Fluorine in PDB 1nmy: Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp

All present enzymatic activity of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp:
2.7.4.9;

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp, PDB code: 1nmy was solved by N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.80 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.258, 101.258, 49.781, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp (pdb code 1nmy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp, PDB code: 1nmy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:14.2 occ:0.50 F A:FDM301 0.0 14.2 0.5 F A:FDM301 0.8 7.8 0.5 C3' A:FDM301 1.4 13.7 0.5 C3' A:FDM301 1.5 9.5 0.5 C4' A:FDM301 2.0 10.3 0.5 C4' A:FDM301 2.4 14.6 0.5 C2' A:FDM301 2.5 14.6 0.5 O A:HOH555 2.5 47.3 1.0 C2' A:FDM301 2.7 10.2 0.5 O4' A:FDM301 2.9 8.9 0.5 O A:HOH510 3.0 50.0 1.0 C1' A:FDM301 3.1 9.1 0.5 C1' A:FDM301 3.1 12.4 0.5 O4' A:FDM301 3.1 12.2 0.5 C5' A:FDM301 3.2 14.5 0.5 CD1 A:TYR151 3.5 15.1 1.0 C5' A:FDM301 3.7 13.0 0.5 O5' A:FDM301 3.8 18.7 0.5 O A:HOH751 3.9 30.1 1.0 O5' A:FDM301 3.9 14.1 0.5 CB A:TYR151 3.9 17.9 1.0 O A:ARG150 3.9 30.1 1.0 CE2 A:PHE105 4.2 16.8 1.0 CG A:TYR151 4.2 16.8 1.0 CD2 A:LEU57 4.3 14.8 1.0 CD2 A:PHE105 4.4 15.7 1.0 CE1 A:TYR151 4.5 15.5 1.0 N1 A:FDM301 4.5 8.2 0.5 OP2 A:FDM301 4.5 14.7 0.5 N1 A:FDM301 4.5 9.9 0.5 O A:HOH512 4.5 99.9 1.0 OD1 A:ASP15 4.6 32.5 0.5 CZ A:PHE105 4.8 13.8 1.0 NH2 A:ARG97 4.8 18.1 1.0 OD2 A:ASP15 4.8 28.7 0.5 P1 A:FDM301 5.0 15.9 0.5 C A:ARG150 5.0 23.9 1.0 O2 A:FDM301 5.0 7.7 0.5

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:7.8 occ:0.50 F A:FDM301 0.0 7.8 0.5 F A:FDM301 0.8 14.2 0.5 C3' A:FDM301 1.4 9.5 0.5 C3' A:FDM301 1.5 13.7 0.5 C2' A:FDM301 2.1 14.6 0.5 C4' A:FDM301 2.4 10.3 0.5 C2' A:FDM301 2.4 10.2 0.5 C4' A:FDM301 2.8 14.6 0.5 C1' A:FDM301 3.0 12.4 0.5 O A:HOH510 3.0 50.0 1.0 C1' A:FDM301 3.0 9.1 0.5 O A:HOH555 3.1 47.3 1.0 O4' A:FDM301 3.2 8.9 0.5 O4' A:FDM301 3.4 12.2 0.5 CE2 A:PHE105 3.4 16.8 1.0 CD1 A:TYR151 3.5 15.1 1.0 C5' A:FDM301 3.7 14.5 0.5 CD2 A:PHE105 3.8 15.7 1.0 CB A:TYR151 3.8 17.9 1.0 CZ A:PHE105 4.0 13.8 1.0 O A:HOH751 4.0 30.1 1.0 C5' A:FDM301 4.1 13.0 0.5 CG A:TYR151 4.1 16.8 1.0 O5' A:FDM301 4.1 14.1 0.5 OD1 A:ASP15 4.2 32.5 0.5 O5' A:FDM301 4.2 18.7 0.5 OD2 A:ASP15 4.3 28.7 0.5 O A:ARG150 4.3 30.1 1.0 O A:HOH512 4.3 99.9 1.0 N1 A:FDM301 4.4 9.9 0.5 NH2 A:ARG97 4.4 18.1 1.0 N1 A:FDM301 4.4 8.2 0.5 CE1 A:TYR151 4.5 15.5 1.0 CG A:PHE105 4.5 12.4 1.0 OP2 A:FDM301 4.6 14.7 0.5 CG A:ASP15 4.7 27.5 0.5 CE1 A:PHE105 4.7 12.8 1.0 CZ A:ARG97 4.7 12.6 1.0 O2 A:FDM301 4.9 7.7 0.5 CD2 A:LEU57 4.9 14.8 1.0 CD1 A:PHE105 4.9 12.6 1.0 O2 A:FDM301 5.0 9.9 0.5

N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie. Structures of Human Thymidylate Kinase in Complex with Prodrugs: Implications For the Structure-Based Design of Novel Compounds Biochemistry V. 42 2568 2003.
ISSN: ISSN 0006-2960
PubMed: 12614151
DOI: 10.1021/BI027302T