Sodium in PDB 5hnj: Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex

The structure of Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex, PDB code: 5hnj was solved by Z.P.Luo, J.Sheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.20 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.692, 45.923, 45.406, 90.00, 100.85, 90.00
R / Rfree (%)	13.4 / 15.5

The binding sites of Sodium atom in the Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex (pdb code 5hnj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex, PDB code: 5hnj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:17.7 occ:0.90 O D:HOH142 2.1 23.2 1.0 O C:HOH117 2.1 20.0 1.0 O C:HOH115 2.1 19.1 1.0 O A:HOH236 2.1 18.3 1.0 O C:HOH139 2.1 25.7 1.0 O C:HOH112 2.1 26.1 1.0 O C:HOH137 4.1 32.2 1.0 O A:HOH238 4.2 31.5 1.0 N4 A:C8 4.2 12.6 1.0 N7 C:G1 4.2 14.1 1.0 O A:HOH239 4.2 30.3 1.0 O4 C:U2 4.3 16.8 1.0 O A:HOH234 4.3 23.1 1.0 O C:HOH133 4.3 37.3 1.0 O6 C:G1 4.4 13.7 1.0 O A:HOH225 4.5 19.1 1.0 O A:HOH217 4.5 21.8 1.0 C5 A:C8 4.8 12.9 1.0 C4 A:C8 4.9 12.1 1.0 N6 D:A7 5.0 17.9 1.0

Sodium binding site 2 out of 2 in the Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Base Pairing and Structure Insights Into the 5-Formylcytosine in Rna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:23.5 occ:0.90 O B:HOH211 2.1 20.2 1.0 O B:HOH205 2.1 18.6 1.0 O A:HOH241 2.2 36.4 1.0 O B:HOH215 2.2 24.8 1.0 O A:HOH235 2.3 37.8 1.0 O D:HOH135 2.4 28.5 1.0 N4 D:C8 4.0 16.2 1.0 O A:HOH210 4.1 23.9 1.0 O A:HOH229 4.2 24.1 1.0 O A:HOH238 4.2 31.5 1.0 O D:HOH129 4.2 33.3 1.0 O4 B:U2 4.2 15.7 1.0 O6 B:G1 4.3 13.6 1.0 N7 B:G1 4.4 14.9 1.0 C5 D:C8 4.6 17.4 1.0 C4 D:C8 4.6 14.1 1.0 O D:HOH124 4.7 32.0 1.0

R.Wang, Z.Luo, K.He, M.O.Delaney, D.Chen, J.Sheng. Base Pairing and Structural Insights Into the 5-Formylcytosine in Rna Duplex. Nucleic Acids Res. V. 44 4968 2016.
ISSN: ESSN 1362-4962
PubMed: 27079978
DOI: 10.1093/NAR/GKW235