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Fluorine in PDB 2vp6: Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

Enzymatic activity of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

All present enzymatic activity of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase:
2.7.1.145;

Protein crystallography data

The structure of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase, PDB code: 2vp6 was solved by N.E.Mikkelsen, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.352, 70.714, 225.396, 90.00, 90.29, 90.00
R / Rfree (%) 25.6 / 28.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase (pdb code 2vp6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase, PDB code: 2vp6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 1 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1211

b:36.2
occ:1.00
 F5 A:5FU1211 0.0 36.2 1.0
C5 A:5FU1211 1.4 36.5 1.0
C4 A:5FU1211 2.4 35.3 1.0
C6 A:5FU1211 2.5 36.3 1.0
O4 A:5FU1211 2.7 36.0 1.0
OE2 A:GLU52 3.6 62.7 1.0
N3 A:5FU1211 3.6 35.4 1.0
N1 A:5FU1211 3.7 35.9 1.0
CH2 A:TRP57 3.7 50.0 1.0
CE A:MET88 3.8 52.4 1.0
CE1 A:PHE114 4.0 41.9 1.0
NH1 A:ARG105 4.0 47.7 1.0
CD1 A:PHE114 4.0 44.5 1.0
CD A:ARG105 4.0 50.6 1.0
CG1 A:VAL84 4.1 41.9 1.0
C2 A:5FU1211 4.1 35.3 1.0
CZ3 A:TRP57 4.4 49.7 1.0
CZ2 A:TRP57 4.5 50.0 1.0
CD A:GLU52 4.5 61.7 1.0
CG A:ARG105 4.6 51.4 1.0
CZ A:PHE114 4.7 42.6 1.0
CB A:ARG105 4.7 52.2 1.0
CB A:ALA110 4.7 47.3 1.0
CG A:PHE114 4.7 45.0 1.0
CA A:ALA110 4.8 47.4 1.0
CZ A:ARG105 4.8 48.5 1.0
NE A:ARG105 4.8 49.6 1.0
O5' A:5FU1211 4.9 45.3 1.0
C1' A:5FU1211 4.9 36.6 1.0
N A:ALA110 5.0 47.8 1.0

Fluorine binding site 2 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 2 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1210

b:47.3
occ:1.00
 F5 B:5FU1210 0.0 47.3 1.0
C5 B:5FU1210 1.3 46.9 1.0
C4 B:5FU1210 2.4 46.4 1.0
C6 B:5FU1210 2.4 48.7 1.0
O4 B:5FU1210 2.6 48.3 1.0
OE2 B:GLU52 3.4 62.8 1.0
N3 B:5FU1210 3.6 46.7 1.0
CH2 B:TRP57 3.6 49.9 1.0
N1 B:5FU1210 3.6 49.2 1.0
CE B:MET88 3.8 52.5 1.0
NH1 B:ARG105 3.9 48.4 1.0
CE1 B:PHE114 3.9 42.1 1.0
CD1 B:PHE114 4.0 44.5 1.0
CD B:ARG105 4.0 50.6 1.0
C2 B:5FU1210 4.1 47.5 1.0
CG1 B:VAL84 4.2 42.0 1.0
CZ3 B:TRP57 4.3 49.8 1.0
CD B:GLU52 4.3 61.8 1.0
CZ2 B:TRP57 4.5 50.1 1.0
CG B:ARG105 4.6 51.3 1.0
CZ B:PHE114 4.6 42.8 1.0
CZ B:ARG105 4.6 48.8 1.0
CB B:ARG105 4.7 52.5 1.0
NE B:ARG105 4.7 49.8 1.0
CG B:PHE114 4.7 45.2 1.0
CB B:ALA110 4.9 47.5 1.0
CG B:GLU52 4.9 61.0 1.0
C1' B:5FU1210 4.9 50.6 1.0
CA B:ALA110 4.9 47.7 1.0

Fluorine binding site 3 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 3 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1210

b:65.8
occ:1.00
 F5 C:5FU1210 0.0 65.8 1.0
C5 C:5FU1210 1.4 66.0 1.0
C6 C:5FU1210 2.4 66.1 1.0
C4 C:5FU1210 2.5 65.1 1.0
O4 C:5FU1210 2.8 65.2 1.0
CH2 C:TRP57 3.2 50.2 1.0
OE2 C:GLU52 3.3 62.7 1.0
N1 C:5FU1210 3.6 66.3 1.0
N3 C:5FU1210 3.7 65.1 1.0
CZ3 C:TRP57 3.8 49.7 1.0
CE C:MET88 3.8 52.5 1.0
CG1 C:VAL84 3.9 42.2 1.0
CZ2 C:TRP57 4.0 50.2 1.0
NH1 C:ARG105 4.1 48.1 1.0
C2 C:5FU1210 4.1 66.0 1.0
CD C:GLU52 4.2 61.9 1.0
CE1 C:PHE114 4.3 42.2 1.0
O5' C:5FU1210 4.3 62.3 1.0
CD1 C:PHE114 4.4 44.6 1.0
CD C:ARG105 4.5 50.7 1.0
CG2 C:VAL84 4.8 42.8 1.0
CG C:GLU52 4.8 61.0 1.0
C1' C:5FU1210 4.9 65.3 1.0
CZ C:PHE114 4.9 43.0 1.0
CG C:PHE114 5.0 45.4 1.0
CZ C:ARG105 5.0 48.9 1.0

Fluorine binding site 4 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 4 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1210

b:58.8
occ:1.00
 F5 D:5FU1210 0.0 58.8 1.0
C5 D:5FU1210 1.4 57.8 1.0
C4 D:5FU1210 2.4 57.8 1.0
C6 D:5FU1210 2.5 57.1 1.0
O4 D:5FU1210 2.7 58.5 1.0
OE2 D:GLU52 3.4 62.6 1.0
N3 D:5FU1210 3.6 57.4 1.0
N1 D:5FU1210 3.7 58.5 1.0
CE1 D:PHE114 3.7 42.1 1.0
CH2 D:TRP57 3.8 50.0 1.0
NH1 D:ARG105 3.8 48.2 1.0
CD1 D:PHE114 3.9 44.4 1.0
CD D:ARG105 4.0 50.7 1.0
CE D:MET88 4.0 52.6 1.0
C2 D:5FU1210 4.1 58.3 1.0
CG1 D:VAL84 4.3 42.0 1.0
CZ D:PHE114 4.3 43.0 1.0
CZ3 D:TRP57 4.4 49.8 1.0
CD D:GLU52 4.4 61.8 1.0
O5' D:5FU1210 4.4 53.9 1.0
CG D:PHE114 4.5 45.3 1.0
CZ D:ARG105 4.6 49.0 1.0
CZ2 D:TRP57 4.6 50.1 1.0
CG D:ARG105 4.6 51.4 1.0
NE D:ARG105 4.7 50.0 1.0
CB D:ARG105 4.8 52.4 1.0
CA D:ALA110 4.9 47.8 1.0
CB D:ALA110 4.9 47.6 1.0
CE2 D:PHE114 5.0 41.5 1.0
C1' D:5FU1210 5.0 59.6 1.0

Fluorine binding site 5 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 5 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1210

b:44.0
occ:1.00
 F5 E:5FU1210 0.0 44.0 1.0
C5 E:5FU1210 1.3 43.2 1.0
C6 E:5FU1210 2.4 43.3 1.0
C4 E:5FU1210 2.4 44.1 1.0
O4 E:5FU1210 2.8 44.4 1.0
OE2 E:GLU52 3.3 62.8 1.0
N1 E:5FU1210 3.6 45.1 1.0
N3 E:5FU1210 3.6 43.9 1.0
CH2 E:TRP57 3.7 50.1 1.0
CE1 E:PHE114 3.7 42.2 1.0
NH1 E:ARG105 3.8 48.1 1.0
CD1 E:PHE114 3.9 44.5 1.0
C2 E:5FU1210 4.0 44.0 1.0
CD E:ARG105 4.1 50.7 1.0
CE E:MET88 4.2 52.6 1.0
CZ3 E:TRP57 4.3 49.8 1.0
CD E:GLU52 4.3 61.8 1.0
CZ E:PHE114 4.4 42.8 1.0
CG1 E:VAL84 4.4 42.0 1.0
CG E:PHE114 4.5 45.3 1.0
CZ E:ARG105 4.6 48.6 1.0
CZ2 E:TRP57 4.6 50.2 1.0
CG E:ARG105 4.7 51.4 1.0
NE E:ARG105 4.7 50.0 1.0
CB E:ARG105 4.8 52.3 1.0
C1' E:5FU1210 4.9 47.3 1.0
CE2 E:PHE114 5.0 41.2 1.0

Fluorine binding site 6 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 6 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1210

b:50.3
occ:1.00
 F5 F:5FU1210 0.0 50.3 1.0
C5 F:5FU1210 1.3 50.1 1.0
C6 F:5FU1210 2.4 50.0 1.0
C4 F:5FU1210 2.5 50.0 1.0
O4 F:5FU1210 2.8 51.0 1.0
OE2 F:GLU52 3.4 62.8 1.0
N1 F:5FU1210 3.6 50.0 1.0
N3 F:5FU1210 3.7 47.9 1.0
CE1 F:PHE114 3.7 42.1 1.0
NH1 F:ARG105 3.8 48.1 1.0
CE F:MET88 3.8 52.7 1.0
CD1 F:PHE114 3.9 44.6 1.0
CD F:ARG105 3.9 50.7 1.0
CH2 F:TRP57 3.9 50.2 1.0
C2 F:5FU1210 4.1 49.7 1.0
CG1 F:VAL84 4.3 42.2 1.0
CD F:GLU52 4.4 62.0 1.0
CG F:ARG105 4.4 51.6 1.0
CZ F:PHE114 4.5 42.9 1.0
CB F:ARG105 4.5 52.5 1.0
CZ3 F:TRP57 4.6 49.9 1.0
CZ F:ARG105 4.6 48.9 1.0
NE F:ARG105 4.6 49.9 1.0
CZ2 F:TRP57 4.7 50.3 1.0
CG F:PHE114 4.7 45.3 1.0
CA F:ALA110 4.7 47.8 1.0
CB F:ALA110 4.8 47.7 1.0
C1' F:5FU1210 4.8 51.9 1.0
N F:ALA110 4.8 48.1 1.0
O5' F:5FU1210 4.8 58.4 1.0
O4' F:5FU1210 4.9 55.4 1.0
CG F:GLU52 5.0 61.2 1.0

Fluorine binding site 7 out of 8 in 2vp6

Go back to Fluorine Binding Sites List in 2vp6
Fluorine binding site 7 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1210

b:83.8
occ:1.00
 F5 G:5FU1210 0.0 83.8 1.0
C5 G:5FU1210 1.3 83.9 1.0
C6 G:5FU1210 2.4 84.4 1.0
C4 G:5FU1210 2.5 83.1 1.0
O4 G:5FU1210 2.8 83.6 1.0
CD1 G:PHE114 3.2 44.5 1.0
CE1 G:PHE114 3.5 42.0 1.0
N1 G:5FU1210 3.6 84.4 1.0
N3 G:5FU1210 3.6 82.2 1.0
CG G:PHE114 3.8 45.5 1.0
CG1 G:VAL84 3.9 42.2 1.0
C2 G:5FU1210 4.1 83.2 1.0
CA G:ALA110 4.2 47.8 1.0
CZ G:PHE114 4.3 42.8 1.0
CB G:PHE114 4.3 46.5 1.0
CB G:ALA110 4.3 47.6 1.0
CH2 G:TRP57 4.4 50.1 1.0
CD2 G:PHE114 4.5 43.3 1.0
OE2 G:GLU52 4.6 62.9 1.0
N G:ALA110 4.6 47.8 1.0
CE G:MET88 4.7 52.8 1.0
NH1 G:ARG105 4.7 48.0 1.0
CE2 G:PHE114 4.7 41.5 1.0
CG2 G:VAL84 4.8 42.9 1.0
C1' G:5FU1210 4.8 85.5 1.0
NE2 G:GLN81 4.9 45.5 1.0
CD G:ARG105 4.9 50.8 1.0
OE1 G:GLN81 4.9 46.6 1.0
CZ3 G:TRP57 4.9 49.8 1.0
CB G:VAL84 5.0 42.7 1.0

Fluorine binding site 8 out of 8 in 2vp6

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Fluorine binding site 8 out of 8 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1210

b:29.1
occ:1.00
 F5 H:5FU1210 0.0 29.1 1.0
C5 H:5FU1210 1.3 27.1 1.0
C6 H:5FU1210 2.3 26.1 1.0
C4 H:5FU1210 2.4 28.6 1.0
O4 H:5FU1210 2.7 31.4 1.0
OE2 H:GLU52 3.4 62.4 1.0
N1 H:5FU1210 3.5 31.1 1.0
N3 H:5FU1210 3.6 28.3 1.0
CE H:MET88 3.7 52.5 1.0
NH1 H:ARG105 3.8 48.1 1.0
CH2 H:TRP57 3.8 49.9 1.0
CE1 H:PHE114 3.9 41.9 1.0
CD1 H:PHE114 4.0 44.3 1.0
CD H:ARG105 4.0 50.8 1.0
C2 H:5FU1210 4.1 30.2 1.0
CG1 H:VAL84 4.2 41.8 1.0
CD H:GLU52 4.4 61.6 1.0
CB H:ARG105 4.5 52.1 1.0
CG H:ARG105 4.5 51.5 1.0
CZ3 H:TRP57 4.5 49.5 1.0
CZ2 H:TRP57 4.6 50.0 1.0
CZ H:ARG105 4.6 48.6 1.0
CZ H:PHE114 4.7 42.7 1.0
CB H:ALA110 4.7 47.5 1.0
NE H:ARG105 4.7 49.6 1.0
CG H:PHE114 4.7 45.2 1.0
CA H:ALA110 4.7 47.5 1.0
N H:ALA110 4.9 47.7 1.0
C1' H:5FU1210 4.9 32.7 1.0
CG H:GLU52 4.9 61.0 1.0

Reference:

N.E.Mikkelsen, B.Munch-Petersen, H.Eklund. Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase. Febs J. V. 275 2151 2008.
ISSN: ISSN 1742-464X
PubMed: 18384378
DOI: 10.1111/J.1742-4658.2008.06369.X
Page generated: Wed Jul 31 16:16:16 2024

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