Sodium in PDB 4pd7: Structure of Vccnt Bound to Zebularine

The structure of Structure of Vccnt Bound to Zebularine, PDB code: 4pd7 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)	39.22 / 2.91
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	119.811, 119.811, 82.658, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 24.7

The binding sites of Sodium atom in the Structure of Vccnt Bound to Zebularine (pdb code 4pd7). 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 Structure of Vccnt Bound to Zebularine, PDB code: 4pd7:

Sodium binding site 1 out of 1 in the Structure of Vccnt Bound to Zebularine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vccnt Bound to Zebularine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:47.6 occ:1.00 O A:HOH603 2.4 27.2 1.0 O A:ILE184 2.4 24.9 1.0 O A:VAL152 2.4 34.7 1.0 OG A:SER183 2.4 34.2 1.0 OD1 A:ASN149 2.4 36.8 1.0 O A:ASN149 2.4 37.4 1.0 CG A:ASN149 3.2 38.3 1.0 C A:ASN149 3.2 34.2 1.0 CB A:SER183 3.3 31.6 1.0 CA A:ASN149 3.3 35.4 1.0 CB A:ASN149 3.4 35.5 1.0 C A:ILE184 3.6 25.2 1.0 C A:VAL152 3.6 31.2 1.0 N A:ILE184 3.9 25.8 1.0 CA A:GLY153 3.9 26.9 1.0 C A:GLY153 3.9 29.5 1.0 C A:SER183 4.0 30.8 1.0 N A:GLN154 4.2 25.5 1.0 N A:GLY153 4.2 31.3 1.0 CA A:ILE184 4.3 24.1 1.0 CA A:SER183 4.3 31.0 1.0 O A:GLY153 4.3 32.0 1.0 O A:GLY180 4.4 36.8 1.0 ND2 A:ASN149 4.5 33.9 1.0 O A:SER183 4.5 28.3 1.0 O A:GLY179 4.5 33.1 1.0 N A:ILE150 4.5 36.1 1.0 CA A:GLY180 4.6 31.8 1.0 N A:ALA185 4.6 31.4 1.0 N A:ASN149 4.8 40.7 1.0 N A:VAL152 4.8 32.9 1.0 CA A:GLN154 4.8 28.9 1.0 CA A:VAL152 4.8 29.5 1.0 CA A:ALA185 4.9 33.2 1.0 C A:GLY180 4.9 32.1 1.0 N A:SER183 5.0 34.0 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