Sodium in PDB 4pd9: Structure of Vccnt-7C8C Bound to Adenosine

The structure of Structure of Vccnt-7C8C Bound to Adenosine, PDB code: 4pd9 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)	48.72 / 3.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	120.001, 120.001, 83.488, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.9

The binding sites of Sodium atom in the Structure of Vccnt-7C8C Bound to Adenosine (pdb code 4pd9). 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-7C8C Bound to Adenosine, PDB code: 4pd9:

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


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-7C8C Bound to Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:71.0 occ:1.00 O A:HOH603 2.4 41.2 1.0 OG A:SER183 2.4 61.0 1.0 O A:ASN149 2.5 63.0 1.0 O A:ILE184 2.5 58.0 1.0 OD1 A:ASN149 2.5 62.4 1.0 O A:VAL152 2.5 71.8 1.0 CG A:ASN149 3.2 63.9 1.0 C A:ASN149 3.2 59.9 1.0 CA A:ASN149 3.3 61.0 1.0 CB A:ASN149 3.3 61.1 1.0 CB A:SER183 3.3 58.3 1.0 C A:ILE184 3.6 56.1 1.0 C A:VAL152 3.6 68.3 1.0 N A:ILE184 3.8 59.0 1.0 C A:GLY153 3.8 66.6 1.0 C A:SER183 3.9 57.6 1.0 O A:GLY153 3.9 69.2 1.0 CA A:GLY153 4.0 64.0 1.0 CA A:ILE184 4.2 57.3 1.0 N A:GLN154 4.2 58.9 1.0 CA A:SER183 4.2 57.8 1.0 N A:GLY153 4.3 68.4 1.0 CA A:GLY180 4.4 49.7 1.0 O A:SER183 4.4 55.1 1.0 O A:GLY179 4.4 64.0 1.0 O A:GLY180 4.5 54.7 1.0 ND2 A:ASN149 4.5 59.5 1.0 N A:ILE150 4.5 64.3 1.0 N A:ALA185 4.7 54.3 1.0 N A:ASN149 4.7 66.3 1.0 CA A:GLN154 4.7 62.3 1.0 N A:VAL152 4.8 70.1 1.0 CA A:VAL152 4.9 66.7 1.0 C A:GLY180 4.9 50.1 1.0 CA A:ALA185 5.0 56.1 1.0 N A:SER183 5.0 60.8 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