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Zinc in PDB 3n9s: Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor:
4.1.2.13;

Protein crystallography data

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor, PDB code: 3n9s was solved by M.Coincon, S.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.28 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.959, 83.436, 139.985, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.4

Other elements in 3n9s:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor (pdb code 3n9s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor, PDB code: 3n9s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3n9s

Go back to Zinc Binding Sites List in 3n9s
Zinc binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:20.3
occ:1.00
 O01 A:TD4308 1.9 27.0 1.0
NE2 A:HIS180 2.1 18.5 1.0
ND1 A:HIS210 2.1 18.5 1.0
NE2 A:HIS83 2.1 22.6 1.0
O13 A:TD4308 2.6 19.3 1.0
N02 A:TD4308 2.8 16.3 1.0
HB3 A:HIS210 2.8 18.0 1.0
CE1 A:HIS180 2.8 29.9 1.0
HE1 A:HIS180 2.9 35.8 1.0
C12 A:TD4308 2.9 18.6 1.0
CE1 A:HIS210 3.0 21.8 1.0
HD22 A:ASN253 3.1 21.1 1.0
CD2 A:HIS83 3.1 15.2 1.0
CG A:HIS210 3.1 16.0 1.0
CE1 A:HIS83 3.1 23.7 1.0
HE1 A:HIS210 3.2 26.0 1.0
CD2 A:HIS180 3.2 18.8 1.0
HD2 A:HIS83 3.2 18.0 1.0
HE1 A:HIS83 3.3 28.3 1.0
CB A:HIS210 3.5 15.1 1.0
HD2 A:HIS180 3.5 22.4 1.0
HD11 A:LEU138 3.8 37.1 1.0
ND2 A:ASN253 3.8 17.7 1.0
C03 A:TD4308 4.0 19.4 1.0
ND1 A:HIS180 4.0 29.9 1.0
HD13 A:LEU138 4.0 37.1 1.0
HD21 A:ASN253 4.1 21.1 1.0
HB2 A:HIS210 4.1 18.0 1.0
NE2 A:HIS210 4.2 16.3 1.0
H A:GLY211 4.2 18.6 1.0
HA A:HIS210 4.2 17.7 1.0
CG A:HIS180 4.2 28.8 1.0
OD1 A:ASP82 4.2 24.7 1.0
CD2 A:HIS210 4.2 15.2 1.0
C04 A:TD4308 4.2 24.6 1.0
ND1 A:HIS83 4.2 21.3 1.0
CG A:HIS83 4.2 23.0 1.0
CD1 A:LEU138 4.3 31.0 1.0
HD12 A:LEU138 4.4 37.1 1.0
OD2 A:ASP82 4.4 25.5 1.0
C14 A:TD4308 4.4 21.3 1.0
CA A:HIS210 4.4 14.9 1.0
HB3 A:ASN253 4.5 16.3 1.0
HB2 A:ASN253 4.7 16.3 1.0
HD1 A:HIS180 4.7 35.7 1.0
CG A:ASP82 4.7 24.8 1.0
N A:GLY211 4.8 15.7 1.0
CG A:ASN253 4.8 17.1 1.0
CB A:ASN253 4.9 13.7 1.0
C05 A:TD4308 4.9 30.7 1.0
HE2 A:HIS210 4.9 19.4 1.0

Zinc binding site 2 out of 2 in 3n9s

Go back to Zinc Binding Sites List in 3n9s
Zinc binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:22.3
occ:1.00
 NE2 B:HIS180 2.0 22.2 1.0
O01 B:TD4311 2.0 24.0 1.0
ND1 B:HIS210 2.1 20.4 1.0
NE2 B:HIS83 2.1 26.4 1.0
O13 B:TD4311 2.6 23.0 1.0
CE1 B:HIS180 2.7 29.8 1.0
HE1 B:HIS180 2.7 35.6 1.0
N02 B:TD4311 2.8 22.9 1.0
HB3 B:HIS210 2.9 24.5 1.0
C12 B:TD4311 2.9 21.5 1.0
CE1 B:HIS210 3.0 23.1 1.0
CE1 B:HIS83 3.0 20.0 1.0
HD22 B:ASN253 3.1 32.3 1.0
CG B:HIS210 3.1 17.5 1.0
CD2 B:HIS83 3.2 24.2 1.0
HE1 B:HIS83 3.2 23.8 1.0
HE1 B:HIS210 3.2 27.6 1.0
CD2 B:HIS180 3.2 23.8 1.0
HD2 B:HIS83 3.4 28.9 1.0
CB B:HIS210 3.5 20.6 1.0
HD2 B:HIS180 3.6 28.4 1.0
ND2 B:ASN253 3.9 27.1 1.0
O B:HOH346 3.9 33.7 1.0
ND1 B:HIS180 3.9 29.0 1.0
C03 B:TD4311 3.9 24.0 1.0
C04 B:TD4311 4.1 24.6 1.0
H B:GLY211 4.1 19.8 1.0
HD21 B:ASN253 4.1 32.3 1.0
HB2 B:HIS210 4.1 24.5 1.0
NE2 B:HIS210 4.2 19.7 1.0
CG B:HIS180 4.2 31.1 1.0
ND1 B:HIS83 4.2 26.1 1.0
HA B:HIS210 4.2 19.1 1.0
CD2 B:HIS210 4.2 19.9 1.0
OD1 B:ASP82 4.2 31.5 1.0
CG B:HIS83 4.3 27.6 1.0
O B:HOH426 4.3 47.8 1.0
C14 B:TD4311 4.3 22.0 1.0
CA B:HIS210 4.5 16.0 1.0
HB3 B:ASN253 4.5 17.1 1.0
OD2 B:ASP82 4.5 35.8 1.0
HD1 B:HIS180 4.6 34.6 1.0
HB2 B:ASN253 4.7 17.1 1.0
N B:GLY211 4.7 16.7 1.0
CG B:ASP82 4.8 30.1 1.0
CG B:ASN253 4.9 22.7 1.0
CB B:ASN253 4.9 14.4 1.0
HE2 B:HIS210 4.9 23.4 1.0
HD1 B:HIS83 4.9 31.2 1.0

Reference:

R.Daher, M.Fonvielle, P.M.Gest, M.E.Guerin, M.Jackson, J.Sygusch, M.Therisod. Rational Design, Synthesis, and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-Phosphate Aldolases. J.Med.Chem. V. 53 7836 2010.
ISSN: ISSN 0022-2623
PubMed: 20929256
DOI: 10.1021/JM1009814
Page generated: Wed Aug 20 12:11:02 2025

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