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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 3n9s

Go back to Calcium Binding Sites List in 3n9s
Calcium 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 Calcium with other atoms in the Ca 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:Ca310

b:24.6
occ:1.00
 OD2 A:ASP104 2.5 19.1 1.0
O A:HOH320 2.6 35.0 1.0
OG A:SER106 2.6 21.9 1.0
OE1 A:GLU134 2.6 29.9 1.0
OD1 A:ASP104 2.7 17.9 1.0
O A:HOH449 2.7 25.5 1.0
O A:HOH638 2.7 34.4 1.0
CG A:ASP104 2.9 24.6 1.0
CD A:GLU134 3.5 34.1 1.0
HB3 A:SER106 3.6 31.5 1.0
CB A:SER106 3.7 26.4 1.0
H A:SER106 3.9 29.4 1.0
HE1 A:HIS83 3.9 28.3 1.0
HD1 A:HIS83 4.0 25.4 1.0
O A:HOH388 4.1 37.6 1.0
OE2 A:GLU134 4.1 30.2 1.0
HD12 A:LEU138 4.2 37.1 1.0
O A:HOH360 4.3 41.2 1.0
HB2 A:SER106 4.3 31.5 1.0
HB3 A:GLU134 4.4 23.8 1.0
HG2 A:GLU134 4.4 24.5 1.0
O A:HOH800 4.4 51.0 1.0
CB A:ASP104 4.4 20.3 1.0
CG A:GLU134 4.5 20.6 1.0
CE1 A:HIS83 4.5 23.7 1.0
O A:HOH632 4.5 36.4 1.0
ND1 A:HIS83 4.6 21.3 1.0
O A:HOH326 4.6 39.3 1.0
N A:SER106 4.6 24.6 1.0
H A:HIS107 4.6 32.5 1.0
CA A:SER106 4.7 24.7 1.0
O A:HOH702 4.7 54.0 1.0
O A:HOH754 4.7 34.2 1.0
HB2 A:ASP104 4.8 24.2 1.0
O A:HOH352 4.8 33.0 1.0
HB3 A:ASP104 4.8 24.2 1.0
HB2 A:LEU138 4.8 43.7 1.0
HE1 A:MET102 4.9 22.7 1.0
HG A:LEU138 4.9 41.8 1.0
CB A:GLU134 4.9 19.9 1.0
ND1 A:HIS107 4.9 37.2 1.0

Calcium binding site 2 out of 2 in 3n9s

Go back to Calcium Binding Sites List in 3n9s
Calcium 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 Calcium with other atoms in the Ca 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:Ca309

b:26.6
occ:1.00
 OE1 B:GLU134 2.5 32.1 1.0
O B:HOH349 2.5 33.9 1.0
OD2 B:ASP104 2.6 24.2 1.0
OD1 B:ASP104 2.6 21.0 1.0
OG B:SER106 2.7 27.1 1.0
O B:HOH436 2.8 40.0 1.0
O B:HOH351 2.8 40.2 1.0
CG B:ASP104 3.0 27.2 1.0
HG B:SER106 3.0 32.3 1.0
HB3 B:SER106 3.3 36.8 1.0
CB B:SER106 3.5 30.8 1.0
CD B:GLU134 3.6 36.6 1.0
H B:SER106 3.9 34.7 1.0
HE1 B:HIS83 4.1 23.8 1.0
HB2 B:SER106 4.1 36.8 1.0
HD1 B:HIS83 4.2 31.2 1.0
O B:HOH346 4.3 33.7 1.0
OE2 B:GLU134 4.3 34.8 1.0
O B:HOH313 4.3 45.8 1.0
HB3 B:GLU134 4.3 26.8 1.0
O B:HOH378 4.4 29.9 1.0
CB B:ASP104 4.5 19.3 1.0
O B:HOH367 4.5 39.3 1.0
HG2 B:GLU134 4.6 30.4 1.0
N B:SER106 4.6 29.0 1.0
CG B:GLU134 4.6 25.5 1.0
CA B:SER106 4.6 30.2 1.0
O B:HOH339 4.7 30.4 1.0
CE1 B:HIS83 4.7 20.0 1.0
H B:HIS107 4.7 35.6 1.0
ND1 B:HIS83 4.7 26.1 1.0
HB2 B:ASP104 4.8 23.0 1.0
HB2 B:LEU138 4.8 50.4 1.0
HB3 B:ASP104 4.9 23.0 1.0
HE1 B:MET102 4.9 29.8 1.0
CB B:GLU134 4.9 22.5 1.0
ND1 B:HIS107 5.0 36.8 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: Tue Jul 8 14:49:50 2025

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