Atomistry » Fluorine » PDB 2fq9-2gtm » 2g07
Atomistry »
  Fluorine »
    PDB 2fq9-2gtm »
      2g07 »

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: Sun Dec 13 11:36:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy