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Sodium in PDB 1e6a: Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase

Enzymatic activity of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase

All present enzymatic activity of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase:
3.6.1.1;

Protein crystallography data

The structure of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase, PDB code: 1e6a was solved by P.Heikinheimo, V.Tuominen, A.-K.Ahonen, A.Teplyakov, B.S.Cooperman, A.A.Baykov, R.Lahti, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.770, 102.340, 115.630, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.2

Other elements in 1e6a:

The structure of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Manganese (Mn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase (pdb code 1e6a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase, PDB code: 1e6a:

Sodium binding site 1 out of 1 in 1e6a

Go back to Sodium Binding Sites List in 1e6a
Sodium binding site 1 out of 1 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4740

b:20.3
occ:0.60
 OD2 A:ASP117 1.9 9.2 0.4
O6 A:POP3001 2.4 9.5 1.0
OD2 A:ASP117 2.4 11.2 0.6
O A:HOH2165 2.5 16.7 1.0
OD2 A:ASP115 2.5 3.8 1.0
F A:F4001 2.6 5.1 1.0
O A:HOH2339 2.7 8.0 1.0
CG A:ASP117 3.0 8.5 0.4
O5 A:POP3001 3.0 7.4 1.0
O A:HOH2338 3.2 11.0 1.0
P2 A:POP3001 3.2 7.2 1.0
MN A:MN2001 3.3 6.8 1.0
CG A:ASP115 3.4 7.9 1.0
CG A:ASP117 3.4 7.8 0.6
MN A:MN2003 3.4 13.0 1.0
O A:HOH2341 3.4 3.2 1.0
CB A:ASP117 3.6 5.2 0.6
CB A:ASP117 3.6 7.0 0.4
OD1 A:ASP117 3.9 14.3 0.4
O A:ASP115 4.0 5.6 1.0
OD1 A:ASP115 4.1 5.3 1.0
CB A:ASP115 4.1 5.5 1.0
O A:HOH2335 4.2 10.8 1.0
O4 A:POP3001 4.3 5.5 1.0
MN A:MN2004 4.3 7.0 1.0
O A:HOH2100 4.3 13.0 1.0
MN A:MN2002 4.4 7.1 1.0
O A:POP3001 4.4 9.4 1.0
O1 A:POP3001 4.5 11.5 1.0
OD1 A:ASP117 4.5 10.9 0.6
O A:HOH2334 4.6 4.3 1.0
OE2 A:GLU58 4.7 9.6 0.6
O3 A:POP3001 4.8 10.1 1.0
P1 A:POP3001 4.8 12.6 1.0
C A:ASP115 4.9 6.0 1.0
CA A:ASP117 4.9 6.3 0.4
CA A:ASP117 4.9 5.7 0.6
OD1 A:ASP152 4.9 6.1 1.0
N A:ASP117 4.9 6.1 0.4
N A:ASP117 5.0 5.5 0.6

Reference:

P.Heikinheimo, V.Tuominen, A.K.Ahonen, A.Teplyakov, B.S.Cooperman, A.A.Baykov, R.Lahti, A.Goldman. Toward A Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase. Proc. Natl. Acad. Sci. V. 98 3121 2001U.S.A..
ISSN: ISSN 0027-8424
PubMed: 11248042
DOI: 10.1073/PNAS.061612498
Page generated: Sun Oct 6 18:21:07 2024

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