Atomistry » Fluorine » PDB 2gtn-2ihj » 2i7d
Atomistry »
  Fluorine »
    PDB 2gtn-2ihj »
      2i7d »

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

Go back to Fluorine Binding Sites List in 2i7d
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

Go back to Fluorine Binding Sites List in 2i7d
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

Go back to Fluorine Binding Sites List in 2i7d
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

Go back to Fluorine Binding Sites List in 2i7d
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

Go back to Fluorine Binding Sites List in 2i7d
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

Go back to Fluorine Binding Sites List in 2i7d
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy