Fluorine in PDB 2no0: C4S Dck Variant of Dck in Complex with Gemcitabine+Adp

All present enzymatic activity of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp:
2.7.1.74;

The structure of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp, PDB code: 2no0 was solved by E.Sabini, S.Hazra, M.Konrad, S.K.Burley, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.300, 132.400, 157.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.1

The binding sites of Fluorine atom in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp (pdb code 2no0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp, PDB code: 2no0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:15.6 occ:1.00 F1 A:GEO302 0.0 15.6 1.0 C2' A:GEO302 1.3 14.3 1.0 F2 A:GEO302 2.2 13.8 1.0 C3' A:GEO302 2.3 15.9 1.0 C1' A:GEO302 2.4 13.5 1.0 N1 A:GEO302 2.7 13.5 1.0 O5' A:GEO302 2.8 19.3 1.0 C6 A:GEO302 2.9 10.7 1.0 O4' A:GEO302 3.0 13.3 1.0 C4' A:GEO302 3.0 14.8 1.0 NH1 A:ARG128 3.0 13.7 1.0 C5' A:GEO302 3.5 17.4 1.0 NH2 A:ARG128 3.5 17.4 1.0 CE2 A:PHE137 3.5 13.8 1.0 O3' A:GEO302 3.6 17.0 1.0 CZ A:PHE137 3.6 16.4 1.0 CZ A:ARG128 3.6 16.1 1.0 CG1 A:ILE30 3.6 10.5 1.0 C2 A:GEO302 3.8 11.9 1.0 O A:HOH398 3.8 25.1 1.0 C5 A:GEO302 4.1 13.2 1.0 O2 A:GEO302 4.2 11.9 1.0 CD1 A:ILE30 4.3 12.3 1.0 CD2 A:PHE137 4.5 12.5 1.0 CE1 A:PHE137 4.6 16.7 1.0 CB A:ILE30 4.6 11.3 1.0 CG2 A:ILE30 4.7 11.1 1.0 N3 A:GEO302 4.7 12.3 1.0 NE A:ARG128 4.8 16.8 1.0 OE2 A:GLU53 4.8 23.6 1.0 OH A:TYR86 4.8 15.0 1.0 C4 A:GEO302 4.8 12.6 1.0 CA A:ILE30 4.9 11.6 1.0 OE1 A:GLU53 4.9 18.0 1.0 O A:HOH419 4.9 19.4 1.0

Fluorine binding site 2 out of 4 in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:13.8 occ:1.00 F2 A:GEO302 0.0 13.8 1.0 C2' A:GEO302 1.3 14.3 1.0 F1 A:GEO302 2.2 15.6 1.0 C1' A:GEO302 2.3 13.5 1.0 C3' A:GEO302 2.4 15.9 1.0 O3' A:GEO302 2.7 17.0 1.0 OH A:TYR86 2.8 15.0 1.0 O A:HOH419 3.0 19.4 1.0 N1 A:GEO302 3.1 13.5 1.0 CD1 A:ILE30 3.1 12.3 1.0 O2 A:GEO302 3.3 11.9 1.0 CG1 A:ILE30 3.3 10.5 1.0 O4' A:GEO302 3.5 13.3 1.0 C2 A:GEO302 3.5 11.9 1.0 C4' A:GEO302 3.5 14.8 1.0 CE2 A:PHE137 3.5 13.8 1.0 C6 A:GEO302 4.0 10.7 1.0 CZ A:TYR86 4.1 15.8 1.0 CD2 A:PHE137 4.2 12.5 1.0 CZ A:PHE137 4.3 16.4 1.0 CG2 A:ILE30 4.5 11.1 1.0 CB A:ILE30 4.5 11.3 1.0 O5' A:GEO302 4.5 19.3 1.0 C5' A:GEO302 4.7 17.4 1.0 N3 A:GEO302 4.7 12.3 1.0 CE1 A:TYR86 4.8 15.0 1.0 CE2 A:TYR86 5.0 17.2 1.0 OE2 A:GLU197 5.0 18.0 1.0

Fluorine binding site 3 out of 4 in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:18.9 occ:1.00 F1 B:GEO302 0.0 18.9 1.0 C2' B:GEO302 1.3 15.2 1.0 F2 B:GEO302 2.2 16.4 1.0 C3' B:GEO302 2.3 16.2 1.0 C1' B:GEO302 2.4 13.9 1.0 N1 B:GEO302 2.7 12.9 1.0 O5' B:GEO302 2.9 18.6 1.0 NH1 B:ARG128 2.9 16.6 1.0 C6 B:GEO302 3.0 14.5 1.0 O4' B:GEO302 3.0 14.8 1.0 C4' B:GEO302 3.0 15.7 1.0 O3' B:GEO302 3.5 18.3 1.0 C5' B:GEO302 3.5 16.6 1.0 NH2 B:ARG128 3.5 17.4 1.0 CZ B:ARG128 3.6 17.7 1.0 CE2 B:PHE137 3.6 16.6 1.0 C2 B:GEO302 3.7 13.7 1.0 O B:HOH404 3.7 23.4 1.0 CG1 B:ILE30 3.7 13.3 1.0 CZ B:PHE137 3.7 14.8 1.0 C5 B:GEO302 4.1 15.9 1.0 O2 B:GEO302 4.2 15.0 1.0 CD1 B:ILE30 4.4 14.2 1.0 CD2 B:PHE137 4.5 16.9 1.0 NE B:ARG128 4.7 14.6 1.0 N3 B:GEO302 4.7 12.9 1.0 CE1 B:PHE137 4.7 14.8 1.0 CB B:ILE30 4.7 12.3 1.0 OE2 B:GLU53 4.7 17.2 1.0 CG2 B:ILE30 4.8 13.6 1.0 C4 B:GEO302 4.8 13.3 1.0 O B:HOH406 4.8 24.4 1.0 OE1 B:GLU53 4.9 19.6 1.0 CA B:ILE30 4.9 13.1 1.0 OH B:TYR86 5.0 16.8 1.0

Fluorine binding site 4 out of 4 in the C4S Dck Variant of Dck in Complex with Gemcitabine+Adp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of C4S Dck Variant of Dck in Complex with Gemcitabine+Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:F302 b:16.4 occ:1.00 F2 B:GEO302 0.0 16.4 1.0 C2' B:GEO302 1.3 15.2 1.0 F1 B:GEO302 2.2 18.9 1.0 C3' B:GEO302 2.3 16.2 1.0 C1' B:GEO302 2.3 13.9 1.0 O3' B:GEO302 2.6 18.3 1.0 OH B:TYR86 2.9 16.8 1.0 O B:HOH406 2.9 24.4 1.0 CD1 B:ILE30 3.1 14.2 1.0 N1 B:GEO302 3.1 12.9 1.0 O2 B:GEO302 3.3 15.0 1.0 CG1 B:ILE30 3.3 13.3 1.0 O4' B:GEO302 3.5 14.8 1.0 C4' B:GEO302 3.5 15.7 1.0 C2 B:GEO302 3.5 13.7 1.0 CE2 B:PHE137 3.7 16.6 1.0 C6 B:GEO302 4.1 14.5 1.0 CZ B:TYR86 4.1 17.3 1.0 CD2 B:PHE137 4.3 16.9 1.0 CZ B:PHE137 4.5 14.8 1.0 CG2 B:ILE30 4.5 13.6 1.0 CB B:ILE30 4.6 12.3 1.0 O5' B:GEO302 4.6 18.6 1.0 C5' B:GEO302 4.6 16.6 1.0 N3 B:GEO302 4.8 12.9 1.0 CE1 B:TYR86 4.8 15.6 1.0 OE2 B:GLU197 5.0 17.3 1.0

E.Sabini, S.Hazra, M.Konrad, A.Lavie. Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained By Structures of the Enzyme in Complex with L- and D-Nucleosides. J.Med.Chem. V. 50 3004 2007.
ISSN: ISSN 0022-2623
PubMed: 17530837
DOI: 10.1021/JM0700215