Sodium in PDB 8ctz: 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H

All present enzymatic activity of 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H:
3.1.26.4;

The structure of 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H, PDB code: 8ctz was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.506, 66.492, 69.182, 90, 107.97, 90
R / Rfree (%)	19.5 / 26.5

The structure of 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H (pdb code 8ctz). 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 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H, PDB code: 8ctz:

Sodium binding site 1 out of 1 in the 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:56.0 occ:1.00 OE2 C:GLU188 2.3 30.0 0.0 OD1 C:ASP71 2.5 40.5 1.0 CD C:GLU188 3.2 30.0 0.0 OE1 C:GLU188 3.4 30.0 0.0 O C:VAL72 3.5 37.7 1.0 CG C:ASP71 3.6 41.8 1.0 OD2 C:ASP71 4.2 46.7 1.0 C C:VAL72 4.4 36.0 1.0 N C:VAL72 4.4 27.7 1.0 CG C:GLU188 4.6 30.0 0.0 CB C:ASP71 4.8 36.5 1.0 C C:ASP71 4.8 32.2 1.0 CA C:ASP71 4.8 35.3 1.0

A.H.Kellum Jr., P.S.Pallan, A.Nilforoushan, S.J.Sturla, M.P.Stone, M.Egli. Conformation and Pairing Properties of An O 6 -Methyl-2'-Deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex Dna. Chem.Res.Toxicol. V. 35 1903 2022.
ISSN: ISSN 0893-228X
PubMed: 35973057
DOI: 10.1021/ACS.CHEMRESTOX.2C00165