Atomistry » Zinc » PDB 3n9n-3nih » 3n9s
Atomistry »
  Zinc »
    PDB 3n9n-3nih »
      3n9s »

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: Sat Oct 26 10:08:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy