Fluorine in PDB 4pd5: Crystal Structure of Vccnt-7C8C Bound to Gemcitabine

The structure of Crystal Structure of Vccnt-7C8C Bound to Gemcitabine, PDB code: 4pd5 was solved by Z.L.Johnson, S.-Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 2.91
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	119.046, 119.046, 82.285, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 25.8

The structure of Crystal Structure of Vccnt-7C8C Bound to Gemcitabine also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Vccnt-7C8C Bound to Gemcitabine (pdb code 4pd5). 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 Vccnt-7C8C Bound to Gemcitabine, PDB code: 4pd5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Vccnt-7C8C Bound to Gemcitabine


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 Vccnt-7C8C Bound to Gemcitabine within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:59.6 occ:1.00 F1 A:GEO501 0.0 59.6 1.0 C2' A:GEO501 1.3 59.6 1.0 F2 A:GEO501 2.2 59.6 1.0 C3' A:GEO501 2.4 59.6 1.0 C1' A:GEO501 2.4 59.6 1.0 N1 A:GEO501 2.6 59.6 1.0 O2 A:GEO501 2.9 59.6 1.0 C2 A:GEO501 2.9 59.6 1.0 CG A:PHE366 3.0 64.9 1.0 O3' A:GEO501 3.1 59.6 1.0 CD2 A:PHE366 3.1 58.9 1.0 NE2 A:GLN154 3.1 56.2 1.0 CB A:PHE366 3.3 64.6 1.0 CD1 A:PHE366 3.4 63.1 1.0 O4' A:GEO501 3.5 59.6 1.0 C4' A:GEO501 3.5 59.6 1.0 C6 A:GEO501 3.5 59.6 1.0 CE2 A:PHE366 3.7 60.9 1.0 N3 A:GEO501 3.9 59.6 1.0 CE1 A:PHE366 4.0 61.5 1.0 CZ A:PHE366 4.1 62.2 1.0 OG A:SER371 4.1 88.2 1.0 CD A:GLN154 4.2 57.9 1.0 CA A:PHE366 4.3 61.5 1.0 C5 A:GEO501 4.4 59.6 1.0 CD1 A:ILE374 4.5 65.6 1.0 O A:PHE366 4.5 66.3 1.0 C4 A:GEO501 4.5 59.6 1.0 O5' A:GEO501 4.6 59.6 1.0 C5' A:GEO501 4.7 59.6 1.0 CG A:GLN154 4.8 49.9 1.0 C A:PHE366 4.9 67.0 1.0 ND2 A:ASN368 5.0 71.5 1.0 OE1 A:GLN154 5.0 57.5 1.0 OE1 A:GLU332 5.0 63.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Vccnt-7C8C Bound to Gemcitabine


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 Vccnt-7C8C Bound to Gemcitabine within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:59.6 occ:1.00 F2 A:GEO501 0.0 59.6 1.0 C2' A:GEO501 1.3 59.6 1.0 F1 A:GEO501 2.2 59.6 1.0 C3' A:GEO501 2.4 59.6 1.0 C1' A:GEO501 2.4 59.6 1.0 O3' A:GEO501 2.6 59.6 1.0 C4' A:GEO501 2.9 59.6 1.0 O4' A:GEO501 3.1 59.6 1.0 CD1 A:ILE374 3.2 65.6 1.0 OG A:SER371 3.4 88.2 1.0 N1 A:GEO501 3.6 59.6 1.0 O2 A:GEO501 3.8 59.6 1.0 ND2 A:ASN368 4.0 71.5 1.0 NE2 A:GLN154 4.0 56.2 1.0 C2 A:GEO501 4.1 59.6 1.0 OD1 A:ASN368 4.3 76.4 1.0 C5' A:GEO501 4.4 59.6 1.0 CB A:SER371 4.5 89.0 1.0 C6 A:GEO501 4.6 59.6 1.0 CG A:ASN368 4.6 75.7 1.0 CG1 A:ILE374 4.7 61.1 1.0 O A:PHE366 4.7 66.3 1.0 CA A:SER371 4.8 88.6 1.0 CB A:PHE366 4.8 64.6 1.0 CG A:PHE366 4.9 64.9 1.0 O5' A:GEO501 5.0 59.6 1.0

Z.L.Johnson, J.H.Lee, K.Lee, M.Lee, D.Y.Kwon, J.Hong, S.Y.Lee. Structural Basis of Nucleoside and Nucleoside Drug Selectivity By Concentrative Nucleoside Transporters. Elife V. 3 03604 2014.
ISSN: ESSN 2050-084X
PubMed: 25082345
DOI: 10.7554/ELIFE.03604