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Sodium in PDB 4pda: Structure of Vccnt-7C8C Bound to Cytidine

Protein crystallography data

The structure of Structure of Vccnt-7C8C Bound to Cytidine, PDB code: 4pda 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) 48.52 / 2.61
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 120.017, 120.017, 82.465, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 23.9

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 4pda

Go back to Sodium Binding Sites List in 4pda
Sodium binding site 1 out of 1 in the Structure of Vccnt-7C8C Bound to Cytidine


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 Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:48.6
occ:1.00
O A:HOH625 2.4 40.1 1.0
O A:ILE184 2.4 45.5 1.0
O A:VAL152 2.4 47.6 1.0
OG A:SER183 2.4 45.4 1.0
O A:ASN149 2.5 43.3 1.0
OD1 A:ASN149 2.5 42.7 1.0
C A:ASN149 3.3 40.1 1.0
CG A:ASN149 3.3 44.2 1.0
CA A:ASN149 3.4 41.2 1.0
CB A:SER183 3.4 42.8 1.0
CB A:ASN149 3.4 41.3 1.0
C A:VAL152 3.6 44.1 1.0
C A:ILE184 3.6 43.5 1.0
C A:GLY153 3.8 45.0 1.0
CA A:GLY153 3.8 42.5 1.0
N A:ILE184 3.9 46.4 1.0
C A:SER183 4.0 42.0 1.0
N A:GLN154 4.1 41.9 1.0
N A:GLY153 4.1 46.8 1.0
O A:GLY153 4.2 47.6 1.0
CA A:ILE184 4.2 44.7 1.0
CA A:SER183 4.3 42.2 1.0
O A:GLY180 4.4 45.6 1.0
O A:SER183 4.5 39.5 1.0
O A:GLY179 4.5 48.1 1.0
CA A:GLY180 4.5 40.6 1.0
N A:ILE150 4.5 48.8 1.0
ND2 A:ASN149 4.6 39.8 1.0
N A:ALA185 4.6 44.0 1.0
CA A:GLN154 4.8 45.2 1.0
N A:ASN149 4.8 46.6 1.0
CA A:VAL152 4.8 42.5 1.0
N A:VAL152 4.8 45.9 1.0
CA A:ALA185 4.9 45.9 1.0
C A:GLY180 4.9 41.0 1.0

Reference:

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
Page generated: Tue Dec 15 06:58:05 2020

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