Sodium in PDB 4hqx: Crystal Structure of Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4)

The structure of Crystal Structure of Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4), PDB code: 4hqx was solved by D.R.Davies, T.E.Edwards, N.Janjic, A.D.Gelinas, C.Zhang, T.C.Jarvis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.430, 59.430, 168.160, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.9

The structure of Crystal Structure of Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4) (pdb code 4hqx). 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 Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4), PDB code: 4hqx:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4)


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 Human Pdgf-Bb in Complex with A Modified Nucleotide Aptamer (Somamer SL4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:44.1 occ:1.00 O C:HOH211 2.3 44.2 1.0 O2 C:DC10 2.4 42.9 1.0 O6 C:DG22 2.4 39.2 1.0 O C:HOH210 2.6 52.9 1.0 O4' C:DC10 3.1 45.5 1.0 C1' C:DC10 3.4 46.3 1.0 C6 C:DG22 3.5 39.2 1.0 C2 C:DC10 3.5 45.0 1.0 N2 C:DG15 3.5 47.7 1.0 C4' C:DC10 3.8 42.9 1.0 N7 C:DG22 3.9 39.5 1.0 N1 C:DC10 4.0 44.6 1.0 N4 C:DC14 4.0 45.0 1.0 OP2 C:A2M21 4.0 38.5 1.0 C5 C:DG22 4.0 39.4 1.0 O C:HOH216 4.3 39.5 1.0 N7 C:A2M21 4.4 35.6 1.0 C8 C:A2M21 4.5 34.9 1.0 C2 C:DA9 4.6 40.2 1.0 N3 C:DA9 4.6 41.5 1.0 O3' C:DC10 4.6 43.5 1.0 O6 C:DG13 4.6 48.2 1.0 N3 C:DC10 4.6 45.6 1.0 N1 C:DG22 4.7 38.4 1.0 C3' C:DC10 4.7 43.2 1.0 C2' C:DC10 4.8 46.1 1.0 C2 C:DG15 4.8 46.6 1.0 C5' C:DC10 4.8 42.2 1.0

D.R.Davies, A.D.Gelinas, C.Zhang, J.C.Rohloff, J.D.Carter, D.O'connell, S.M.Waugh, S.K.Wolk, W.S.Mayfield, A.B.Burgin, T.E.Edwards, L.J.Stewart, L.Gold, N.Janjic, T.C.Jarvis. Unique Motifs and Hydrophobic Interactions Shape the Binding of Modified Dna Ligands to Protein Targets. Proc.Natl.Acad.Sci.Usa V. 109 19971 2012.
ISSN: ISSN 0027-8424
PubMed: 23139410
DOI: 10.1073/PNAS.1213933109