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Fluorine in PDB 2vpp: Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines

Enzymatic activity of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines

All present enzymatic activity of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines:
2.7.1.145;

Protein crystallography data

The structure of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines, PDB code: 2vpp was solved by W.Knecht, N.E.Mikkelsen, A.Clausen, M.Willer, Z.Gojkovic, J.Piskur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.106, 62.298, 68.078, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines (pdb code 2vpp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines, PDB code: 2vpp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2vpp

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Fluorine binding site 1 out of 4 in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1210

b:17.2
occ:1.00
 F1 A:GEO1210 0.0 17.2 1.0
C2' A:GEO1210 1.3 16.1 1.0
F2 A:GEO1210 2.2 15.1 1.0
C1' A:GEO1210 2.3 14.5 1.0
C3' A:GEO1210 2.4 14.8 1.0
O3' A:GEO1210 2.5 16.3 1.0
O A:HOH2050 2.7 28.9 1.0
OH A:TYR70 2.8 19.0 1.0
N1 A:GEO1210 3.1 12.6 1.0
O2 A:GEO1210 3.4 11.8 1.0
CD1 A:ILE29 3.4 13.7 1.0
O4' A:GEO1210 3.4 17.1 1.0
C4' A:GEO1210 3.5 14.7 1.0
CE2 A:PHE114 3.5 14.2 1.0
C2 A:GEO1210 3.6 12.6 1.0
CG1 A:ILE29 3.6 15.0 1.0
CZ A:TYR70 4.0 16.6 1.0
C6 A:GEO1210 4.1 11.1 1.0
CD2 A:PHE114 4.2 13.2 1.0
CZ A:PHE114 4.3 14.8 1.0
CE1 A:TYR70 4.5 15.6 1.0
O A:HOH2119 4.6 37.9 1.0
O5' A:GEO1210 4.7 19.4 1.0
C5' A:GEO1210 4.7 14.8 1.0
N3 A:GEO1210 4.8 12.1 1.0
CB A:ILE29 4.9 14.6 1.0
CG2 A:ILE29 4.9 12.5 1.0

Fluorine binding site 2 out of 4 in 2vpp

Go back to Fluorine Binding Sites List in 2vpp
Fluorine binding site 2 out of 4 in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1210

b:15.1
occ:1.00
 F2 A:GEO1210 0.0 15.1 1.0
C2' A:GEO1210 1.3 16.1 1.0
F1 A:GEO1210 2.2 17.2 1.0
C3' A:GEO1210 2.3 14.8 1.0
C1' A:GEO1210 2.3 14.5 1.0
N1 A:GEO1210 2.7 12.6 1.0
C6 A:GEO1210 2.9 11.1 1.0
O4' A:GEO1210 2.9 17.1 1.0
NH1 A:ARG105 3.0 11.1 1.0
C4' A:GEO1210 3.1 14.7 1.0
O5' A:GEO1210 3.1 19.4 1.0
CE2 A:PHE114 3.4 14.2 1.0
CZ A:PHE114 3.4 14.8 1.0
O3' A:GEO1210 3.4 16.3 1.0
CZ A:ARG105 3.6 13.7 1.0
C2 A:GEO1210 3.7 12.6 1.0
NH2 A:ARG105 3.7 14.1 1.0
C5' A:GEO1210 3.8 14.8 1.0
CG1 A:ILE29 3.8 15.0 1.0
C5 A:GEO1210 4.0 12.3 1.0
O A:HOH2137 4.1 21.6 1.0
O2 A:GEO1210 4.3 11.8 1.0
CD2 A:PHE114 4.3 13.2 1.0
CE1 A:PHE114 4.4 13.9 1.0
CD1 A:ILE29 4.5 13.7 1.0
OE2 A:GLU52 4.5 17.4 1.0
N3 A:GEO1210 4.6 12.1 1.0
NE A:ARG105 4.6 15.7 1.0
O A:HOH2050 4.7 28.9 1.0
C4 A:GEO1210 4.8 13.5 1.0
OE1 A:GLU52 4.8 16.9 1.0
OH A:TYR70 4.9 19.0 1.0
CB A:ILE29 4.9 14.6 1.0

Fluorine binding site 3 out of 4 in 2vpp

Go back to Fluorine Binding Sites List in 2vpp
Fluorine binding site 3 out of 4 in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1207

b:24.2
occ:1.00
 F1 B:GEO1207 0.0 24.2 1.0
C2' B:GEO1207 1.3 20.7 1.0
F2 B:GEO1207 2.1 20.7 1.0
C3' B:GEO1207 2.3 21.2 1.0
C1' B:GEO1207 2.4 19.7 1.0
O3' B:GEO1207 2.4 20.1 1.0
OH B:TYR70 2.6 22.2 1.0
O B:HOH2088 2.9 30.3 1.0
CD1 B:ILE29 3.0 20.6 1.0
N1 B:GEO1207 3.2 15.9 1.0
O2 B:GEO1207 3.4 14.8 1.0
CG1 B:ILE29 3.4 20.3 1.0
O4' B:GEO1207 3.5 22.1 1.0
C4' B:GEO1207 3.5 21.5 1.0
C2 B:GEO1207 3.6 15.3 1.0
CE2 B:PHE114 3.8 14.2 1.0
CZ B:TYR70 3.8 21.0 1.0
C6 B:GEO1207 4.2 16.1 1.0
CE1 B:TYR70 4.3 21.4 1.0
CZ B:PHE114 4.4 13.4 1.0
CD2 B:PHE114 4.5 14.5 1.0
CG2 B:ILE29 4.6 19.5 1.0
CB B:ILE29 4.6 20.6 1.0
C5' B:GEO1207 4.7 23.4 1.0
CE2 B:TYR70 4.8 21.6 1.0
O5' B:GEO1207 4.8 23.6 1.0
N3 B:GEO1207 4.8 15.0 1.0

Fluorine binding site 4 out of 4 in 2vpp

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Fluorine binding site 4 out of 4 in the Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Drosophila Melanogaster Deoxyribonucleoside Kinase Successfully Activates Gemcitabine in Transduced Cancer Cell Lines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1207

b:20.7
occ:1.00
 F2 B:GEO1207 0.0 20.7 1.0
C2' B:GEO1207 1.3 20.7 1.0
F1 B:GEO1207 2.1 24.2 1.0
C3' B:GEO1207 2.3 21.2 1.0
C1' B:GEO1207 2.4 19.7 1.0
N1 B:GEO1207 2.8 15.9 1.0
C6 B:GEO1207 3.1 16.1 1.0
O4' B:GEO1207 3.1 22.1 1.0
C4' B:GEO1207 3.2 21.5 1.0
NH1 B:ARG105 3.2 18.1 1.0
CZ B:PHE114 3.3 13.4 1.0
O3' B:GEO1207 3.4 20.1 1.0
CE2 B:PHE114 3.4 14.2 1.0
O5' B:GEO1207 3.4 23.6 1.0
CG1 B:ILE29 3.4 20.3 1.0
C2 B:GEO1207 3.7 15.3 1.0
CZ B:ARG105 3.7 21.4 1.0
NH2 B:ARG105 3.7 20.6 1.0
C5' B:GEO1207 3.9 23.4 1.0
CD1 B:ILE29 3.9 20.6 1.0
O B:HOH2100 4.1 26.1 1.0
C5 B:GEO1207 4.1 13.8 1.0
O2 B:GEO1207 4.2 14.8 1.0
CE1 B:PHE114 4.3 16.1 1.0
CD2 B:PHE114 4.4 14.5 1.0
CB B:ILE29 4.5 20.6 1.0
N3 B:GEO1207 4.6 15.0 1.0
O B:HOH2088 4.6 30.3 1.0
OH B:TYR70 4.6 22.2 1.0
CG2 B:ILE29 4.7 19.5 1.0
NE B:ARG105 4.7 22.2 1.0
C4 B:GEO1207 4.8 14.6 1.0
OE2 B:GLU52 4.8 28.3 1.0
CA B:ILE29 4.9 20.8 1.0

Reference:

W.Knecht, N.E.Mikkelsen, A.Clausen, M.Willer, H.Eklund, Z.Gojkovic, J.Piskur. Drosophila Melanogaster Deoxyribonucleoside Kinase Activates Gemcitabine. Biochem.Biophys.Res.Commun. V. 382 430 2009.
ISSN: ISSN 0006-291X
PubMed: 19285960
DOI: 10.1016/J.BBRC.2009.03.041
Page generated: Sun Dec 13 11:40:34 2020

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