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Fluorine in PDB 2g07: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride

Enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride:
3.1.1.5;

Protein crystallography data

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride, PDB code: 2g07 was solved by E.Bitto, C.A.Bingman, G.E.Wesenberg, G.N.Phillips Jr., Center Foreukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.42 / 2.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 134.834, 134.834, 38.945, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 25.9

Other elements in 2g07:

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride (pdb code 2g07). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride, PDB code: 2g07:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 1 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F49

b:37.5
occ:1.00
 F1 A:BFD49 0.0 37.5 1.0
BE A:BFD49 1.5 38.5 1.0
MG A:MG601 2.0 29.0 1.0
F3 A:BFD49 2.4 38.3 1.0
F2 A:BFD49 2.5 38.9 1.0
OD1 A:BFD49 2.7 36.6 1.0
OD2 A:BFD49 3.0 39.5 1.0
O A:ASP51 3.0 34.8 1.0
O A:HOH666 3.1 16.4 1.0
O A:HOH681 3.1 29.9 1.0
CB A:ASP51 3.1 33.2 1.0
CG A:BFD49 3.2 34.8 1.0
N A:ASP51 3.3 33.5 1.0
O A:HOH676 3.3 24.9 1.0
O A:HOH846 3.4 26.8 1.0
CA A:ASP51 3.5 34.7 1.0
C A:ASP51 3.7 35.2 1.0
CG A:ASP51 4.1 36.5 1.0
OD2 A:ASP51 4.1 40.1 1.0
O A:HOH874 4.1 32.0 1.0
OD1 A:ASP238 4.2 35.4 1.0
O A:HOH742 4.3 27.0 1.0
C A:PHE50 4.3 34.0 1.0
N A:PHE50 4.5 34.4 1.0
OG A:SER164 4.7 33.9 1.0
CB A:BFD49 4.7 34.6 1.0
NZ A:LYS213 4.9 33.3 1.0
CA A:PHE50 4.9 34.3 1.0

Fluorine binding site 2 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 2 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F49

b:38.9
occ:1.00
 F2 A:BFD49 0.0 38.9 1.0
BE A:BFD49 1.5 38.5 1.0
F3 A:BFD49 2.4 38.3 1.0
OD1 A:BFD49 2.5 36.6 1.0
F1 A:BFD49 2.5 37.5 1.0
OG A:SER164 2.6 33.9 1.0
N A:ASP51 2.8 33.5 1.0
N A:PHE50 3.1 34.4 1.0
CB A:SER164 3.2 33.9 1.0
CG A:BFD49 3.5 34.8 1.0
CA A:SER164 3.5 33.5 1.0
CA A:PHE50 3.5 34.3 1.0
CB A:PHE50 3.5 34.4 1.0
C A:PHE50 3.6 34.0 1.0
CB A:ASP51 3.8 33.2 1.0
O A:HOH681 3.8 29.9 1.0
CA A:ASP51 3.8 34.7 1.0
OD2 A:BFD49 3.9 39.5 1.0
OD2 A:ASP51 3.9 40.1 1.0
N A:ALA165 4.0 34.1 1.0
CG A:ASP51 4.0 36.5 1.0
MG A:MG601 4.1 29.0 1.0
C A:BFD49 4.2 35.5 1.0
C A:SER164 4.3 34.3 1.0
O A:PHE163 4.4 34.7 1.0
O A:ASP51 4.5 34.8 1.0
CA A:BFD49 4.5 34.5 1.0
N A:GLY166 4.5 36.1 1.0
NZ A:LYS213 4.5 33.3 1.0
CB A:BFD49 4.6 34.6 1.0
N A:SER164 4.7 34.4 1.0
C A:ASP51 4.7 35.2 1.0
CG A:PHE50 4.7 35.9 1.0
O A:PHE50 4.8 33.7 1.0
C A:PHE163 4.9 34.7 1.0
O A:HOH676 4.9 24.9 1.0
CD2 A:PHE50 4.9 32.3 1.0
OD1 A:ASP51 4.9 38.6 1.0

Fluorine binding site 3 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 3 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F49

b:38.3
occ:1.00
 F3 A:BFD49 0.0 38.3 1.0
BE A:BFD49 1.5 38.5 1.0
F1 A:BFD49 2.4 37.5 1.0
OD1 A:BFD49 2.4 36.6 1.0
F2 A:BFD49 2.4 38.9 1.0
O A:HOH676 2.7 24.9 1.0
NZ A:LYS213 2.9 33.3 1.0
N A:ALA165 3.0 34.1 1.0
O A:HOH681 3.6 29.9 1.0
CG A:BFD49 3.6 34.8 1.0
CE A:LYS213 3.7 32.5 1.0
CA A:SER164 3.7 33.5 1.0
O A:HOH666 3.8 16.4 1.0
CB A:ALA165 3.8 34.5 1.0
C A:SER164 3.9 34.3 1.0
OG A:SER164 3.9 33.9 1.0
CA A:ALA165 3.9 34.6 1.0
MG A:MG601 3.9 29.0 1.0
OD2 A:BFD49 4.2 39.5 1.0
O A:PHE163 4.2 34.7 1.0
CB A:SER164 4.4 33.9 1.0
OD1 A:ASP242 4.4 36.0 1.0
O A:HOH622 4.5 23.7 1.0
N A:GLY166 4.6 36.1 1.0
C A:ALA165 4.6 34.8 1.0
CB A:BFD49 4.8 34.6 1.0
N A:SER164 4.8 34.4 1.0
N A:PHE50 4.8 34.4 1.0
N A:ASP51 4.9 33.5 1.0
C A:PHE163 4.9 34.7 1.0
O A:HOH742 4.9 27.0 1.0

Fluorine binding site 4 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 4 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F49

b:30.5
occ:1.00
 F1 B:BFD49 0.0 30.5 1.0
BE B:BFD49 1.5 36.1 1.0
F3 B:BFD49 2.4 33.1 1.0
F2 B:BFD49 2.5 36.9 1.0
OD1 B:BFD49 2.5 34.3 1.0
O B:HOH674 2.7 21.4 1.0
N B:ALA165 2.9 34.1 1.0
NZ B:LYS213 2.9 35.5 1.0
O B:HOH720 3.3 40.9 1.0
CB B:ALA165 3.5 34.3 1.0
CE B:LYS213 3.7 33.4 1.0
CA B:ALA165 3.7 34.4 1.0
CG B:BFD49 3.7 35.5 1.0
CA B:SER164 3.7 33.3 1.0
C B:SER164 3.8 34.5 1.0
OG B:SER164 3.8 29.9 1.0
O B:HOH669 3.9 23.8 1.0
MG B:MG602 4.1 33.8 1.0
OD2 B:BFD49 4.2 39.6 1.0
O B:PHE163 4.2 34.6 1.0
CB B:SER164 4.3 33.6 1.0
N B:GLY166 4.4 35.8 1.0
C B:ALA165 4.4 34.7 1.0
O B:HOH638 4.5 27.7 1.0
OD1 B:ASP242 4.6 34.9 1.0
O B:HOH735 4.8 29.9 1.0
N B:SER164 4.8 34.5 1.0
CB B:BFD49 4.9 32.7 1.0
CB B:ASP51 5.0 33.7 1.0
C B:PHE163 5.0 34.9 1.0
N B:ASP51 5.0 33.5 1.0

Fluorine binding site 5 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 5 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F49

b:36.9
occ:1.00
 F2 B:BFD49 0.0 36.9 1.0
BE B:BFD49 1.6 36.1 1.0
MG B:MG602 2.0 33.8 1.0
F1 B:BFD49 2.5 30.5 1.0
F3 B:BFD49 2.5 33.1 1.0
OD1 B:BFD49 2.8 34.3 1.0
OD2 B:BFD49 2.8 39.6 1.0
CB B:ASP51 3.0 33.7 1.0
O B:ASP51 3.1 35.7 1.0
O B:HOH669 3.1 23.8 1.0
O B:HOH720 3.1 40.9 1.0
CG B:BFD49 3.2 35.5 1.0
O B:HOH863 3.2 28.9 1.0
N B:ASP51 3.4 33.5 1.0
O B:HOH674 3.4 21.4 1.0
CA B:ASP51 3.5 34.5 1.0
C B:ASP51 3.7 35.1 1.0
CG B:ASP51 4.1 35.9 1.0
OD1 B:ASP238 4.1 39.3 1.0
OD2 B:ASP51 4.1 37.7 1.0
O B:HOH735 4.3 29.9 1.0
C B:PHE50 4.4 34.0 1.0
N B:PHE50 4.6 34.0 1.0
CB B:BFD49 4.6 32.7 1.0
OG B:SER164 4.7 29.9 1.0
NZ B:LYS213 4.8 35.5 1.0
CA B:PHE50 5.0 34.1 1.0

Fluorine binding site 6 out of 6 in 2g07

Go back to Fluorine Binding Sites List in 2g07
Fluorine binding site 6 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Phospho- Enzyme Intermediate Analog with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F49

b:33.1
occ:1.00
 F3 B:BFD49 0.0 33.1 1.0
BE B:BFD49 1.5 36.1 1.0
OD1 B:BFD49 2.4 34.3 1.0
F1 B:BFD49 2.4 30.5 1.0
F2 B:BFD49 2.5 36.9 1.0
OG B:SER164 2.5 29.9 1.0
N B:ASP51 2.9 33.5 1.0
N B:PHE50 3.1 34.0 1.0
CB B:SER164 3.2 33.6 1.0
CG B:BFD49 3.3 35.5 1.0
CA B:SER164 3.5 33.3 1.0
CA B:PHE50 3.6 34.1 1.0
CB B:PHE50 3.6 33.6 1.0
C B:PHE50 3.7 34.0 1.0
OD2 B:BFD49 3.7 39.6 1.0
CB B:ASP51 3.7 33.7 1.0
O B:HOH720 3.8 40.9 1.0
CA B:ASP51 3.9 34.5 1.0
N B:ALA165 3.9 34.1 1.0
OD2 B:ASP51 4.1 37.7 1.0
CG B:ASP51 4.1 35.9 1.0
MG B:MG602 4.2 33.8 1.0
C B:SER164 4.2 34.5 1.0
C B:BFD49 4.2 34.8 1.0
O B:PHE163 4.3 34.6 1.0
NZ B:LYS213 4.4 35.5 1.0
CA B:BFD49 4.4 34.0 1.0
CB B:BFD49 4.5 32.7 1.0
N B:GLY166 4.5 35.8 1.0
N B:SER164 4.6 34.5 1.0
O B:ASP51 4.6 35.7 1.0
C B:ASP51 4.7 35.1 1.0
C B:PHE163 4.8 34.9 1.0
CG B:PHE50 4.8 34.6 1.0
O B:PHE50 4.8 33.9 1.0
O B:HOH674 4.8 21.4 1.0
CA B:ALA165 5.0 34.4 1.0

Reference:

E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.Mccoy, G.N.Phillips. Structure of Pyrimidine 5'-Nucleotidase Type 1. Insight Into Mechanism of Action and Inhibition During Lead Poisoning. J.Biol.Chem. V. 281 20521 2006.
ISSN: ISSN 0021-9258
PubMed: 16672222
DOI: 10.1074/JBC.M602000200
Page generated: Wed Jul 31 14:26:30 2024

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