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Fluorine in PDB 2g08: X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride

Enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride

All present enzymatic activity of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride:
3.1.1.5;

Protein crystallography data

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride, PDB code: 2g08 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) 67.52 / 2.35
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 135.044, 135.044, 39.049, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 26

Other elements in 2g08:

The structure of X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum Fluoride (pdb code 2g08). 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, Product- Transition Complex Analog with Aluminum Fluoride, PDB code: 2g08:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 1 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:32.3
occ:1.00
F1 A:AF3501 0.0 32.3 1.0
AL A:AF3501 1.7 35.7 1.0
OD1 A:ASP49 2.5 38.4 1.0
OG A:SER164 2.6 41.1 1.0
O A:HOH502 2.7 32.1 1.0
N A:ASP51 2.8 39.5 1.0
N A:PHE50 2.9 40.0 1.0
F3 A:AF3501 2.9 35.4 1.0
F2 A:AF3501 2.9 35.8 1.0
CB A:PHE50 3.2 39.2 1.0
CA A:PHE50 3.3 39.4 1.0
CB A:SER164 3.3 40.5 1.0
CG A:ASP49 3.5 39.1 1.0
C A:PHE50 3.5 39.5 1.0
OD2 A:ASP51 3.6 45.1 1.0
CA A:SER164 3.7 40.6 1.0
CB A:ASP51 3.9 40.8 1.0
CA A:ASP51 3.9 40.9 1.0
CG A:ASP51 3.9 41.1 1.0
C A:ASP49 4.0 39.0 1.0
OD2 A:ASP49 4.0 39.9 1.0
N A:ALA165 4.2 41.4 1.0
MG A:MG500 4.3 35.1 1.0
C A:SER164 4.4 41.4 1.0
O A:PHE163 4.4 38.8 1.0
CA A:ASP49 4.5 38.5 1.0
CG A:PHE50 4.5 38.6 1.0
N A:GLY166 4.5 41.5 1.0
CB A:ASP49 4.6 37.4 1.0
NZ A:LYS213 4.6 39.6 1.0
O A:ASP51 4.7 41.6 1.0
O A:PHE50 4.7 40.4 1.0
O A:HOH664 4.7 24.8 1.0
C A:ASP51 4.8 41.2 1.0
CD2 A:PHE50 4.8 38.4 1.0
N A:SER164 4.8 40.3 1.0
OD1 A:ASP51 4.8 41.5 1.0
C A:PHE163 5.0 40.0 1.0

Fluorine binding site 2 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 2 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.8
occ:1.00
F2 A:AF3501 0.0 35.8 1.0
AL A:AF3501 1.7 35.7 1.0
MG A:MG500 2.0 35.1 1.0
O A:HOH502 2.3 32.1 1.0
OD1 A:ASP49 2.8 38.4 1.0
O A:HOH619 2.8 24.2 1.0
O A:HOH503 2.9 25.6 1.0
O A:HOH664 2.9 24.8 1.0
F3 A:AF3501 2.9 35.4 1.0
F1 A:AF3501 2.9 32.3 1.0
OD2 A:ASP49 3.1 39.9 1.0
O A:ASP51 3.1 41.6 1.0
CG A:ASP49 3.3 39.1 1.0
CB A:ASP51 3.3 40.8 1.0
N A:ASP51 3.6 39.5 1.0
O A:HOH507 3.7 42.8 1.0
CA A:ASP51 3.7 40.9 1.0
C A:ASP51 3.8 41.2 1.0
O A:HOH716 3.8 42.7 1.0
O A:HOH506 3.9 41.0 1.0
OD1 A:ASP238 3.9 40.1 1.0
OD2 A:ASP51 4.0 45.1 1.0
CG A:ASP51 4.2 41.1 1.0
C A:PHE50 4.5 39.5 1.0
N A:PHE50 4.6 40.0 1.0
CB A:ASP49 4.7 37.4 1.0
NZ A:LYS213 4.9 39.6 1.0
CG A:ASP238 4.9 40.2 1.0

Fluorine binding site 3 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 3 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.4
occ:1.00
F3 A:AF3501 0.0 35.4 1.0
AL A:AF3501 1.7 35.7 1.0
O A:HOH664 2.4 24.8 1.0
O A:HOH502 2.4 32.1 1.0
OD1 A:ASP49 2.5 38.4 1.0
NZ A:LYS213 2.6 39.6 1.0
F1 A:AF3501 2.9 32.3 1.0
F2 A:AF3501 2.9 35.8 1.0
N A:ALA165 3.0 41.4 1.0
CE A:LYS213 3.3 36.8 1.0
CB A:ALA165 3.6 41.7 1.0
CG A:ASP49 3.7 39.1 1.0
CA A:SER164 3.8 40.6 1.0
CA A:ALA165 3.8 41.6 1.0
C A:SER164 3.9 41.4 1.0
O A:PHE163 4.0 38.8 1.0
O A:HOH619 4.1 24.2 1.0
OG A:SER164 4.1 41.1 1.0
O A:HOH650 4.3 39.7 1.0
OD1 A:ASP242 4.3 34.8 1.0
O A:HOH506 4.4 41.0 1.0
OD2 A:ASP49 4.4 39.9 1.0
CB A:SER164 4.5 40.5 1.0
MG A:MG500 4.5 35.1 1.0
C A:ALA165 4.6 41.3 1.0
N A:GLY166 4.6 41.5 1.0
CB A:ASP49 4.7 37.4 1.0
CD A:LYS213 4.8 34.4 1.0
N A:SER164 4.8 40.3 1.0
O A:HOH716 4.8 42.7 1.0
C A:PHE163 4.8 40.0 1.0
N A:PHE50 4.9 40.0 1.0

Fluorine binding site 4 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 4 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:37.9
occ:1.00
F1 B:AF3601 0.0 37.9 1.0
AL B:AF3601 1.7 38.8 1.0
MG B:MG600 2.0 34.9 1.0
O B:HOH831 2.2 33.1 1.0
F3 B:AF3601 2.9 38.8 1.0
OD1 B:ASP49 2.9 39.9 1.0
F2 B:AF3601 2.9 34.9 1.0
O B:HOH602 2.9 23.6 1.0
O B:HOH603 2.9 32.0 1.0
OD2 B:ASP49 3.1 41.8 1.0
O B:ASP51 3.1 41.8 1.0
CB B:ASP51 3.1 40.4 1.0
O B:HOH679 3.1 31.3 1.0
CG B:ASP49 3.3 40.0 1.0
N B:ASP51 3.6 39.5 1.0
CA B:ASP51 3.7 40.8 1.0
C B:ASP51 3.8 41.2 1.0
O B:HOH761 3.9 38.2 1.0
OD1 B:ASP238 4.0 40.8 1.0
OD2 B:ASP51 4.0 44.5 1.0
O B:HOH721 4.0 41.7 1.0
CG B:ASP51 4.1 41.0 1.0
C B:PHE50 4.5 39.5 1.0
N B:PHE50 4.7 39.8 1.0
CB B:ASP49 4.8 37.7 1.0
NZ B:LYS213 4.9 39.8 1.0
CG B:ASP238 5.0 40.4 1.0

Fluorine binding site 5 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 5 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:34.9
occ:1.00
F2 B:AF3601 0.0 34.9 1.0
AL B:AF3601 1.7 38.8 1.0
O B:HOH831 2.5 33.1 1.0
OG B:SER164 2.6 39.7 1.0
OD1 B:ASP49 2.7 39.9 1.0
N B:ASP51 2.9 39.5 1.0
F1 B:AF3601 2.9 37.9 1.0
F3 B:AF3601 2.9 38.8 1.0
N B:PHE50 3.0 39.8 1.0
CB B:SER164 3.2 39.9 1.0
CB B:PHE50 3.3 38.9 1.0
OD2 B:ASP51 3.4 44.5 1.0
CA B:PHE50 3.4 39.3 1.0
C B:PHE50 3.6 39.5 1.0
CG B:ASP49 3.6 40.0 1.0
CA B:SER164 3.6 40.4 1.0
CB B:ASP51 3.7 40.4 1.0
CG B:ASP51 3.8 41.0 1.0
CA B:ASP51 3.9 40.8 1.0
OD2 B:ASP49 4.1 41.8 1.0
N B:ALA165 4.1 41.3 1.0
C B:ASP49 4.2 39.0 1.0
C B:SER164 4.3 41.2 1.0
MG B:MG600 4.4 34.9 1.0
N B:GLY166 4.4 41.4 1.0
O B:PHE163 4.5 38.9 1.0
CG B:PHE50 4.6 38.2 1.0
NZ B:LYS213 4.6 39.8 1.0
CA B:ASP49 4.6 38.6 1.0
CB B:ASP49 4.7 37.7 1.0
O B:ASP51 4.7 41.8 1.0
OD1 B:ASP51 4.7 40.9 1.0
O B:PHE50 4.8 40.3 1.0
N B:SER164 4.8 40.3 1.0
C B:ASP51 4.8 41.2 1.0
CD2 B:PHE50 4.9 37.8 1.0
O B:HOH679 4.9 31.3 1.0

Fluorine binding site 6 out of 6 in 2g08

Go back to Fluorine Binding Sites List in 2g08
Fluorine binding site 6 out of 6 in the X-Ray Structure of Mouse Pyrimidine 5'-Nucleotidase Type 1, Product- Transition Complex Analog with Aluminum 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, Product- Transition Complex Analog with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:38.8
occ:1.00
F3 B:AF3601 0.0 38.8 1.0
AL B:AF3601 1.7 38.8 1.0
O B:HOH831 2.4 33.1 1.0
O B:HOH679 2.4 31.3 1.0
OD1 B:ASP49 2.6 39.9 1.0
NZ B:LYS213 2.6 39.8 1.0
F1 B:AF3601 2.9 37.9 1.0
F2 B:AF3601 2.9 34.9 1.0
N B:ALA165 3.1 41.3 1.0
CE B:LYS213 3.3 38.0 1.0
CB B:ALA165 3.6 41.7 1.0
CG B:ASP49 3.7 40.0 1.0
CA B:ALA165 3.9 41.6 1.0
CA B:SER164 3.9 40.4 1.0
C B:SER164 4.0 41.2 1.0
O B:HOH602 4.0 23.6 1.0
O B:PHE163 4.2 38.9 1.0
OG B:SER164 4.2 39.7 1.0
O B:HOH761 4.2 38.2 1.0
O B:HOH687 4.2 36.5 1.0
OD1 B:ASP242 4.3 34.9 1.0
OD2 B:ASP49 4.4 41.8 1.0
MG B:MG600 4.4 34.9 1.0
C B:ALA165 4.5 41.3 1.0
CB B:SER164 4.6 39.9 1.0
N B:GLY166 4.6 41.4 1.0
CB B:ASP49 4.8 37.7 1.0
O B:HOH721 4.8 41.7 1.0
CD B:LYS213 4.8 36.2 1.0
N B:SER164 4.9 40.3 1.0
N B:PHE50 5.0 39.8 1.0
C B:PHE163 5.0 40.1 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 Oct 28 14:44:53 2020

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