Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Class II Fructose-Biphosphate Aldolase From Helicobacter Pylori, PDB code: 3c4u:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na308 b:13.0 occ:1.00 NE2 A:HIS80 3.0 9.8 1.0 OE2 A:GLU132 3.2 11.4 1.0 NZ A:LYS251 3.2 8.4 1.0 OE1 A:GLU132 3.3 8.0 1.0 OD1 A:ASP82 3.3 12.3 1.0 ND2 A:ASN253 3.4 7.3 1.0 OE1 A:GLN47 3.4 10.7 1.0 CD A:GLU132 3.5 10.6 1.0 SD A:MET102 3.7 10.6 1.0 NE2 A:HIS210 3.7 5.7 1.0 CD2 A:HIS80 3.7 7.5 1.0 CE1 A:HIS210 3.8 11.2 1.0 CB A:MET102 3.9 6.0 1.0 CG A:MET102 4.0 6.8 1.0 CE1 A:HIS80 4.1 10.3 1.0 OD1 A:ASN253 4.2 4.7 1.0 CG A:ASN253 4.2 5.3 1.0 N A:HIS83 4.2 7.6 1.0 CA A:ASP82 4.3 7.2 1.0 CG A:ASP82 4.3 10.5 1.0 CD A:GLN47 4.3 6.5 1.0 ND1 A:HIS83 4.3 10.1 1.0 CE A:LYS251 4.4 9.8 1.0 CE1 A:HIS83 4.6 10.9 1.0 O A:LEU81 4.7 6.1 1.0 NE2 A:GLN47 4.7 7.0 1.0 CB A:ASP82 4.7 9.8 1.0 C A:ASP82 4.8 6.9 1.0 CG A:GLU132 4.8 3.4 1.0 CD2 A:HIS210 4.8 12.3 1.0 CE A:MET102 4.9 8.5 1.0 O A:HOH384 4.9 15.1 1.0 ND1 A:HIS210 4.9 12.2 1.0 CG A:HIS80 5.0 8.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na308 b:13.2 occ:1.00 OD1 B:ASP82 3.2 15.3 1.0 NE2 B:HIS80 3.2 12.6 1.0 ND2 B:ASN253 3.3 7.1 1.0 OE2 B:GLU132 3.3 12.8 1.0 NZ B:LYS251 3.4 14.2 1.0 OE1 B:GLN47 3.5 14.1 1.0 OE1 B:GLU132 3.5 7.6 1.0 SD B:MET102 3.6 10.6 1.0 NE2 B:HIS210 3.6 5.2 1.0 CD B:GLU132 3.7 14.1 1.0 CE1 B:HIS210 3.7 9.2 1.0 CD2 B:HIS80 3.9 10.8 1.0 CG B:MET102 3.9 8.1 1.0 CB B:MET102 3.9 6.2 1.0 N B:HIS83 4.1 7.6 1.0 ND1 B:HIS83 4.1 10.5 1.0 CG B:ASP82 4.2 14.5 1.0 CG B:ASN253 4.2 5.4 1.0 CA B:ASP82 4.2 8.6 1.0 OD1 B:ASN253 4.2 7.4 1.0 CE1 B:HIS80 4.3 14.8 1.0 CE1 B:HIS83 4.3 10.6 1.0 CD B:GLN47 4.3 7.4 1.0 CE B:LYS251 4.6 11.0 1.0 NE2 B:GLN47 4.6 5.5 1.0 CB B:ASP82 4.6 8.5 1.0 C B:ASP82 4.7 8.0 1.0 O B:HOH396 4.7 13.2 1.0 CE B:MET102 4.7 10.7 1.0 CD2 B:HIS210 4.8 12.8 1.0 ND1 B:HIS210 4.8 11.4 1.0 O B:LEU81 4.8 6.3 1.0 CG B:HIS83 4.9 9.7 1.0 CG B:GLU132 4.9 8.1 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