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Sodium 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
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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor (pdb code 3c52). 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor, PDB code: 3c52:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c52

Go back to Sodium Binding Sites List in 3c52
Sodium 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 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:43.4
occ:1.00
OD1 A:ASP82 2.9 27.6 1.0
NE2 A:HIS80 3.1 18.2 1.0
ND2 A:ASN253 3.2 20.0 1.0
OE1 A:GLU132 3.2 22.4 1.0
NZ A:LYS251 3.2 22.8 1.0
CE1 A:HIS210 3.3 27.0 1.0
NE2 A:HIS210 3.4 25.7 1.0
OE2 A:GLU132 3.4 32.9 1.0
CD A:GLU132 3.6 24.7 1.0
OE1 A:GLN47 3.6 24.1 1.0
SD A:MET102 3.6 29.5 1.0
CD2 A:HIS80 3.6 19.9 1.0
CG A:ASP82 3.8 25.7 1.0
CB A:MET102 4.0 20.1 1.0
CG A:ASN253 4.1 24.8 1.0
CA A:ASP82 4.1 21.4 1.0
OD1 A:ASN253 4.2 20.6 1.0
CE1 A:HIS80 4.2 21.4 1.0
CG A:MET102 4.3 26.2 1.0
CD A:GLN47 4.3 29.2 1.0
CB A:ASP82 4.4 25.1 1.0
NE2 A:GLN47 4.4 23.0 1.0
CE A:LYS251 4.4 29.4 1.0
ND1 A:HIS210 4.4 29.8 1.0
N A:HIS83 4.5 24.3 1.0
CD2 A:HIS210 4.6 22.1 1.0
O2 A:PGH404 4.6 42.0 1.0
O A:LEU81 4.7 21.3 1.0
CE A:MET102 4.8 26.5 1.0
OD2 A:ASP82 4.8 34.4 1.0
C A:ASP82 4.9 22.5 1.0
CG A:HIS80 4.9 18.4 1.0
CG1 A:VAL208 4.9 19.2 1.0
CG A:GLU132 4.9 22.2 1.0

Sodium binding site 2 out of 2 in 3c52

Go back to Sodium Binding Sites List in 3c52
Sodium 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 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 Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:47.0
occ:1.00
OD1 B:ASP82 2.9 32.0 1.0
CE1 B:HIS210 3.1 31.1 1.0
ND2 B:ASN253 3.1 27.4 1.0
NE2 B:HIS80 3.2 22.2 1.0
OE1 B:GLU132 3.2 28.2 1.0
NE2 B:HIS210 3.2 23.4 1.0
OE2 B:GLU132 3.3 26.9 1.0
NZ B:LYS251 3.4 29.4 1.0
CD B:GLU132 3.6 26.2 1.0
SD B:MET102 3.6 34.0 1.0
CD2 B:HIS80 3.6 17.4 1.0
OE1 B:GLN47 3.8 29.3 1.0
CG B:ASP82 3.8 25.3 1.0
CB B:MET102 3.9 19.0 1.0
CG B:MET102 4.0 26.1 1.0
CG B:ASN253 4.1 29.8 1.0
CA B:ASP82 4.2 22.2 1.0
ND1 B:HIS210 4.2 32.8 1.0
OD1 B:ASN253 4.3 25.9 1.0
CE B:LYS251 4.3 26.3 1.0
CE1 B:HIS80 4.3 23.6 1.0
CB B:ASP82 4.4 20.9 1.0
NE2 B:GLN47 4.4 28.1 1.0
CD B:GLN47 4.4 27.4 1.0
CD2 B:HIS210 4.5 27.2 1.0
N B:HIS83 4.5 25.8 1.0
OD2 B:ASP82 4.7 32.1 1.0
O B:LEU81 4.7 22.1 1.0
CE B:MET102 4.8 27.7 1.0
O2 B:PGH404 4.9 50.5 1.0
C B:ASP82 4.9 23.5 1.0
CG B:GLU132 4.9 23.0 1.0
CG B:HIS80 4.9 22.5 1.0
CG B:HIS210 5.0 28.2 1.0
CG1 B:VAL208 5.0 24.8 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: Tue Dec 15 06:03:59 2020

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