Fluorine in PDB 1p62: Structure of Human Dck Complexed with Gemcitabine and Adp-Mg

All present enzymatic activity of Structure of Human Dck Complexed with Gemcitabine and Adp-Mg:
2.7.1.74;

The structure of Structure of Human Dck Complexed with Gemcitabine and Adp-Mg, PDB code: 1p62 was solved by E.Sabini, S.Ort, C.Monnerjahn, M.Konrad, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.200, 81.200, 94.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.7

The structure of Structure of Human Dck Complexed with Gemcitabine and Adp-Mg also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Structure of Human Dck Complexed with Gemcitabine and Adp-Mg (pdb code 1p62). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Human Dck Complexed with Gemcitabine and Adp-Mg, PDB code: 1p62:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Human Dck Complexed with Gemcitabine and Adp-Mg


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 Dck Complexed with Gemcitabine and Adp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:25.9 occ:1.00 F1 B:GEO302 0.0 25.9 1.0 C2' B:GEO302 1.3 26.8 1.0 F2 B:GEO302 2.1 26.2 1.0 C1' B:GEO302 2.3 25.4 1.0 C3' B:GEO302 2.4 27.3 1.0 N1 B:GEO302 2.7 24.2 1.0 O4' B:GEO302 2.9 27.8 1.0 C6 B:GEO302 2.9 25.5 1.0 NH1 B:ARG128 3.0 24.1 1.0 O5' B:GEO302 3.1 31.9 1.0 C4' B:GEO302 3.1 28.4 1.0 CE2 B:PHE137 3.5 24.0 1.0 O3' B:GEO302 3.5 27.2 1.0 CZ B:PHE137 3.6 23.0 1.0 C5' B:GEO302 3.7 25.5 1.0 NH2 B:ARG128 3.7 23.3 1.0 CZ B:ARG128 3.7 22.6 1.0 CG1 B:ILE30 3.8 24.2 1.0 C2 B:GEO302 3.8 24.5 1.0 O B:HOH414 3.8 21.5 1.0 C5 B:GEO302 4.1 26.4 1.0 O2 B:GEO302 4.3 20.8 1.0 CD1 B:ILE30 4.3 27.0 1.0 CD2 B:PHE137 4.3 20.2 1.0 OE2 B:GLU53 4.5 30.7 1.0 CE1 B:PHE137 4.5 23.3 1.0 O B:HOH416 4.7 25.7 1.0 N3 B:GEO302 4.7 21.4 1.0 OH B:TYR86 4.8 24.0 1.0 C4 B:GEO302 4.9 21.5 1.0 NE B:ARG128 4.9 23.1 1.0 CB B:ILE30 4.9 23.2 1.0 OE1 B:GLU53 4.9 23.8 1.0 O B:HOH418 4.9 31.1 1.0

Fluorine binding site 2 out of 2 in the Structure of Human Dck Complexed with Gemcitabine and Adp-Mg


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 Dck Complexed with Gemcitabine and Adp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:26.2 occ:1.00 F2 B:GEO302 0.0 26.2 1.0 C2' B:GEO302 1.3 26.8 1.0 F1 B:GEO302 2.1 25.9 1.0 C1' B:GEO302 2.3 25.4 1.0 C3' B:GEO302 2.4 27.3 1.0 O3' B:GEO302 2.7 27.2 1.0 OH B:TYR86 2.8 24.0 1.0 O B:HOH416 2.8 25.7 1.0 N1 B:GEO302 3.1 24.2 1.0 CD1 B:ILE30 3.2 27.0 1.0 O2 B:GEO302 3.4 20.8 1.0 CE2 B:PHE137 3.4 24.0 1.0 O4' B:GEO302 3.5 27.8 1.0 CG1 B:ILE30 3.5 24.2 1.0 C2 B:GEO302 3.5 24.5 1.0 C4' B:GEO302 3.5 28.4 1.0 C6 B:GEO302 4.0 25.5 1.0 CD2 B:PHE137 4.1 20.2 1.0 CZ B:TYR86 4.2 26.3 1.0 CZ B:PHE137 4.3 23.0 1.0 O5' B:GEO302 4.6 31.9 1.0 N3 B:GEO302 4.7 21.4 1.0 C5' B:GEO302 4.8 25.5 1.0 CB B:ILE30 4.8 23.2 1.0 OE2 B:GLU197 5.0 27.2 1.0

E.Sabini, S.Ort, C.Monnerjahn, M.Konrad, A.Lavie. Structure of Human Dck Suggests Strategies to Improve Anticancer and Antiviral Therapy Nat.Struct.Biol. V. 10 513 2003.
ISSN: ISSN 1072-8368
PubMed: 12808445
DOI: 10.1038/NSB942