Silver 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:

Potassium

(K)

2 atoms

The binding sites of Silver 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 Silver atom.
In total 4 binding sites of Silver where determined in the Crystal Structure of Dna Duplex Containing 4-Thiothymine-2AG(I)-4- Thiothymine Base Pairs, PDB code: 5xuv:
Jump to Silver binding site number: 1; 2; 3; 4;

Silver binding site 1 out of 4 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 Silver with other atoms in the Ag 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:Ag101 b:33.6 occ:1.00 N3 B:8RO19 2.1 35.0 1.0 N3 A:8RO6 2.1 35.9 1.0 AG B:AG102 2.8 35.8 1.0 O2 A:8RO6 2.8 35.4 1.0 C2 A:8RO6 2.8 34.6 1.0 C2 B:8RO19 2.9 38.0 1.0 O2 B:8RO19 2.9 39.9 1.0 AG B:AG101 3.0 33.2 1.0 C4 B:8RO19 3.1 38.0 1.0 C4 A:8RO6 3.2 38.4 1.0 S4 B:8RO19 3.3 37.2 1.0 N1 A:DA5 3.5 36.4 1.0 S4 A:8RO6 3.5 34.6 1.0 C6 A:DA5 3.6 34.5 1.0 N6 A:DA5 3.6 37.0 1.0 N3 A:8RO7 3.8 31.0 1.0 N3 B:DT20 3.8 36.5 1.0 O2 A:8RO7 4.0 33.7 1.0 K A:K103 4.0 36.4 1.0 AG A:AG102 4.0 35.5 1.0 N3 B:8RO18 4.0 37.3 1.0 C2 A:8RO7 4.1 33.9 1.0 C2 A:DA5 4.2 37.1 1.0 N1 A:8RO6 4.2 33.6 1.0 N1 B:8RO19 4.2 38.1 1.0 C4 B:DT20 4.4 35.2 1.0 C5 B:8RO19 4.4 37.6 1.0 C2 B:DT20 4.4 39.1 1.0 O4 B:DT20 4.4 39.9 1.0 O2 B:DT20 4.4 38.7 1.0 C5 A:DA5 4.5 35.4 1.0 C5 A:8RO6 4.5 34.2 1.0 S4 B:8RO18 4.5 35.4 1.0 C4 B:8RO18 4.5 36.1 1.0 C4 A:8RO7 4.6 36.9 1.0 C2 B:8RO18 4.6 36.8 1.0 O2 B:8RO18 4.6 36.4 1.0 C6 B:8RO19 4.8 38.6 1.0 C6 A:8RO6 4.8 36.2 1.0 S4 A:8RO7 4.8 34.7 1.0 N3 A:DA5 4.9 36.5 1.0 C4 A:DA5 5.0 37.0 1.0

Silver binding site 2 out of 4 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 Silver with other atoms in the Ag 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:Ag102 b:35.5 occ:1.00 S4 B:8RO18 2.4 35.4 1.0 S4 A:8RO7 2.5 34.7 1.0 S4 A:8RO6 2.8 34.6 1.0 AG B:AG101 2.8 33.2 1.0 O B:HOH208 2.8 41.3 1.0 AG B:AG102 3.2 35.8 1.0 C4 A:8RO6 3.2 38.4 1.0 C4 B:8RO18 3.2 36.1 1.0 N6 B:DA17 3.3 31.5 1.0 C4 A:8RO7 3.3 36.9 1.0 N3 B:8RO18 3.4 37.3 1.0 N3 A:8RO7 3.5 31.0 1.0 N3 A:8RO6 3.6 35.9 1.0 C6 B:DA17 3.9 34.9 1.0 AG A:AG101 4.0 33.6 1.0 C5 A:8RO6 4.1 34.2 1.0 O B:HOH202 4.3 35.5 1.0 C5 B:DA17 4.5 33.6 1.0 C7 A:8RO6 4.6 37.9 1.0 N1 B:DA17 4.6 33.9 1.0 N7 B:DA17 4.6 35.6 1.0 C5 B:8RO18 4.7 36.7 1.0 C2 B:8RO18 4.7 36.8 1.0 C2 A:8RO6 4.7 34.6 1.0 C5 A:8RO7 4.7 36.5 1.0 C2 A:8RO7 4.8 33.9 1.0

Silver binding site 3 out of 4 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 Silver with other atoms in the Ag binding site number 3 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 B:Ag101 b:33.2 occ:1.00 N3 B:8RO18 2.2 37.3 1.0 N3 A:8RO7 2.2 31.0 1.0 AG A:AG102 2.8 35.5 1.0 O2 B:8RO18 2.8 36.4 1.0 C2 B:8RO18 2.9 36.8 1.0 O2 A:8RO7 2.9 33.7 1.0 C2 A:8RO7 3.0 33.9 1.0 AG A:AG101 3.0 33.6 1.0 C4 B:8RO18 3.2 36.1 1.0 C4 A:8RO7 3.2 36.9 1.0 N1 B:DA17 3.4 33.9 1.0 S4 A:8RO7 3.5 34.7 1.0 S4 B:8RO18 3.5 35.4 1.0 C6 B:DA17 3.6 34.9 1.0 N3 B:8RO19 3.6 35.0 1.0 N6 B:DA17 3.6 31.5 1.0 O2 B:8RO19 3.8 39.9 1.0 N3 A:8RO6 3.9 35.9 1.0 N3 A:DT8 3.9 33.2 1.0 C2 B:8RO19 3.9 38.0 1.0 AG B:AG102 3.9 35.8 1.0 K A:K104 4.0 37.0 1.0 C2 B:DA17 4.1 34.8 1.0 N1 B:8RO18 4.2 33.1 1.0 N1 A:8RO7 4.3 34.6 1.0 C4 B:8RO19 4.4 38.0 1.0 C5 B:DA17 4.4 33.6 1.0 C4 A:8RO6 4.4 38.4 1.0 O2 A:DT8 4.4 37.7 1.0 C2 A:8RO6 4.5 34.6 1.0 C2 A:DT8 4.5 37.4 1.0 S4 A:8RO6 4.5 34.6 1.0 C5 B:8RO18 4.5 36.7 1.0 C5 A:8RO7 4.5 36.5 1.0 O2 A:8RO6 4.5 35.4 1.0 C4 A:DT8 4.6 32.4 1.0 O4 A:DT8 4.6 35.5 1.0 S4 B:8RO19 4.7 37.2 1.0 C6 B:8RO18 4.8 33.6 1.0 N3 B:DA17 4.8 34.2 1.0 C6 A:8RO7 4.9 37.3 1.0 C4 B:DA17 4.9 33.3 1.0 N1 B:8RO19 5.0 38.1 1.0

Silver binding site 4 out of 4 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 Silver with other atoms in the Ag binding site number 4 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 B:Ag102 b:35.8 occ:1.00 S4 A:8RO6 2.4 34.6 1.0 S4 B:8RO19 2.4 37.2 1.0 S4 B:8RO18 2.7 35.4 1.0 AG A:AG101 2.8 33.6 1.0 AG A:AG102 3.2 35.5 1.0 C4 B:8RO18 3.2 36.1 1.0 C4 A:8RO6 3.2 38.4 1.0 C4 B:8RO19 3.2 38.0 1.0 N3 A:8RO6 3.3 35.9 1.0 N6 A:DA5 3.3 37.0 1.0 N3 B:8RO19 3.4 35.0 1.0 N3 B:8RO18 3.6 37.3 1.0 AG B:AG101 3.9 33.2 1.0 C6 A:DA5 4.0 34.5 1.0 C5 B:8RO18 4.1 36.7 1.0 O A:HOH209 4.3 41.1 1.0 C5 A:DA5 4.5 35.4 1.0 C7 B:8RO18 4.6 36.0 1.0 C5 A:8RO6 4.6 34.2 1.0 C5 B:8RO19 4.6 37.6 1.0 N7 A:DA5 4.7 35.0 1.0 C2 A:8RO6 4.7 34.6 1.0 N1 A:DA5 4.7 36.4 1.0 C2 B:8RO18 4.7 36.8 1.0 C2 B:8RO19 4.7 38.0 1.0 O4 B:DT20 5.0 39.9 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