Atomistry » Sodium » PDB 3n0u-3nrv » 3n9s
Atomistry »
  Sodium »
    PDB 3n0u-3nrv »
      3n9s »

Sodium 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:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3n9s

Go back to Sodium Binding Sites List in 3n9s
Sodium 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 Sodium with other atoms in the Na 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:Na311

b:31.3
occ:1.00
 HE2 A:HIS80 2.3 16.2 1.0
HD21 A:ASN253 2.4 21.1 1.0
OD1 A:ASP82 2.8 24.7 1.0
HZ1 A:LYS251 2.8 21.0 1.0
HZ2 A:LYS251 2.8 21.0 1.0
HE1 A:HIS210 2.8 26.0 1.0
OE2 A:GLU132 3.0 17.9 1.0
NE2 A:HIS80 3.1 13.7 1.0
OE1 A:GLU132 3.2 18.4 1.0
NZ A:LYS251 3.2 17.6 1.0
HB2 A:MET102 3.3 19.1 1.0
HE2 A:HIS210 3.3 19.4 1.0
ND2 A:ASN253 3.3 17.7 1.0
CE1 A:HIS210 3.3 21.8 1.0
HA A:ASP82 3.3 22.4 1.0
CD A:GLU132 3.4 19.0 1.0
HD2 A:HIS80 3.4 20.1 1.0
NE2 A:HIS210 3.5 16.3 1.0
SD A:MET102 3.5 19.8 1.0
HZ3 A:LYS251 3.6 21.0 1.0
CD2 A:HIS80 3.6 16.9 1.0
HD22 A:ASN253 3.7 21.1 1.0
H A:HIS83 3.7 23.4 1.0
OE1 A:GLN47 3.8 19.6 1.0
CG A:ASP82 3.8 24.8 1.0
HE21 A:GLN47 3.9 24.6 1.0
CB A:MET102 3.9 16.0 1.0
HG3 A:MET102 4.0 16.9 1.0
HG11 A:VAL208 4.1 10.1 1.0
HB3 A:MET102 4.1 19.1 1.0
CG A:MET102 4.1 14.2 1.0
CG A:ASN253 4.2 17.1 1.0
CE1 A:HIS80 4.2 17.2 1.0
CA A:ASP82 4.2 18.8 1.0
OD1 A:ASN253 4.2 15.3 1.0
NE2 A:GLN47 4.4 20.7 1.0
ND1 A:HIS210 4.4 18.5 1.0
HE3 A:MET102 4.4 22.7 1.0
CB A:ASP82 4.5 18.8 1.0
CD A:GLN47 4.5 18.2 1.0
CE A:LYS251 4.5 16.7 1.0
HE3 A:LYS251 4.5 19.9 1.0
N A:HIS83 4.5 19.6 1.0
HB2 A:ASP82 4.5 22.4 1.0
HE1 A:HIS80 4.5 20.5 1.0
CE A:MET102 4.6 19.0 1.0
CG A:GLU132 4.7 18.0 1.0
CD2 A:HIS210 4.7 15.2 1.0
OD2 A:ASP82 4.7 25.5 1.0
O A:LEU81 4.7 15.5 1.0
HB3 A:GLU132 4.8 24.2 1.0
HE1 A:MET102 4.8 22.7 1.0
O01 A:TD4308 4.8 27.0 1.0
HG2 A:GLU132 4.9 21.4 1.0
CG A:HIS80 4.9 17.2 1.0
C A:ASP82 5.0 21.0 1.0
CG1 A:VAL208 5.0 8.6 1.0

Sodium binding site 2 out of 2 in 3n9s

Go back to Sodium Binding Sites List in 3n9s
Sodium 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 Sodium with other atoms in the Na 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:Na310

b:33.1
occ:1.00
 HD21 B:ASN253 2.4 32.3 1.0
HE2 B:HIS80 2.4 23.9 1.0
HE1 B:HIS210 2.8 27.6 1.0
OD1 B:ASP82 2.8 31.5 1.0
HZ1 B:LYS251 2.8 23.0 1.0
HZ2 B:LYS251 2.9 23.0 1.0
OE2 B:GLU132 3.1 21.0 1.0
OE1 B:GLU132 3.2 21.8 1.0
NE2 B:HIS80 3.2 20.0 1.0
HB2 B:MET102 3.2 29.3 1.0
HE2 B:HIS210 3.2 23.4 1.0
ND2 B:ASN253 3.2 27.1 1.0
NZ B:LYS251 3.3 19.3 1.0
CE1 B:HIS210 3.3 23.1 1.0
HA B:ASP82 3.3 19.1 1.0
CD B:GLU132 3.4 21.6 1.0
SD B:MET102 3.4 24.0 1.0
NE2 B:HIS210 3.5 19.7 1.0
HD2 B:HIS80 3.6 25.2 1.0
HZ3 B:LYS251 3.6 23.0 1.0
HD22 B:ASN253 3.6 32.3 1.0
H B:HIS83 3.7 26.3 1.0
CD2 B:HIS80 3.8 21.1 1.0
CG B:ASP82 3.8 30.1 1.0
OE1 B:GLN47 3.8 21.9 1.0
CB B:MET102 3.9 24.6 1.0
HE21 B:GLN47 4.0 26.9 1.0
HB3 B:MET102 4.0 29.3 1.0
HG11 B:VAL208 4.0 17.5 1.0
CG B:MET102 4.1 19.7 1.0
CA B:ASP82 4.2 16.1 1.0
CG B:ASN253 4.2 22.7 1.0
HG3 B:MET102 4.2 23.5 1.0
CE1 B:HIS80 4.3 20.9 1.0
OD1 B:ASN253 4.3 19.4 1.0
ND1 B:HIS210 4.4 20.4 1.0
N B:HIS83 4.4 22.0 1.0
CB B:ASP82 4.4 19.6 1.0
HE3 B:MET102 4.5 29.8 1.0
NE2 B:GLN47 4.5 22.5 1.0
HB2 B:ASP82 4.5 23.4 1.0
O01 B:TD4311 4.5 24.0 1.0
CD B:GLN47 4.5 25.7 1.0
CE B:MET102 4.6 25.0 1.0
HE1 B:HIS80 4.6 24.9 1.0
HE3 B:LYS251 4.6 24.4 1.0
CE B:LYS251 4.6 20.4 1.0
CD2 B:HIS210 4.7 19.9 1.0
HE1 B:MET102 4.7 29.8 1.0
OD2 B:ASP82 4.7 35.8 1.0
HB3 B:GLU132 4.8 20.9 1.0
CG B:GLU132 4.8 20.4 1.0
C B:ASP82 4.9 20.1 1.0
CG1 B:VAL208 4.9 14.7 1.0
O B:LEU81 4.9 20.1 1.0
HG2 B:GLU132 5.0 24.3 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: Mon Oct 7 11:46:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy