.8 1.0
CA A:ASP185 4.8 22.4 1.0
O A:HOH322 4.8 37.8 1.0
CD A:LYS213 4.8 24.7 1.0
CA A:HIS211 4.9 20.5 1.0

Zinc binding site 2 out of 4 in 3cqk

Go back to Zinc Binding Sites List in 3cqk
Zinc binding site 2 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate


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+ and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn286

b:74.1
occ:1.00
 NE2 A:HIS206 2.4 33.1 1.0
O A:HOH328 2.7 43.1 1.0
CD2 A:HIS206 3.1 31.3 1.0
CE1 A:HIS206 3.5 35.1 1.0
CE1 A:HIS173 3.8 38.0 1.0
O A:HOH296 4.2 51.1 1.0
ND1 A:HIS173 4.3 35.1 1.0
CG A:HIS206 4.3 28.7 1.0
CD2 A:LEU169 4.4 23.5 1.0
ND1 A:HIS206 4.5 34.7 1.0
NE2 A:HIS173 4.8 37.0 1.0

Zinc binding site 3 out of 4 in 3cqk

Go back to Zinc Binding Sites List in 3cqk
Zinc binding site 3 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate


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+ and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn285

b:55.6
occ:1.00
 ND1 B:HIS211 2.0 37.2 1.0
OD2 B:ASP185 2.2 37.5 1.0
OE2 B:GLU155 2.3 39.3 1.0
OE2 B:GLU251 2.3 51.0 1.0
CG B:HIS211 3.0 35.8 1.0
CE1 B:HIS211 3.0 36.0 1.0
CG B:ASP185 3.2 36.9 1.0
CB B:HIS211 3.3 35.6 1.0
CD B:GLU251 3.3 48.1 1.0
CD B:GLU155 3.5 38.3 1.0
CB B:ASP185 3.6 35.6 1.0
OE1 B:GLU251 3.6 52.1 1.0
NE2 B:HIS211 4.1 37.0 1.0
CD2 B:HIS211 4.1 36.1 1.0
OD1 B:ASP185 4.3 39.0 1.0
OE1 B:GLU155 4.3 42.6 1.0
NZ B:LYS213 4.3 43.0 1.0
CG B:GLU155 4.4 37.4 1.0
ND2 B:ASN188 4.4 38.8 1.0
NE2 B:GLN115 4.7 37.5 1.0
CG B:GLU251 4.7 47.5 1.0
CA B:ASP185 4.7 35.4 1.0
CA B:HIS211 4.8 35.6 1.0
CE B:LYS213 4.8 43.5 1.0
CD B:LYS213 5.0 43.9 1.0
CB B:GLU251 5.0 45.3 1.0

Zinc binding site 4 out of 4 in 3cqk

Go back to Zinc Binding Sites List in 3cqk
Zinc binding site 4 out of 4 in the Crystal Structure of L-Xylulose-5-Phosphate 3-Epimerase Ulae (Form B) Complex with ZN2+ and Sulfate


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+ and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn286

b:76.1
occ:1.00
 O B:HOH349 2.5 51.0 1.0
NE2 B:HIS206 2.5 41.2 1.0
CD2 B:HIS206 3.3 37.9 1.0
CE1 B:HIS173 3.3 34.4 1.0
CE1 B:HIS206 3.5 42.0 1.0
ND1 B:HIS173 3.9 33.3 1.0
NE2 B:HIS173 4.3 35.1 1.0
CG B:HIS206 4.5 34.8 1.0
CD2 B:LEU169 4.6 24.9 1.0
ND1 B:HIS206 4.6 39.6 1.0

Reference:

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
Page generated: Thu Oct 24 11:55:04 2024

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