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Zinc in PDB 3c56: Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor

Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor

All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, 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-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor, PDB code: 3c56 was solved by M.Coincon, J.Sygusch, P.Potvin-Dulude, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.222, 62.005, 65.615, 82.90, 79.77, 71.03
R / Rfree (%) 17.2 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor (pdb code 3c56). 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 N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor, PDB code: 3c56:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3c56

Go back to Zinc Binding Sites List in 3c56
Zinc binding site 1 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, 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 N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:31.2
occ:1.00
 ND1 A:HIS210 2.2 24.8 1.0
NE2 A:HIS83 2.2 27.0 1.0
NE2 A:HIS180 2.2 58.2 1.0
O3 A:PH4309 2.5 29.4 1.0
O2 A:PH4309 2.9 39.0 1.0
CD2 A:HIS83 2.9 18.9 1.0
CE1 A:HIS180 3.0 56.7 1.0
N3 A:PH4309 3.0 35.4 1.0
CE1 A:HIS210 3.0 26.3 1.0
CD2 A:HIS180 3.2 52.4 1.0
C2 A:PH4309 3.2 35.5 1.0
CG A:HIS210 3.3 24.1 1.0
CE1 A:HIS83 3.3 24.5 1.0
CB A:HIS210 3.7 21.3 1.0
ND2 A:ASN253 3.9 21.9 1.0
ND1 A:HIS180 4.0 54.2 1.0
C5 A:PH4309 4.1 26.6 1.0
CG A:HIS180 4.1 49.3 1.0
C4 A:PH4309 4.1 32.2 1.0
CD1 A:LEU138 4.1 45.4 1.0
NE2 A:HIS210 4.2 24.2 1.0
CG A:HIS83 4.2 22.8 1.0
OD1 A:ASP82 4.3 26.3 1.0
CD2 A:HIS210 4.3 30.5 1.0
ND1 A:HIS83 4.3 25.8 1.0
C1 A:PH4309 4.4 38.7 1.0
OD2 A:ASP82 4.6 37.6 1.0
CA A:HIS210 4.6 20.7 1.0
N A:GLY211 4.6 23.4 1.0
CG A:ASP82 4.9 28.1 1.0
CG A:ASN253 5.0 27.3 1.0

Zinc binding site 2 out of 2 in 3c56

Go back to Zinc Binding Sites List in 3c56
Zinc binding site 2 out of 2 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, 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 N-(3-Hydroxypropyl)-Glycolohydroxamic Acid Bisphosphate, A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:35.8
occ:1.00
 NE2 B:HIS180 2.2 46.0 1.0
NE2 B:HIS83 2.2 25.2 1.0
ND1 B:HIS210 2.2 23.2 1.0
O3 B:PH4309 2.6 33.5 1.0
CE1 B:HIS180 2.7 48.6 1.0
O2 B:PH4309 2.8 49.7 1.0
CD2 B:HIS83 2.9 25.6 1.0
N3 B:PH4309 3.0 39.6 1.0
C2 B:PH4309 3.1 43.0 1.0
CD2 B:HIS180 3.1 47.2 1.0
CE1 B:HIS210 3.2 25.4 1.0
CG B:HIS210 3.2 19.4 1.0
CE1 B:HIS83 3.3 26.5 1.0
CB B:HIS210 3.5 22.5 1.0
ND1 B:HIS180 3.7 49.8 1.0
ND2 B:ASN253 4.0 21.4 1.0
CG B:HIS180 4.0 48.0 1.0
C4 B:PH4309 4.1 35.5 1.0
CG B:HIS83 4.2 27.5 1.0
C5 B:PH4309 4.2 31.9 1.0
NE2 B:HIS210 4.3 30.1 1.0
ND1 B:HIS83 4.3 29.0 1.0
OD1 B:ASP82 4.3 23.0 1.0
CD2 B:HIS210 4.3 28.5 1.0
CD1 B:LEU138 4.4 44.8 1.0
C1 B:PH4309 4.4 45.8 1.0
CA B:HIS210 4.4 18.5 1.0
N B:GLY211 4.6 19.7 1.0
OD2 B:ASP82 4.6 36.8 1.0
CG B:ASP82 4.9 24.8 1.0
O B:HOH706 5.0 37.9 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: Wed Dec 16 04:10:09 2020

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