Sodium 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:

Fluorine

(F)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Vccnt-7C8C Bound to Gemcitabine, PDB code: 4pd5:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na502 b:70.1 occ:1.00 O A:HOH603 2.4 47.3 1.0 OG A:SER183 2.4 64.1 1.0 O A:VAL152 2.4 61.1 1.0 OD1 A:ASN149 2.5 59.0 1.0 O A:ASN149 2.5 59.6 1.0 O A:ILE184 2.5 60.0 1.0 CG A:ASN149 3.2 60.5 1.0 C A:ASN149 3.2 56.4 1.0 CB A:ASN149 3.3 57.7 1.0 CA A:ASN149 3.3 57.5 1.0 CB A:SER183 3.4 61.5 1.0 C A:ILE184 3.6 58.0 1.0 C A:VAL152 3.6 57.7 1.0 N A:ILE184 3.8 60.9 1.0 C A:GLY153 3.8 52.7 1.0 CA A:GLY153 3.9 50.1 1.0 C A:SER183 3.9 60.7 1.0 O A:GLY153 4.1 55.3 1.0 CA A:ILE184 4.2 59.2 1.0 N A:GLN154 4.2 52.9 1.0 N A:GLY153 4.2 54.5 1.0 CA A:SER183 4.2 61.0 1.0 CA A:GLY180 4.3 53.3 1.0 O A:GLY179 4.3 69.2 1.0 O A:GLY180 4.4 58.3 1.0 O A:SER183 4.4 58.3 1.0 ND2 A:ASN149 4.5 56.1 1.0 N A:ILE150 4.5 71.2 1.0 N A:ALA185 4.6 60.8 1.0 N A:ASN149 4.7 62.9 1.0 CA A:GLN154 4.8 56.2 1.0 C A:GLY180 4.8 53.6 1.0 CA A:VAL152 4.8 56.0 1.0 N A:VAL152 4.8 59.4 1.0 N A:SER183 4.9 64.0 1.0 CA A:ALA185 5.0 62.7 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