Fluorine in PDB 1e6a: 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;

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

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

Manganese	(Mn)	8 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase, PDB code: 1e6a:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F4001 b:5.1 occ:1.00 MN A:MN2001 2.1 6.8 1.0 MN A:MN2002 2.1 7.1 1.0 NA A:NA4740 2.6 20.3 0.6 OD2 A:ASP117 2.7 9.2 0.4 O6 A:POP3001 2.8 9.5 1.0 O5 A:POP3001 2.9 7.4 1.0 P2 A:POP3001 2.9 7.2 1.0 O4 A:POP3001 2.9 5.5 1.0 O A:HOH2336 3.0 2.2 1.0 CB A:ASP117 3.0 7.0 0.4 CB A:ASP117 3.1 5.2 0.6 OD1 A:ASP120 3.1 6.8 1.0 O A:HOH2334 3.1 4.3 1.0 OD2 A:ASP115 3.2 3.8 1.0 O A:HOH2335 3.2 10.8 1.0 CG A:ASP117 3.3 8.5 0.4 OD2 A:ASP117 3.4 11.2 0.6 OD2 A:ASP120 3.5 3.9 1.0 CG A:ASP117 3.6 7.8 0.6 CG A:ASP120 3.7 3.8 1.0 CG A:ASP115 4.0 7.9 1.0 O A:PRO118 4.0 6.2 0.6 O A:PRO118 4.0 6.6 0.5 OD1 A:ASP115 4.1 5.3 1.0 OD1 A:ASP152 4.3 6.1 1.0 O A:HOH2337 4.3 4.5 1.0 CA A:ASP117 4.4 6.3 0.4 CA A:ASP117 4.4 5.7 0.6 O A:POP3001 4.5 9.4 1.0 OD1 A:ASP117 4.6 14.3 0.4 OD1 A:ASP117 4.6 10.9 0.6 C A:ASP117 4.7 5.8 0.6 C A:ASP117 4.7 6.5 0.4 O A:HOH2338 4.8 11.0 1.0 O A:HOH2341 4.8 3.2 1.0 MN A:MN2004 4.9 7.0 1.0 MN A:MN2003 4.9 13.0 1.0 OH A:TYR93 4.9 5.6 1.0 O A:HOH2096 4.9 9.6 1.0 O A:HOH2165 4.9 16.7 1.0 O A:HOH2339 4.9 8.0 1.0 N A:PRO118 5.0 6.6 0.5

Fluorine binding site 2 out of 2 in the Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fluoride-Inhibited Substrate Complex of Saccharomyces Cerevisiae Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:F4010 b:7.9 occ:1.00 MN B:MN2005 2.1 5.0 1.0 MN B:MN2006 2.2 6.4 1.0 OD2 B:ASP1117 2.6 11.2 0.6 O1 B:POP3002 2.7 10.8 0.8 O1 B:PO43004 2.7 6.6 0.2 O3 B:PO43004 2.8 8.8 0.2 O4 B:PO43004 2.8 6.9 0.2 P1 B:POP3002 2.9 9.1 0.8 O B:HOH2294 2.9 3.4 1.0 O3 B:POP3002 2.9 5.4 0.8 O2 B:POP3002 2.9 5.8 0.8 P B:PO43004 2.9 9.3 0.2 CB B:ASP1117 3.0 7.2 0.6 O B:HOH2295 3.0 5.6 1.0 CB B:ASP1117 3.0 7.4 0.4 O B:HOH2297 3.1 2.2 1.0 OD2 B:ASP1115 3.1 6.6 1.0 OD1 B:ASP1120 3.1 4.0 1.0 OD2 B:ASP1117 3.2 13.5 0.4 CG B:ASP1117 3.2 6.9 0.6 CG B:ASP1117 3.4 8.5 0.4 OD2 B:ASP1120 3.5 4.2 1.0 CG B:ASP1120 3.7 4.6 1.0 CG B:ASP1115 4.0 8.5 1.0 O B:PRO1118 4.1 6.2 1.0 OD1 B:ASP1115 4.2 8.6 1.0 O B:HOH2296 4.3 4.0 1.0 OD1 B:ASP1152 4.3 5.1 1.0 OD1 B:ASP1117 4.4 13.5 0.6 CA B:ASP1117 4.4 6.4 0.4 CA B:ASP1117 4.4 6.5 0.6 O2 B:PO43004 4.5 6.3 0.2 OD1 B:ASP1117 4.5 8.9 0.4 O B:POP3002 4.5 8.8 0.8 O B:HOH2299 4.5 8.4 1.0 O B:HOH2115 4.6 14.5 1.0 O B:HOH2301 4.7 2.4 1.0 MN B:MN2007 4.7 9.8 0.9 C B:ASP1117 4.8 6.0 0.4 C B:ASP1117 4.8 5.9 0.6 MN B:MN2008 4.9 6.1 1.0 O B:HOH2053 4.9 11.1 1.0 OH B:TYR1093 4.9 8.4 1.0

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