Sodium in PDB 8cty: 12-Mer Dna Structure of Exbim Bound to Rnase-H

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

The structure of 12-Mer Dna Structure of Exbim Bound to Rnase-H, PDB code: 8cty 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)	32.73 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.976, 65.834, 95.723, 84.54, 88.2, 62.49
R / Rfree (%)	19.6 / 26.1

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

Chlorine

(Cl)

1 atom

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

Sodium binding site 1 out of 1 in the 12-Mer Dna Structure of Exbim 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 Bound to Rnase-H within 5.0Å range: probe atom residue distance (Å) B Occ F:Na201 b:42.6 occ:1.00 OE2 F:GLU109 2.2 44.2 1.0 OD1 F:ASP71 2.2 33.8 1.0 OD1 F:ASN132 2.4 40.0 1.0 O3' M:DG12 2.4 45.0 1.0 O F:HOH309 2.6 32.0 1.0 CD F:GLU109 3.2 39.5 1.0 CG F:ASP71 3.2 38.7 1.0 CG F:ASN132 3.4 37.9 1.0 C3' M:DG12 3.4 43.3 1.0 OE1 F:GLU109 3.5 37.9 1.0 O F:HOH306 3.6 37.1 1.0 ND2 F:ASN132 3.7 38.8 1.0 OD2 F:ASP71 3.9 43.2 1.0 C4' M:DG12 4.1 46.2 1.0 CA F:ASP71 4.2 35.8 1.0 CB F:ASP71 4.2 37.2 1.0 N F:VAL72 4.2 35.9 1.0 CG F:GLU109 4.5 38.0 1.0 N F:ASN132 4.6 29.6 1.0 CB F:ASN132 4.7 38.6 1.0 C2' M:DG12 4.7 41.3 1.0 O F:VAL70 4.7 31.1 1.0 N F:SER133 4.8 32.6 1.0 C5' M:DG12 4.8 45.0 1.0 C F:ASP71 4.8 36.9 1.0 C F:ASN132 4.9 31.8 1.0 CA F:ASN132 4.9 33.1 1.0 CB F:SER133 5.0 30.8 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