Fluorine in PDB 3rdp: Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt

All present enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt:
2.7.1.21;

The structure of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt, PDB code: 3rdp was solved by L.Pernot, R.Perozzo, Y.Westermaier, M.Martic, S.Ametamey, L.Scapozza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.26 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	114.187, 118.283, 108.871, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.4

The binding sites of Fluorine atom in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt (pdb code 3rdp). 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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt, PDB code: 3rdp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:39.2 occ:1.00 F A:NMF601 0.0 39.2 1.0 C14 A:NMF601 1.3 39.2 1.0 C12 A:NMF601 2.4 39.2 1.0 C11 A:NMF601 2.8 39.2 1.0 C13 A:NMF601 2.8 39.2 1.0 C6 A:NMF601 3.1 39.2 1.0 C5 A:NMF601 3.5 39.2 1.0 CD A:ARG222 3.5 24.5 1.0 N1 A:NMF601 3.6 39.2 1.0 O3 A:NMF601 3.8 39.2 1.0 NE A:ARG222 3.9 22.7 1.0 CD1 A:ILE97 4.0 22.3 1.0 NH1 A:ARG222 4.1 23.0 1.0 CZ A:ARG222 4.2 22.6 1.0 CG A:HIS58 4.5 34.8 1.0 CZ3 A:TRP88 4.5 25.5 1.0 CD2 A:HIS58 4.6 38.0 1.0 C3 A:NMF601 4.6 39.2 1.0 ND1 A:HIS58 4.7 33.6 1.0 CB A:HIS58 4.7 33.0 1.0 CG A:ARG222 4.8 21.6 1.0 C1 A:NMF601 4.8 39.2 1.0 CG1 A:ILE97 4.9 20.2 1.0 NE2 A:HIS58 4.9 36.5 1.0 CE1 A:HIS58 5.0 37.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with N-Methyl-Fhbt within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:41.2 occ:1.00 F B:NMF601 0.0 41.2 1.0 C14 B:NMF601 1.3 41.2 1.0 C12 B:NMF601 2.4 41.2 1.0 C13 B:NMF601 2.8 41.2 1.0 C11 B:NMF601 2.9 41.2 1.0 C6 B:NMF601 3.1 41.2 1.0 CG B:ARG222 3.4 62.6 1.0 C5 B:NMF601 3.6 41.2 1.0 N1 B:NMF601 3.7 41.2 1.0 O3 B:NMF601 3.7 41.2 1.0 NE B:ARG222 3.9 60.6 1.0 CD B:ARG222 4.1 58.2 1.0 CD1 B:ILE97 4.1 38.9 1.0 CB B:ARG222 4.4 62.7 1.0 CD2 B:HIS58 4.5 32.4 1.0 CG B:HIS58 4.5 32.0 1.0 CZ3 B:TRP88 4.7 30.0 1.0 CB B:HIS58 4.8 32.2 1.0 C3 B:NMF601 4.8 41.2 1.0 CZ B:ARG222 4.8 62.0 1.0 NE2 B:HIS58 4.9 35.3 1.0 ND1 B:HIS58 4.9 33.3 1.0 C1 B:NMF601 5.0 41.2 1.0

M.Martic, L.Pernot, Y.Westermaier, R.Perozzo, T.G.Kraljevic, S.Kristafor, S.Raic-Malic, L.Scapozza, S.Ametamey. Synthesis, Crystal Structure, and in Vitro Biological Evaluation of C-6 Pyrimidine Derivatives: New Lead Structures For Monitoring Gene Expression in Vivo. Nucleosides Nucleotides V. 30 293 2011NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 21623543
DOI: 10.1080/15257770.2011.581258