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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

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