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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3c4u:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

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 3c4u

Go back to Sodium Binding Sites List in 3c4u
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 3c4u

Go back to Sodium Binding Sites List in 3c4u
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

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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