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Calcium in PDB 3c52: Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, A Competitive Inhibitor

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, A Competitive Inhibitor

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor, PDB code: 3c52 was solved by M.Coincon, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.242, 85.305, 90.818, 90.00, 100.16, 90.00
R / Rfree (%) 20.4 / 24.9

Other elements in 3c52:

The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor (pdb code 3c52). 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor, PDB code: 3c52:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3c52

Go back to Calcium Binding Sites List in 3c52
Calcium binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:55.3
occ:1.00
 O A:HOH501 2.5 32.9 1.0
O A:HOH756 2.5 28.4 1.0
OD2 A:ASP104 2.7 30.6 1.0
OG A:SER106 2.9 36.3 1.0
OD1 A:ASP104 3.0 23.8 1.0
OE1 A:GLU134 3.2 45.1 1.0
CG A:ASP104 3.2 28.1 1.0
OE2 A:GLU134 3.6 54.5 1.0
CD A:GLU134 3.6 44.3 1.0
CB A:SER106 4.1 33.0 1.0
CE1 A:HIS83 4.4 26.8 1.0
ND1 A:HIS83 4.5 22.5 1.0
CB A:ASP104 4.7 26.2 1.0
CD1 A:LEU138 4.7 49.9 1.0
CG A:GLU134 4.8 41.4 1.0
O A:HOH524 5.0 34.8 1.0
O A:HOH513 5.0 48.3 1.0

Calcium binding site 2 out of 2 in 3c52

Go back to Calcium Binding Sites List in 3c52
Calcium binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with Phosphoglycolohydroxamic Acid, 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:74.6
occ:1.00
 OD2 B:ASP104 2.8 35.2 1.0
OG B:SER106 2.9 45.1 1.0
OE1 B:GLU134 3.0 60.5 1.0
OD1 B:ASP104 3.3 35.1 1.0
OE2 B:GLU134 3.4 45.7 1.0
CG B:ASP104 3.5 28.7 1.0
CD B:GLU134 3.5 49.3 1.0
CD2 B:LEU138 3.8 74.0 1.0
CB B:SER106 4.1 43.1 1.0
CG B:LEU138 4.2 65.7 1.0
CE1 B:HIS83 4.8 36.5 1.0
CG B:GLU134 4.9 31.9 1.0
CD1 B:LEU138 4.9 71.1 1.0
CB B:ASP104 4.9 29.2 1.0
ND1 B:HIS83 5.0 33.8 1.0

Reference:

M.Fonvielle, M.Coincon, R.Daher, N.Desbenoit, K.Kosieradzka, N.Barilone, B.Gicquel, J.Sygusch, M.Jackson, M.Therisod. Synthesis and Biochemical Evaluation of Selective Inhibitors of Class II Fructose Bisphosphate Aldolases: Towards New Synthetic Antibiotics. Chemistry V. 14 8521 2008.
ISSN: ISSN 0947-6539
PubMed: 18688832
DOI: 10.1002/CHEM.200800857
Page generated: Sat Jul 13 08:33:14 2024

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