Potassium 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:

Sodium

(Na)

1 atom

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H, PDB code: 8ctz:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K205 b:68.3 occ:1.00 O C:TYR174 3.6 38.9 1.0 N C:TYR174 3.7 35.3 1.0 CA C:THR173 4.0 42.2 1.0 CD2 C:TYR174 4.2 28.0 1.0 CE2 C:TYR174 4.2 33.0 1.0 CB C:THR173 4.3 36.1 1.0 NZ C:LYS143 4.3 37.0 1.0 C C:THR173 4.4 36.5 1.0 CG C:TYR174 4.5 35.5 1.0 CZ C:TYR174 4.5 33.9 1.0 C C:TYR174 4.5 42.3 1.0 CA C:TYR174 4.6 40.3 1.0 CG2 C:THR173 4.6 41.0 1.0 CD1 C:TYR174 4.8 33.4 1.0 CE1 C:TYR174 4.8 33.1 1.0 O C:HIS172 4.9 37.0 1.0

Potassium binding site 2 out of 2 in the 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 12-Mer Dna Structure of Exbim & O6ME-G Bound to Rnase-H within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:59.8 occ:1.00 O B:HOH305 3.3 35.3 1.0 O2 D:DC11 3.4 44.7 1.0 N2 E:DG2 3.5 39.0 1.0 O4' D:DG12 3.9 55.0 1.0 OG1 B:THR135 3.9 35.3 1.0 OP1 D:DG12 4.1 39.1 1.0 C5' D:DG12 4.2 51.7 1.0 N2 D:DG10 4.4 41.3 1.0 OD1 B:ASN106 4.4 34.6 1.0 CB B:THR135 4.5 32.9 1.0 C4' D:DG12 4.5 56.8 1.0 O B:HOH309 4.6 51.5 1.0 O5' D:DG12 4.6 51.9 1.0 C2 D:DC11 4.7 41.1 1.0 O3' D:DC11 4.7 54.9 1.0 OG B:SER133 4.7 39.6 1.0 C2 E:DG2 4.8 35.4 1.0 P D:DG12 4.8 64.9 1.0 N B:THR135 4.8 35.8 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