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Zinc 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:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 3c52

Go back to Zinc Binding Sites List in 3c52
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:38.0
occ:1.00
 NE2 A:HIS83 2.0 27.2 1.0
NE2 A:HIS180 2.1 39.9 1.0
ND1 A:HIS210 2.1 29.8 1.0
O2 A:PGH404 2.2 42.0 1.0
CE1 A:HIS180 2.7 41.1 1.0
O1 A:PGH404 2.7 37.6 1.0
CD2 A:HIS83 2.9 24.1 1.0
CE1 A:HIS210 3.0 27.0 1.0
CE1 A:HIS83 3.0 26.8 1.0
N2 A:PGH404 3.1 37.6 1.0
CD2 A:HIS180 3.1 41.6 1.0
C1 A:PGH404 3.2 35.1 1.0
CG A:HIS210 3.3 26.1 1.0
O A:HOH621 3.7 42.7 1.0
CB A:HIS210 3.7 24.2 1.0
ND1 A:HIS180 3.7 45.4 1.0
CG A:HIS180 3.9 39.3 1.0
ND2 A:ASN253 4.1 20.0 1.0
CG A:HIS83 4.1 27.5 1.0
ND1 A:HIS83 4.1 22.5 1.0
NE2 A:HIS210 4.1 25.7 1.0
OD1 A:ASP82 4.2 27.6 1.0
CD2 A:HIS210 4.3 22.1 1.0
CD1 A:LEU138 4.4 49.9 1.0
C2 A:PGH404 4.6 24.3 1.0
CA A:HIS210 4.6 22.2 1.0
OD2 A:ASP82 4.6 34.4 1.0
N A:GLY211 4.7 23.2 1.0
CG A:ASP82 4.8 25.7 1.0

Zinc binding site 2 out of 2 in 3c52

Go back to Zinc Binding Sites List in 3c52
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:40.0
occ:1.00
 NE2 B:HIS180 2.0 41.3 1.0
NE2 B:HIS83 2.1 38.3 1.0
O2 B:PGH404 2.1 50.5 1.0
ND1 B:HIS210 2.3 32.8 1.0
CE1 B:HIS180 2.8 43.7 1.0
O1 B:PGH404 3.0 47.5 1.0
CE1 B:HIS83 3.0 36.5 1.0
N2 B:PGH404 3.0 45.8 1.0
C1 B:PGH404 3.1 46.7 1.0
CD2 B:HIS180 3.1 43.1 1.0
CD2 B:HIS83 3.1 33.3 1.0
CE1 B:HIS210 3.2 31.1 1.0
CG B:HIS210 3.3 28.2 1.0
CB B:HIS210 3.6 31.5 1.0
ND1 B:HIS180 3.9 47.5 1.0
ND2 B:ASN253 4.1 27.4 1.0
ND1 B:HIS83 4.1 33.8 1.0
CG B:HIS180 4.1 42.6 1.0
CG B:HIS83 4.2 29.8 1.0
OD1 B:ASP82 4.2 32.0 1.0
C2 B:PGH404 4.2 44.1 1.0
NE2 B:HIS210 4.3 23.4 1.0
CD2 B:HIS210 4.4 27.2 1.0
CA B:HIS210 4.6 32.4 1.0
OD2 B:ASP82 4.6 32.1 1.0
N B:GLY211 4.7 34.9 1.0
CG B:ASP82 4.9 25.3 1.0
CD2 B:LEU138 4.9 74.0 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: Thu Oct 24 11:43:16 2024

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