Atomistry » Sodium » PDB 4owe-4pd7 » 4pd5
Atomistry »
  Sodium »
    PDB 4owe-4pd7 »
      4pd5 »

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

Protein crystallography data

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

Other elements in 4pd5:

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

Fluorine (F) 2 atoms

Sodium Binding Sites:

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 4pd5

Go back to Sodium Binding Sites List in 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

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: Mon Oct 7 17:40:54 2024

Last articles

Mn in 8XK0
Mn in 8XHV
Mn in 8XJW
Mn in 8XJX
Mn in 8VUK
Mn in 8RE9
Mn in 8RE6
Mn in 8RE7
Mn in 8RE8
Mn in 8RE5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy