Potassium in PDB 5xuv: Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs

The structure of Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs, PDB code: 5xuv was solved by J.Kondo, T.Sugawara, H.Saneyoshi, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.22 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.213, 40.487, 66.432, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.2

The structure of Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs also contains other interesting chemical elements:

Silver

(Ag)

4 atoms

The binding sites of Potassium atom in the Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs (pdb code 5xuv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs, PDB code: 5xuv:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:36.4 occ:1.00 O2 A:8RO6 2.7 35.4 1.0 O2 B:8RO19 2.7 39.9 1.0 O B:HOH206 2.7 43.2 1.0 O2 B:DT20 2.9 38.7 1.0 O4' A:8RO7 3.1 35.9 1.0 O2 A:8RO7 3.2 33.7 1.0 C2 B:DT20 3.5 39.1 1.0 O4' B:DT20 3.6 43.3 1.0 C1' A:8RO7 3.6 37.4 1.0 C2 A:8RO7 3.7 33.9 1.0 O A:HOH214 3.8 40.0 1.0 C2 B:8RO19 3.8 38.0 1.0 C2 A:8RO6 3.8 34.6 1.0 N1 A:8RO7 3.9 34.6 1.0 AG A:AG101 4.0 33.6 1.0 C4' A:8RO7 4.0 39.0 1.0 N1 B:DT20 4.2 42.1 1.0 C1' B:DT20 4.2 42.3 1.0 N3 B:DT20 4.3 36.5 1.0 N3 B:8RO19 4.5 35.0 1.0 K A:K104 4.6 37.0 1.0 C4' B:DT20 4.6 47.3 1.0 N3 A:8RO7 4.6 31.0 1.0 N3 A:8RO6 4.7 35.9 1.0 C1' A:8RO6 4.7 37.1 1.0 N1 B:8RO19 4.8 38.1 1.0 N1 A:8RO6 4.8 33.6 1.0 C1' B:8RO19 4.8 41.8 1.0 C2 A:DA5 4.8 37.1 1.0 O A:HOH212 4.9 43.3 1.0 C5' A:8RO7 4.9 40.0 1.0 N1 A:DA5 4.9 36.4 1.0 C6 A:8RO7 5.0 37.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:37.0 occ:1.00 O A:HOH214 2.6 40.0 1.0 O2 A:DT8 2.7 37.7 1.0 O2 A:8RO7 2.7 33.7 1.0 O A:HOH204 2.7 41.6 1.0 O2 B:8RO18 2.8 36.4 1.0 O4' B:8RO19 3.2 34.8 1.0 O2 B:8RO19 3.3 39.9 1.0 C2 A:DT8 3.4 37.4 1.0 C1' B:8RO19 3.7 41.8 1.0 O4' A:DT8 3.7 40.9 1.0 C2 B:8RO19 3.8 38.0 1.0 C2 A:8RO7 3.8 33.9 1.0 AG B:AG101 4.0 33.2 1.0 C2 B:8RO18 4.0 36.8 1.0 C4' B:8RO19 4.0 41.2 1.0 N1 B:8RO19 4.0 38.1 1.0 N1 A:DT8 4.1 40.4 1.0 C1' A:DT8 4.1 41.5 1.0 N3 A:DT8 4.1 33.2 1.0 K A:K103 4.6 36.4 1.0 N3 A:8RO7 4.6 31.0 1.0 C2 B:DA17 4.6 34.8 1.0 N3 B:8RO19 4.7 35.0 1.0 N1 A:8RO7 4.8 34.6 1.0 N3 B:8RO18 4.8 37.3 1.0 C1' A:8RO7 4.8 37.4 1.0 C4' A:DT8 4.8 43.6 1.0 N1 B:DA17 4.8 33.9 1.0 C5' B:8RO19 4.9 40.7 1.0 C1' B:8RO18 4.9 37.2 1.0 N1 B:8RO18 5.0 33.1 1.0

J.Kondo, T.Sugawara, H.Saneyoshi, A.Ono. Crystal Structure of A Dna Duplex Containing Four Ag(I) Ions in Consecutive Dinuclear Ag(I)-Mediated Base Pairs: 4-Thiothymine-2AG(I)-4-Thiothymine Chem. Commun. (Camb.) V. 53 11747 2017.
ISSN: ESSN 1364-548X
PubMed: 28991300
DOI: 10.1039/C7CC06153F