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Fluorine in PDB 2i7d: Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+

Protein crystallography data

The structure of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+, PDB code: 2i7d was solved by A.Rinaldo-Matthis, K.Wallden, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.10 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.623, 47.153, 62.384, 68.92, 81.69, 74.99
R / Rfree (%) 16.6 / 19.6

Other elements in 2i7d:

The structure of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ 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 Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ (pdb code 2i7d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+, PDB code: 2i7d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2i7d

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Fluorine binding site 1 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:6.9
occ:1.00
 F1 A:ALF400 0.0 6.9 1.0
AL A:ALF400 1.8 5.7 1.0
MG A:MG728 2.0 4.9 1.0
F3 A:ALF400 2.4 9.2 1.0
F4 A:ALF400 2.7 6.5 1.0
O3' A:DUR300 2.7 7.8 1.0
OD1 A:ASP10 2.8 5.1 1.0
OD2 A:ASP10 2.9 5.5 1.0
O A:HOH729 2.9 5.5 1.0
O A:HOH731 3.0 6.5 1.0
O A:ASP12 3.0 5.5 1.0
CB A:ASP12 3.1 5.2 1.0
CG A:ASP10 3.1 4.1 1.0
N A:ASP12 3.3 4.8 1.0
C2' A:DUR300 3.3 9.7 1.0
CA A:ASP12 3.5 5.1 1.0
C3' A:DUR300 3.5 7.8 1.0
F2 A:ALF400 3.5 9.6 1.0
C A:ASP12 3.6 4.9 1.0
OD2 A:ASP12 3.7 7.3 1.0
CG A:ASP12 3.9 6.1 1.0
OD1 A:ASP145 4.1 5.5 1.0
C1' A:DUR300 4.2 9.3 1.0
C A:MET11 4.3 3.9 1.0
O2 A:DUR300 4.4 9.5 1.0
N A:MET11 4.5 4.7 1.0
CB A:ASP10 4.7 4.8 1.0
C4' A:DUR300 4.8 9.6 1.0
N A:GLY13 4.9 4.9 1.0
CA A:MET11 4.9 5.1 1.0

Fluorine binding site 2 out of 8 in 2i7d

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Fluorine binding site 2 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:9.6
occ:1.00
 F2 A:ALF400 0.0 9.6 1.0
AL A:ALF400 1.8 5.7 1.0
F3 A:ALF400 2.4 9.2 1.0
F4 A:ALF400 2.6 6.5 1.0
OD1 A:ASP10 2.6 5.1 1.0
N A:SER100 2.8 7.1 1.0
O3' A:DUR300 2.8 7.8 1.0
NZ A:LYS134 2.8 6.1 1.0
CA A:THR99 3.1 6.2 1.0
OG1 A:THR99 3.2 7.2 1.0
C A:THR99 3.4 6.0 1.0
CE A:LYS134 3.5 6.2 1.0
F1 A:ALF400 3.5 6.9 1.0
CB A:THR99 3.6 6.2 1.0
C3' A:DUR300 3.7 7.8 1.0
CA A:SER100 3.9 7.9 1.0
CG A:ASP10 3.9 4.1 1.0
CB A:SER100 3.9 9.0 1.0
OG A:SER100 3.9 9.7 1.0
O A:CYS98 4.1 5.8 1.0
N A:THR99 4.3 5.5 1.0
O A:SER100 4.3 8.8 1.0
O A:THR99 4.6 7.2 1.0
C A:CYS98 4.6 5.9 1.0
C A:SER100 4.6 7.8 1.0
N A:MET11 4.6 4.7 1.0
OD2 A:ASP10 4.7 5.5 1.0
C2' A:DUR300 4.8 9.7 1.0
O A:HOH760 4.8 10.9 1.0
O A:HOH729 4.8 5.5 1.0
CB A:ASP10 4.8 4.8 1.0
C4' A:DUR300 4.9 9.6 1.0
CA A:ASP10 5.0 4.6 1.0
OD2 A:ASP12 5.0 7.3 1.0

Fluorine binding site 3 out of 8 in 2i7d

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Fluorine binding site 3 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:9.2
occ:1.00
 F3 A:ALF400 0.0 9.2 1.0
AL A:ALF400 1.8 5.7 1.0
F1 A:ALF400 2.4 6.9 1.0
F2 A:ALF400 2.4 9.6 1.0
O A:HOH729 2.7 5.5 1.0
O3' A:DUR300 2.8 7.8 1.0
OD1 A:ASP10 2.9 5.1 1.0
C3' A:DUR300 3.1 7.8 1.0
C2' A:DUR300 3.4 9.7 1.0
O A:HOH760 3.5 10.9 1.0
MG A:MG728 3.5 4.9 1.0
NZ A:LYS134 3.6 6.1 1.0
F4 A:ALF400 3.6 6.5 1.0
CG A:ASP10 3.7 4.1 1.0
OD2 A:ASP10 3.9 5.5 1.0
O A:HOH859 4.3 19.6 1.0
OD2 A:ASP144 4.3 6.9 1.0
CE A:LYS134 4.4 6.2 1.0
O A:HOH731 4.4 6.5 1.0
CZ A:PHE44 4.5 10.2 1.0
OD1 A:ASP144 4.5 6.1 1.0
C4' A:DUR300 4.6 9.6 1.0
OG A:SER100 4.7 9.7 1.0
CB A:SER100 4.8 9.0 1.0
N A:SER100 4.8 7.1 1.0
C1' A:DUR300 4.8 9.3 1.0
CG A:ASP144 4.8 5.0 1.0

Fluorine binding site 4 out of 8 in 2i7d

Go back to Fluorine Binding Sites List in 2i7d
Fluorine binding site 4 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:6.5
occ:1.00
 F4 A:ALF400 0.0 6.5 1.0
AL A:ALF400 1.8 5.7 1.0
F2 A:ALF400 2.6 9.6 1.0
O3' A:DUR300 2.6 7.8 1.0
OD1 A:ASP10 2.7 5.1 1.0
F1 A:ALF400 2.7 6.9 1.0
OG1 A:THR99 2.7 7.2 1.0
N A:ASP12 2.8 4.8 1.0
N A:MET11 3.0 4.7 1.0
OD2 A:ASP12 3.3 7.3 1.0
CB A:MET11 3.3 6.4 1.0
CA A:MET11 3.4 5.1 1.0
CG A:ASP10 3.5 4.1 1.0
C A:MET11 3.5 3.9 1.0
F3 A:ALF400 3.6 9.2 1.0
CB A:THR99 3.7 6.2 1.0
NZ A:LYS112 3.7 6.5 1.0
CG A:ASP12 3.8 6.1 1.0
CB A:ASP12 3.9 5.2 1.0
CA A:ASP12 3.9 5.1 1.0
OD2 A:ASP10 4.1 5.5 1.0
C3' A:DUR300 4.1 7.8 1.0
C A:ASP10 4.2 4.3 1.0
CA A:THR99 4.2 6.2 1.0
CG A:MET11 4.3 7.4 1.0
MG A:MG728 4.4 4.9 1.0
N A:SER100 4.5 7.1 1.0
CA A:ASP10 4.5 4.6 1.0
O A:ASP12 4.6 5.5 1.0
CB A:ASP10 4.6 4.8 1.0
OD1 A:ASP12 4.7 6.8 1.0
NZ A:LYS134 4.7 6.1 1.0
O A:MET11 4.8 5.1 1.0
C A:ASP12 4.8 4.9 1.0
C2' A:DUR300 4.8 9.7 1.0
CE A:LYS112 4.9 7.0 1.0
C A:THR99 4.9 6.0 1.0
C4' A:DUR300 5.0 9.6 1.0

Fluorine binding site 5 out of 8 in 2i7d

Go back to Fluorine Binding Sites List in 2i7d
Fluorine binding site 5 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:10.1
occ:1.00
 F1 B:ALF401 0.0 10.1 1.0
AL B:ALF401 1.8 7.3 1.0
F3 B:ALF401 2.4 10.4 1.0
F4 B:ALF401 2.5 7.8 1.0
O B:HOH730 2.7 7.5 1.0
O3' B:DUR301 2.8 8.8 1.0
OD1 B:ASP10 2.8 7.7 1.0
C3' B:DUR301 3.1 9.8 1.0
C2' B:DUR301 3.3 10.7 1.0
O B:HOH1038 3.6 12.4 1.0
MG B:MG729 3.6 6.8 1.0
F2 B:ALF401 3.6 8.1 1.0
NZ B:LYS134 3.6 7.6 1.0
CG B:ASP10 3.6 6.8 1.0
OD2 B:ASP10 3.8 6.9 1.0
O B:HOH878 4.2 20.3 1.0
OD1 B:ASP144 4.3 8.3 1.0
CE B:LYS134 4.4 6.4 1.0
OD2 B:ASP144 4.5 7.7 1.0
O B:HOH733 4.5 8.7 1.0
C4' B:DUR301 4.6 10.8 1.0
CZ B:PHE44 4.7 12.0 1.0
CB B:SER100 4.7 9.6 1.0
N B:SER100 4.7 7.8 1.0
OG B:SER100 4.7 10.0 1.0
C1' B:DUR301 4.8 10.6 1.0
CG B:ASP144 4.8 7.0 1.0
CB B:ASP10 5.0 6.1 1.0

Fluorine binding site 6 out of 8 in 2i7d

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Fluorine binding site 6 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:8.1
occ:1.00
 F2 B:ALF401 0.0 8.1 1.0
AL B:ALF401 1.8 7.3 1.0
O3' B:DUR301 2.6 8.8 1.0
F3 B:ALF401 2.6 10.4 1.0
OD1 B:ASP10 2.6 7.7 1.0
F4 B:ALF401 2.7 7.8 1.0
OG1 B:THR99 2.8 7.1 1.0
N B:ASP12 2.8 6.3 1.0
N B:MET11 3.0 6.6 1.0
OD2 B:ASP12 3.3 8.5 1.0
CB B:MET11 3.3 7.7 1.0
CA B:MET11 3.4 6.6 1.0
CG B:ASP10 3.5 6.8 1.0
C B:MET11 3.5 5.9 1.0
F1 B:ALF401 3.6 10.1 1.0
NZ B:LYS112 3.7 7.5 1.0
CB B:THR99 3.7 6.6 1.0
CG B:ASP12 3.8 6.9 1.0
CB B:ASP12 3.9 7.1 1.0
CA B:ASP12 3.9 6.5 1.0
OD2 B:ASP10 4.0 6.9 1.0
C3' B:DUR301 4.0 9.8 1.0
C B:ASP10 4.1 6.7 1.0
CA B:THR99 4.2 6.3 1.0
MG B:MG729 4.4 6.8 1.0
CG B:MET11 4.4 8.9 1.0
CA B:ASP10 4.5 6.0 1.0
N B:SER100 4.5 7.8 1.0
CB B:ASP10 4.6 6.1 1.0
O B:ASP12 4.6 8.2 1.0
OD1 B:ASP12 4.7 8.4 1.0
C2' B:DUR301 4.7 10.7 1.0
O B:MET11 4.7 6.7 1.0
C B:ASP12 4.8 6.6 1.0
NZ B:LYS134 4.8 7.6 1.0
CE B:LYS112 4.9 7.7 1.0
C B:THR99 4.9 6.7 1.0
C4' B:DUR301 5.0 10.8 1.0

Fluorine binding site 7 out of 8 in 2i7d

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Fluorine binding site 7 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:10.4
occ:1.00
 F3 B:ALF401 0.0 10.4 1.0
AL B:ALF401 1.8 7.3 1.0
F1 B:ALF401 2.4 10.1 1.0
OD1 B:ASP10 2.6 7.7 1.0
F2 B:ALF401 2.6 8.1 1.0
N B:SER100 2.7 7.8 1.0
O3' B:DUR301 2.8 8.8 1.0
NZ B:LYS134 2.9 7.6 1.0
CA B:THR99 3.1 6.3 1.0
OG1 B:THR99 3.2 7.1 1.0
C B:THR99 3.3 6.7 1.0
CE B:LYS134 3.6 6.4 1.0
F4 B:ALF401 3.6 7.8 1.0
CB B:THR99 3.7 6.6 1.0
C3' B:DUR301 3.7 9.8 1.0
CA B:SER100 3.8 8.7 1.0
CB B:SER100 3.8 9.6 1.0
CG B:ASP10 3.9 6.8 1.0
OG B:SER100 3.9 10.0 1.0
O B:CYS98 4.1 6.7 1.0
O B:SER100 4.2 9.9 1.0
N B:THR99 4.3 6.5 1.0
C B:SER100 4.5 8.6 1.0
O B:THR99 4.6 7.4 1.0
C B:CYS98 4.6 6.3 1.0
OD2 B:ASP10 4.6 6.9 1.0
N B:MET11 4.7 6.6 1.0
C2' B:DUR301 4.7 10.7 1.0
O B:HOH1038 4.8 12.4 1.0
O B:HOH730 4.8 7.5 1.0
CB B:ASP10 4.8 6.1 1.0
C4' B:DUR301 4.8 10.8 1.0
CA B:ASP10 5.0 6.0 1.0

Fluorine binding site 8 out of 8 in 2i7d

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Fluorine binding site 8 out of 8 in the Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Human Cytosolic Deoxyribonucleotidase in Complex with Deoxyuridine, ALF4 and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:7.8
occ:1.00
 F4 B:ALF401 0.0 7.8 1.0
AL B:ALF401 1.8 7.3 1.0
MG B:MG729 2.0 6.8 1.0
F1 B:ALF401 2.5 10.1 1.0
F2 B:ALF401 2.7 8.1 1.0
O3' B:DUR301 2.7 8.8 1.0
OD1 B:ASP10 2.8 7.7 1.0
OD2 B:ASP10 2.8 6.9 1.0
O B:HOH730 3.0 7.5 1.0
O B:ASP12 3.0 8.2 1.0
O B:HOH733 3.0 8.7 1.0
CG B:ASP10 3.1 6.8 1.0
CB B:ASP12 3.1 7.1 1.0
N B:ASP12 3.2 6.3 1.0
C2' B:DUR301 3.3 10.7 1.0
CA B:ASP12 3.4 6.5 1.0
C3' B:DUR301 3.5 9.8 1.0
F3 B:ALF401 3.6 10.4 1.0
C B:ASP12 3.6 6.6 1.0
OD2 B:ASP12 3.8 8.5 1.0
CG B:ASP12 3.9 6.9 1.0
OD1 B:ASP145 4.0 7.2 1.0
C1' B:DUR301 4.2 10.6 1.0
C B:MET11 4.3 5.9 1.0
O2 B:DUR301 4.4 10.2 1.0
N B:MET11 4.5 6.6 1.0
CB B:ASP10 4.6 6.1 1.0
C4' B:DUR301 4.8 10.8 1.0
CA B:MET11 4.9 6.6 1.0
N B:GLY13 4.9 7.0 1.0

Reference:

K.Wallden, A.Rinaldo-Matthis, B.Ruzzenente, C.Rampazzo, V.Bianchi, P.Nordlund. Structures of Human and Murine Cytosolic Deoxyribonucleotidase: Insights Into Substrate Specificity and Catalysis To Be Published.
Page generated: Wed Jul 31 14:50:32 2024

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