Silver in PDB 5ix7: Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array

The structure of Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array, PDB code: 5ix7 was solved by J.Kondo, Y.Tada, T.Dairaku, Y.Hattori, H.Saneyoshi, A.Ono, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.11 / 1.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	30.150, 30.150, 118.420, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 18.9

The structure of Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Bromine	(Br)	1 atom

The binding sites of Silver atom in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array (pdb code 5ix7). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 6 binding sites of Silver where determined in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array, PDB code: 5ix7:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6;

Silver binding site 1 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


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 Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:13.9 occ:0.50 N7 A:DG7 2.3 12.4 1.0 AG A:AG102 3.2 11.4 1.0 C5 A:DG7 3.3 16.9 1.0 O2 A:DC9 3.3 10.0 1.0 O6 A:DG7 3.3 12.3 1.0 C8 A:DG7 3.4 15.5 1.0 O A:HOH237 3.5 26.3 0.2 H8 A:DG7 3.5 18.6 1.0 C6 A:DG7 3.6 16.1 1.0 C2 A:DC9 3.7 12.0 1.0 N3 A:DC9 3.8 12.4 1.0 N3 A:CBR6 3.9 9.5 1.0 H42 A:CBR6 4.0 6.3 1.0 C4 A:DG7 4.5 14.8 1.0 N9 A:DG7 4.5 14.6 1.0 O2 A:CBR6 4.5 13.8 1.0 N4 A:CBR6 4.6 5.3 1.0 C2 A:CBR6 4.6 15.1 1.0 C4 A:CBR6 4.6 9.2 1.0 O A:HOH248 4.6 18.5 0.2 H1' A:DC9 4.6 21.8 1.0 K A:K107 4.6 12.8 1.0 N1 A:DC9 4.7 13.8 1.0 C4 A:DC9 4.8 13.0 1.0

Silver binding site 2 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


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 Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:11.4 occ:1.00 N3 A:CBR6 2.2 9.5 1.0 H42 A:CBR6 2.7 6.3 1.0 C2 A:CBR6 3.0 15.1 1.0 O2 A:CBR6 3.0 13.8 1.0 C4 A:CBR6 3.1 9.2 1.0 AG A:AG103 3.1 11.3 1.0 AG A:AG101 3.2 13.9 0.5 N4 A:CBR6 3.3 5.3 1.0 O4 A:DT5 3.6 13.8 1.0 N3 A:DT5 3.7 14.7 1.0 C4 A:DT5 3.8 12.1 1.0 K A:K107 4.0 12.8 1.0 N7 A:DG7 4.1 12.4 1.0 H41 A:CBR6 4.2 6.3 1.0 N1 A:CBR6 4.3 18.2 1.0 O6 A:DG7 4.3 12.3 1.0 C5 A:CBR6 4.5 15.3 1.0 C2 A:DT5 4.5 13.8 1.0 C5 A:DG7 4.6 16.9 1.0 C6 A:DG7 4.7 16.1 1.0 C5 A:DT5 4.8 14.1 1.0 C6 A:CBR6 4.9 18.2 1.0 O2 A:DT5 4.9 15.3 1.0 C8 A:DG7 4.9 15.5 1.0

Silver binding site 3 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


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 Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:11.3 occ:1.00 N3 A:DT5 2.2 14.7 1.0 C2 A:DT5 3.0 13.8 1.0 O2 A:DT5 3.0 15.3 1.0 H42 A:DC4 3.1 15.0 1.0 AG A:AG102 3.1 11.4 1.0 C4 A:DT5 3.1 12.1 1.0 AG A:AG104 3.2 14.7 1.0 O4 A:DT5 3.2 13.8 1.0 N3 A:DC4 3.6 13.6 1.0 N4 A:DC4 3.7 12.5 1.0 C4 A:DC4 4.0 16.1 1.0 N3 A:CBR6 4.1 9.5 1.0 O2 A:CBR6 4.2 13.8 1.0 N1 A:DT5 4.3 13.8 1.0 C2 A:CBR6 4.3 15.1 1.0 H41 A:DC4 4.4 15.0 1.0 C5 A:DT5 4.5 14.1 1.0 C2 A:DC4 4.5 14.7 1.0 O2 A:DC4 4.8 16.9 1.0 H42 A:CBR6 4.8 6.3 1.0 C6 A:DT5 4.8 17.2 1.0 C4 A:CBR6 4.8 9.2 1.0 K A:K108 4.9 32.6 1.0

Silver binding site 4 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


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 Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:14.7 occ:1.00 N3 A:DC4 2.4 13.6 1.0 H42 A:DC4 2.9 15.0 1.0 O2 A:DC4 3.1 16.9 1.0 C2 A:DC4 3.1 14.7 1.0 O6 A:DG2 3.1 15.9 1.0 N1 A:DG2 3.1 14.6 1.0 AG A:AG103 3.2 11.3 1.0 C6 A:DG2 3.3 14.9 1.0 C4 A:DC4 3.3 16.1 1.0 AG A:AG105 3.4 16.4 1.0 N4 A:DC4 3.5 12.5 1.0 K A:K108 3.8 32.6 1.0 N3 A:DT5 4.0 14.7 1.0 O2 A:DT5 4.0 15.3 1.0 C2 A:DG2 4.1 14.3 1.0 H22 A:DG2 4.2 17.0 1.0 C2 A:DT5 4.3 13.8 1.0 C5 A:DG2 4.4 17.9 1.0 N1 A:DC4 4.4 13.3 1.0 H41 A:DC4 4.4 15.0 1.0 N2 A:DG2 4.5 14.2 1.0 C5 A:DC4 4.7 16.4 1.0 C4 A:DT5 4.8 12.1 1.0 O4 A:DT5 5.0 13.8 1.0 N3 A:DG2 5.0 13.7 1.0

Silver binding site 5 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:16.4 occ:1.00 N1 A:DG2 2.2 14.6 1.0 H22 A:DG2 2.5 17.0 1.0 O6 A:DG1 2.8 17.8 1.0 C2 A:DG2 3.1 14.3 1.0 N2 A:DG2 3.1 14.2 1.0 C6 A:DG2 3.1 14.9 1.0 AG A:AG106 3.2 18.1 0.5 O6 A:DG2 3.2 15.9 1.0 AG A:AG104 3.4 14.7 1.0 C6 A:DG1 3.5 16.1 1.0 N7 A:DG1 3.8 13.3 1.0 C5 A:DG1 3.9 15.5 1.0 H21 A:DG2 4.1 17.0 1.0 N3 A:DG2 4.4 13.7 1.0 C5 A:DG2 4.4 17.9 1.0 N1 A:DG1 4.6 18.5 1.0 O2 A:DC4 4.6 16.9 1.0 H1 A:DG1 4.8 22.1 1.0 C4 A:DG2 4.8 18.1 1.0 N3 A:DC4 4.8 13.6 1.0 C8 A:DG1 4.9 15.8 1.0 C2 A:DC4 5.0 14.7 1.0

Silver binding site 6 out of 6 in the Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Crystal Structure of Metallo-Dna Nanowire with Infinite One- Dimensional Silver Array within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:18.1 occ:0.50 N7 A:DG1 2.3 13.3 1.0 O A:HOH239 2.8 35.4 0.5 AG A:AG105 3.2 16.4 1.0 C8 A:DG1 3.2 15.8 1.0 C5 A:DG1 3.3 15.5 1.0 H8 A:DG1 3.4 19.0 1.0 H22 A:DG2 3.4 17.0 1.0 O6 A:DG1 3.5 17.8 1.0 N2 A:DG2 3.5 14.2 1.0 C6 A:DG1 3.8 16.1 1.0 C2 A:DG2 3.8 14.3 1.0 N1 A:DG2 3.8 14.6 1.0 H21 A:DG2 4.0 17.0 1.0 N9 A:DG1 4.4 20.4 1.0 C4 A:DG1 4.5 18.6 1.0 N3 A:DG2 4.5 13.7 1.0 C6 A:DG2 4.7 14.9 1.0

J.Kondo, Y.Tada, T.Dairaku, Y.Hattori, H.Saneyoshi, A.Ono, Y.Tanaka. A Metallo-Dna Nanowire with Uninterrupted One-Dimensional Silver Array Nat Chem V. 9 956 2017.
ISSN: ESSN 1755-4349
PubMed: 28937663
DOI: 10.1038/NCHEM.2808