Sodium in PDB 6ycs: Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide

The structure of Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide, PDB code: 6ycs was solved by M.Hyjek-Skladanowska, T.A.Vickers, A.Napiorkowska, B.Anderson, M.Tanowitz, S.T.Crooke, X.Liang, P.P.Seth, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.68 / 3.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.143, 102.143, 83.813, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 31.8

The binding sites of Sodium atom in the Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide (pdb code 6ycs). 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 Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide, PDB code: 6ycs:

Sodium binding site 1 out of 1 in the Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Transcription Cofactor PC4 Dna-Binding Domain in Complex with Full Phosphorothioate 5-10-5 2'-O-Methyl Dna Gapmer Antisense Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:57.5 occ:1.00 O5' E:GS14 3.3 85.1 0.5 C5' E:GS13 3.5 81.3 0.5 C3' E:GS13 3.6 84.0 0.5 C5' E:GS13 3.6 81.3 0.5 CA A:ARG100 3.7 72.2 0.7 CA A:ARG100 3.7 72.2 0.3 O B:HOH202 3.7 62.9 1.0 O5' E:GS14 3.7 85.1 0.5 O3' E:GS13 3.7 84.7 0.5 C4' E:GS13 3.7 82.8 0.5 CB A:ARG100 3.8 75.1 0.7 C3' E:GS13 3.8 84.0 0.5 C4' E:GS13 3.8 82.8 0.5 O5' F:OKQ1 3.8 74.0 1.0 OP1 E:GS14 3.8 85.0 0.5 CB A:ARG100 3.8 75.2 0.3 P E:GS14 4.0 85.0 0.5 N A:ARG100 4.1 70.9 1.0 O3' E:GS13 4.2 84.7 0.5 S2P E:GS14 4.2 85.2 0.5 C5' E:GS14 4.2 85.3 0.5 C5' F:OKQ1 4.2 72.9 1.0 C5' E:GS14 4.2 85.3 0.5 S2P E:GS13 4.3 77.6 0.5 P E:GS14 4.3 85.0 0.5 O A:GLY99 4.4 67.2 1.0 OP1 E:GS13 4.4 77.8 0.5 O5' E:GS13 4.4 79.8 0.5 C A:GLY99 4.4 67.5 1.0 O A:HOH302 4.4 69.6 1.0 O5' E:GS13 4.6 79.8 0.5 C4' E:GS14 4.6 85.8 0.5 C4' E:GS14 4.7 85.8 0.5 C6 F:OKQ1 4.7 68.4 1.0 P E:GS13 4.8 78.3 0.5 C A:ARG100 4.9 71.3 1.0 C5 F:OKQ1 4.9 68.8 1.0 P E:GS13 5.0 78.3 0.5

M.Hyjek-Skladanowska, T.A.Vickers, A.Napiorkowska, B.A.Anderson, M.Tanowitz, S.T.Crooke, X.H.Liang, P.P.Seth, M.Nowotny. Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids For Proteins. J.Am.Chem.Soc. V. 142 7456 2020.
ISSN: ESSN 1520-5126
PubMed: 32202774
DOI: 10.1021/JACS.9B13524