Zinc in PDB 3c4u: Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori

All present enzymatic activity of Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori:
4.1.2.13;

The structure of Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori, PDB code: 3c4u 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)	33.40 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.023, 82.560, 91.272, 90.00, 99.66, 90.00
R / Rfree (%)	18.6 / 20.7

The structure of Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori (pdb code 3c4u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori, PDB code: 3c4u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:11.8 occ:1.00 NE2 A:HIS180 2.2 12.6 1.0 OE1 A:GLU134 2.2 12.3 1.0 NE2 A:HIS83 2.3 10.2 1.0 ND1 A:HIS210 2.4 12.2 1.0 O A:HOH356 2.5 7.7 1.0 OE2 A:GLU134 2.7 13.0 1.0 CD A:GLU134 2.7 12.7 1.0 CD2 A:HIS180 3.1 15.9 1.0 CE1 A:HIS83 3.1 10.9 1.0 CE1 A:HIS180 3.2 13.8 1.0 CE1 A:HIS210 3.2 11.2 1.0 CD2 A:HIS83 3.3 9.6 1.0 CG A:HIS210 3.4 11.1 1.0 CB A:HIS210 3.8 6.6 1.0 CG A:GLU134 4.2 8.0 1.0 O A:HOH412 4.2 12.7 1.0 ND1 A:HIS83 4.3 10.1 1.0 CG A:HIS180 4.3 15.8 1.0 O A:HOH359 4.3 20.2 1.0 ND1 A:HIS180 4.3 12.8 1.0 OD2 A:ASP104 4.3 10.6 1.0 CE A:MET102 4.3 8.5 1.0 CG A:HIS83 4.4 8.6 1.0 NE2 A:HIS210 4.4 5.7 1.0 CD2 A:HIS210 4.5 12.3 1.0 O A:HOH418 4.6 15.6 1.0 CG A:ASP104 4.8 11.8 1.0 CB A:GLU134 4.8 8.0 1.0 OD1 A:ASP104 5.0 9.7 1.0

Zinc binding site 2 out of 2 in the Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:10.8 occ:1.00 NE2 B:HIS180 2.2 11.6 1.0 OE1 B:GLU134 2.2 10.5 1.0 NE2 B:HIS83 2.2 10.1 1.0 ND1 B:HIS210 2.4 11.4 1.0 O B:HOH560 2.4 7.6 1.0 OE2 B:GLU134 2.7 13.2 1.0 CD B:GLU134 2.8 10.5 1.0 CE1 B:HIS180 3.1 12.1 1.0 CD2 B:HIS180 3.1 11.8 1.0 CE1 B:HIS83 3.1 10.6 1.0 CE1 B:HIS210 3.3 9.2 1.0 CD2 B:HIS83 3.3 8.7 1.0 CG B:HIS210 3.5 9.6 1.0 CB B:HIS210 3.8 9.7 1.0 CG B:GLU134 4.2 8.5 1.0 ND1 B:HIS180 4.2 11.3 1.0 O B:HOH587 4.3 20.7 1.0 CG B:HIS180 4.3 15.0 1.0 O B:HOH443 4.3 17.7 1.0 ND1 B:HIS83 4.3 10.5 1.0 CE B:MET102 4.3 10.7 1.0 OD2 B:ASP104 4.4 12.8 1.0 CG B:HIS83 4.4 9.7 1.0 NE2 B:HIS210 4.4 5.2 1.0 CD2 B:HIS210 4.5 12.8 1.0 O B:HOH392 4.7 19.0 1.0 CG B:ASP104 4.8 9.9 1.0 CB B:GLU134 4.8 9.0 1.0 O B:HOH391 5.0 19.9 1.0 OD1 B:ASP104 5.0 8.5 1.0

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