Silver in PDB 9khw: A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm

The structure of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm, PDB code: 9khw was solved by H.Kanazawa, J.Kondo, G.Romolini, C.Cerretani, A.Lanza, Z.Huang, T.Vosch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.82 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.215, 53.171, 27.215, 90, 103.67, 90
R / Rfree (%)	16.3 / 16.4

The structure of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Silver atom in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm (pdb code 9khw). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 28 binding sites of Silver where determined in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm, PDB code: 9khw:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:9.1 occ:0.95 N7 A:DG3 2.3 11.3 1.0 N7 A:DG12 2.4 11.7 1.0 AG A:AG103 2.8 9.9 1.0 AG A:AG104 2.8 8.6 1.0 AG A:AG102 2.8 9.1 1.0 O6 A:DG12 2.8 12.2 1.0 AG A:AG105 2.9 8.7 1.0 C5 A:DG12 3.1 12.0 1.0 O6 A:DG3 3.1 9.5 1.0 C5 A:DG3 3.2 9.2 1.0 O2 A:DC4 3.2 9.2 1.0 C6 A:DG12 3.2 12.3 1.0 C8 A:DG3 3.4 9.3 1.0 C6 A:DG3 3.5 10.2 1.0 C2 A:DC4 3.5 8.0 1.0 N3 A:DC4 3.5 9.0 1.0 C8 A:DG12 3.6 14.1 1.0 O2 A:DC2 3.7 13.3 1.0 N3 A:DC11 4.0 8.6 1.0 AG A:AG106 4.1 8.5 1.0 O2 A:DC11 4.1 10.9 1.0 C2 A:DC2 4.2 9.2 1.0 N3 A:DC2 4.3 11.4 1.0 C2 A:DC11 4.4 10.0 1.0 C4 A:DG12 4.4 12.7 1.0 C4 A:DG3 4.4 10.4 1.0 C4 A:DC4 4.5 7.6 1.0 O2 A:DC13 4.5 8.7 1.0 N1 A:DC4 4.5 8.7 1.0 N9 A:DG3 4.6 9.3 1.0 N1 A:DG12 4.6 12.9 1.0 N9 A:DG12 4.6 15.8 1.0 N3 A:DC13 4.8 11.1 1.0 N1 A:DG3 4.9 10.0 1.0 AG A:AG107 4.9 8.8 0.9 C4 A:DC11 4.9 11.2 1.0

Silver binding site 2 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:9.1 occ:0.96 N3 A:DC2 2.3 11.4 1.0 O2 A:DC13 2.6 8.7 1.0 AG A:AG103 2.7 9.9 1.0 AG A:AG101 2.8 9.1 0.9 AG A:AG106 2.8 8.5 1.0 AG A:AG105 2.8 8.7 1.0 AG A:AG107 2.9 8.8 0.9 C2 A:DC2 3.0 9.2 1.0 O6 A:DG3 3.0 9.5 1.0 O2 A:DC2 3.1 13.3 1.0 C4 A:DC2 3.2 6.9 1.0 N1 A:DG14 3.3 10.6 1.0 O6 A:DG14 3.3 9.2 1.0 N4 A:DC2 3.4 13.0 1.0 C2 A:DC13 3.5 12.0 1.0 C6 A:DG14 3.5 12.8 1.0 N3 A:DC13 3.7 11.1 1.0 AG A:AG104 3.9 8.6 1.0 C6 A:DG3 3.9 10.2 1.0 N7 A:DG12 4.1 11.7 1.0 C2 A:DG14 4.2 10.9 1.0 N7 A:DG3 4.2 11.3 1.0 N1 A:DC2 4.3 11.4 1.0 C5 A:DG3 4.4 9.2 1.0 C5 A:DC2 4.5 9.9 1.0 N2 A:DG14 4.5 11.0 1.0 C8 A:DG12 4.6 14.1 1.0 C5 A:DG14 4.7 12.9 1.0 O2 A:DC1 4.7 10.2 1.0 N1 A:DC13 4.7 11.9 1.0 N3 A:DC4 4.8 9.0 1.0 AG A:AG108 4.8 8.8 0.9 N3 A:DC10 4.8 9.5 1.0 C6 A:DC2 4.9 11.4 1.0 C4 A:DC13 5.0 11.5 1.0

Silver binding site 3 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:9.9 occ:1.00 N3 A:DC13 2.3 11.1 1.0 O2 A:DC11 2.4 10.9 1.0 AG A:AG104 2.7 8.6 1.0 AG A:AG102 2.7 9.1 1.0 AG A:AG101 2.8 9.1 0.9 AG A:AG106 2.8 8.5 1.0 N7 A:DG12 2.9 11.7 1.0 C2 A:DC13 3.1 12.0 1.0 O2 A:DC13 3.2 8.7 1.0 C4 A:DC13 3.3 11.5 1.0 C8 A:DG12 3.3 14.1 1.0 C2 A:DC11 3.3 10.0 1.0 N4 A:DC13 3.4 10.9 1.0 N3 A:DC10 3.5 9.5 1.0 N3 A:DC11 3.6 8.6 1.0 C5 A:DG12 3.7 12.0 1.0 O6 A:DG14 3.9 9.2 1.0 AG A:AG105 3.9 8.7 1.0 C2 A:DC10 4.0 8.5 1.0 O2 A:DC10 4.1 9.3 1.0 C4 A:DC10 4.1 8.6 1.0 N9 A:DG12 4.2 15.8 1.0 O6 A:DG3 4.3 9.5 1.0 N4 A:DC10 4.3 9.2 1.0 C6 A:DG12 4.4 12.3 1.0 C4 A:DG12 4.4 12.7 1.0 N1 A:DC13 4.5 11.9 1.0 O6 A:DG12 4.5 12.2 1.0 N1 A:DC11 4.6 11.0 1.0 C5 A:DC13 4.6 10.7 1.0 O2 A:DC4 4.7 9.2 1.0 C6 A:DG14 4.8 12.8 1.0 AG A:AG107 4.9 8.8 0.9 AG A:AG108 4.9 8.8 0.9 N1 A:DC10 4.9 9.6 1.0 C4 A:DC11 4.9 11.2 1.0 C1' A:DC11 5.0 12.2 1.0 N3 A:DC2 5.0 11.4 1.0

Silver binding site 4 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:8.6 occ:0.96 O2 A:DC4 2.4 9.2 1.0 N3 A:DC11 2.4 8.6 1.0 O2 A:DC10 2.5 9.3 1.0 AG A:AG103 2.7 9.9 1.0 AG A:AG101 2.8 9.1 0.9 AG A:AG105 2.8 8.7 1.0 AG A:AG106 2.9 8.5 1.0 AG A:AG108 3.1 8.8 0.9 O2 A:DC11 3.2 10.9 1.0 C2 A:DC11 3.2 10.0 1.0 C2 A:DC10 3.2 8.5 1.0 C2 A:DC4 3.3 8.0 1.0 C4 A:DC11 3.4 11.2 1.0 N4 A:DC11 3.5 10.8 1.0 N3 A:DC10 3.6 9.5 1.0 O6 A:DG12 3.6 12.2 1.0 N3 A:DC4 3.6 9.0 1.0 N7 A:DG5 3.7 8.4 1.0 AG A:AG102 3.9 9.1 1.0 C8 A:DG5 3.9 9.6 1.0 C6 A:DG12 4.1 12.3 1.0 N7 A:DG12 4.1 11.7 1.0 C5 A:DG12 4.3 12.0 1.0 N1 A:DC10 4.4 9.6 1.0 C5 A:DG5 4.4 8.8 1.0 N1 A:DC11 4.6 11.0 1.0 N1 A:DC4 4.6 8.7 1.0 N9 A:DG5 4.7 8.6 1.0 C5 A:DC11 4.8 9.9 1.0 N7 A:DG3 4.8 11.3 1.0 C1' A:DC10 4.8 8.8 1.0 C4 A:DC10 4.8 8.6 1.0 C2' A:DC10 4.8 9.9 1.0 N3 A:DC13 4.9 11.1 1.0 AG A:AG107 4.9 8.8 0.9 C4 A:DC4 5.0 7.6 1.0

Silver binding site 5 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:8.7 occ:0.96 N3 A:DC4 2.3 9.0 1.0 O2 A:DC2 2.6 13.3 1.0 AG A:AG107 2.8 8.8 0.9 AG A:AG104 2.8 8.6 1.0 AG A:AG102 2.8 9.1 1.0 AG A:AG106 2.8 8.5 1.0 AG A:AG108 2.9 8.8 0.9 AG A:AG101 2.9 9.1 0.9 C2 A:DC4 3.2 8.0 1.0 C4 A:DC4 3.2 7.6 1.0 O2 A:DC4 3.2 9.2 1.0 AG A:AG110 3.2 9.2 0.9 N4 A:DC4 3.3 10.9 1.0 C2 A:DC2 3.6 9.2 1.0 O6 A:DG5 3.7 8.9 1.0 N3 A:DC2 3.9 11.4 1.0 AG A:AG103 3.9 9.9 1.0 N7 A:DG3 4.0 11.3 1.0 N7 A:DG5 4.1 8.4 1.0 C6 A:DG5 4.2 9.5 1.0 AG A:AG109 4.2 9.0 0.9 N3 A:DC1 4.2 8.4 1.0 O2 A:DC1 4.3 10.2 1.0 C5 A:DG5 4.3 8.8 1.0 O2 A:DC10 4.4 9.3 1.0 N1 A:DC4 4.5 8.7 1.0 C5 A:DC4 4.5 8.0 1.0 O6 A:DG14 4.6 9.2 1.0 C2 A:DC1 4.7 8.9 1.0 C8 A:DG3 4.7 9.3 1.0 N1 A:DG14 4.8 10.6 1.0 C5 A:DG3 4.8 9.2 1.0 O6 A:DG3 4.8 9.5 1.0 N1 A:DC2 4.9 11.4 1.0 O6 A:DG12 4.9 12.2 1.0 N3 A:DC10 4.9 9.5 1.0

Silver binding site 6 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:8.5 occ:0.97 N3 A:DC10 2.3 9.5 1.0 O6 A:DG14 2.4 9.2 1.0 AG A:AG108 2.7 8.8 0.9 AG A:AG102 2.8 9.1 1.0 AG A:AG107 2.8 8.8 0.9 AG A:AG103 2.8 9.9 1.0 AG A:AG105 2.8 8.7 1.0 AG A:AG104 2.9 8.6 1.0 AG A:AG109 3.0 9.0 0.9 C2 A:DC10 3.1 8.5 1.0 O2 A:DC10 3.2 9.3 1.0 C4 A:DC10 3.3 8.6 1.0 C6 A:DG14 3.4 12.8 1.0 N4 A:DC10 3.4 9.2 1.0 N1 A:DG14 3.7 10.6 1.0 O6 A:DG9 3.9 9.3 1.0 N3 A:DC13 3.9 11.1 1.0 AG A:AG101 4.1 9.1 0.9 AG A:AG110 4.2 9.2 0.9 O2 A:DC13 4.2 8.7 1.0 C6 A:DG9 4.3 9.1 1.0 C2 A:DC13 4.3 12.0 1.0 N1 A:DA15 4.5 9.6 1.0 N1 A:DC10 4.5 9.6 1.0 O2 A:DC11 4.5 10.9 1.0 N1 A:DG9 4.5 9.7 1.0 C4 A:DC13 4.6 11.5 1.0 C5 A:DC10 4.6 8.6 1.0 N3 A:DC2 4.7 11.4 1.0 C5 A:DG14 4.7 12.9 1.0 N7 A:DG5 4.7 8.4 1.0 O2 A:DC2 4.7 13.3 1.0 N4 A:DC13 4.7 10.9 1.0 N6 A:DA15 4.8 10.2 1.0 AG A:AG111 4.8 8.9 1.0 O2 A:DC4 4.9 9.2 1.0 N3 A:DC4 4.9 9.0 1.0 N3 A:DC11 5.0 8.6 1.0 C6 A:DA15 5.0 11.2 1.0

Silver binding site 7 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:8.8 occ:0.95 O2 A:DC1 2.3 10.2 1.0 N1 A:DG14 2.4 10.6 1.0 AG A:AG109 2.7 9.0 0.9 AG A:AG105 2.8 8.7 1.0 AG A:AG106 2.8 8.5 1.0 AG A:AG110 2.9 9.2 0.9 AG A:AG102 2.9 9.1 1.0 O6 A:DG14 3.1 9.2 1.0 C6 A:DG14 3.2 12.8 1.0 O2 A:DC2 3.2 13.3 1.0 N3 A:DC2 3.2 11.4 1.0 C2 A:DC1 3.3 8.9 1.0 C2 A:DG14 3.3 10.9 1.0 C2 A:DA15 3.3 8.5 1.0 N1 A:DA15 3.4 9.6 1.0 N2 A:DG14 3.4 11.0 1.0 C2 A:DC2 3.5 9.2 1.0 N3 A:DC1 3.6 8.4 1.0 AG A:AG108 3.7 8.8 0.9 C4 A:DC2 4.3 6.9 1.0 N3 A:DA15 4.3 11.1 1.0 C6 A:DA15 4.4 11.2 1.0 C5 A:DG14 4.5 12.9 1.0 N1 A:DC1 4.5 8.9 1.0 N4 A:DC2 4.6 13.0 1.0 N3 A:DG14 4.6 11.6 1.0 O6 A:DG9 4.7 9.3 1.0 N4 A:DC4 4.7 10.9 1.0 N1 A:DC2 4.8 11.4 1.0 N3 A:DC4 4.8 9.0 1.0 AG A:AG104 4.9 8.6 1.0 O6 A:DG5 4.9 8.9 1.0 AG A:AG103 4.9 9.9 1.0 O2 A:DC13 4.9 8.7 1.0 C4 A:DC1 4.9 9.1 1.0 AG A:AG101 4.9 9.1 0.9 C4 A:DG14 5.0 12.6 1.0 C1' A:DC1 5.0 10.1 1.0 N6 A:DA15 5.0 10.2 1.0 N3 A:DC10 5.0 9.5 1.0

Silver binding site 8 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag108 b:8.8 occ:0.92 N7 A:DG5 2.2 8.4 1.0 AG A:AG106 2.7 8.5 1.0 O2 A:DC10 2.8 9.3 1.0 AG A:AG110 2.8 9.2 0.9 AG A:AG111 2.8 8.9 1.0 AG A:AG109 2.8 9.0 0.9 AG A:AG105 2.9 8.7 1.0 AG A:AG104 3.1 8.6 1.0 C5 A:DG5 3.2 8.8 1.0 C8 A:DG5 3.3 9.6 1.0 O6 A:DG5 3.3 8.9 1.0 N1 A:DG9 3.3 9.7 1.0 C2 A:DC10 3.5 8.5 1.0 C6 A:DG5 3.6 9.5 1.0 N3 A:DC10 3.6 9.5 1.0 AG A:AG107 3.7 8.8 0.9 O6 A:DG9 3.7 9.3 1.0 C6 A:DG9 3.9 9.1 1.0 N3 A:DC4 3.9 9.0 1.0 O2 A:DC4 4.0 9.2 1.0 C2 A:DG9 4.2 8.1 1.0 O2 A:DC6 4.2 10.2 1.0 N2 A:DG9 4.2 10.2 1.0 AG A:AG112 4.2 9.1 0.9 C2 A:DC4 4.4 8.0 1.0 C4 A:DG5 4.4 7.5 1.0 N9 A:DG5 4.4 8.6 1.0 AG A:AG113 4.7 9.4 0.9 C2 A:DC6 4.7 8.5 1.0 N3 A:DC6 4.7 9.5 1.0 O6 A:DG14 4.8 9.2 1.0 N1 A:DC10 4.8 9.6 1.0 AG A:AG102 4.8 9.1 1.0 C4 A:DC10 4.9 8.6 1.0 C4 A:DC4 4.9 7.6 1.0 AG A:AG103 4.9 9.9 1.0 N1 A:DG5 5.0 7.8 1.0 N3 A:DC1 5.0 8.4 1.0

Silver binding site 9 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag109 b:9.0 occ:0.93 O6 A:DG9 2.2 9.3 1.0 N1 A:DA15 2.3 9.6 1.0 AG A:AG107 2.7 8.8 0.9 AG A:AG110 2.8 9.2 0.9 AG A:AG108 2.8 8.8 0.9 AG A:AG111 2.9 8.9 1.0 AG A:AG106 3.0 8.5 1.0 AG A:AG113 3.1 9.4 0.9 C6 A:DG9 3.2 9.1 1.0 C2 A:DA15 3.2 8.5 1.0 C6 A:DA15 3.3 11.2 1.0 N6 A:DA15 3.3 10.2 1.0 O6 A:DG14 3.5 9.2 1.0 N1 A:DG9 3.6 9.7 1.0 O6 A:DG7 3.8 9.1 1.0 N1 A:DG14 4.0 10.6 1.0 C6 A:DG14 4.0 12.8 1.0 N3 A:DC10 4.1 9.5 1.0 O2 A:DC1 4.1 10.2 1.0 N1 A:DA16 4.2 8.7 1.0 AG A:AG105 4.2 8.7 1.0 C6 A:DG7 4.3 7.5 1.0 C5 A:DG9 4.5 8.7 1.0 AG A:AG112 4.5 9.1 0.9 N3 A:DA15 4.5 11.1 1.0 C5 A:DA15 4.6 12.3 1.0 O2 A:DC10 4.7 9.3 1.0 N4 A:DC10 4.7 9.2 1.0 N3 A:DC1 4.7 8.4 1.0 C2 A:DC10 4.7 8.5 1.0 C4 A:DC10 4.7 8.6 1.0 C2 A:DA16 4.8 8.8 1.0 C2 A:DC1 4.8 8.9 1.0 N6 A:DA16 4.8 9.3 1.0 C6 A:DA16 4.8 8.0 1.0 O6 A:DG5 4.9 8.9 1.0 N7 A:DG5 4.9 8.4 1.0 C5 A:DG7 4.9 9.6 1.0 C2 A:DG9 4.9 8.1 1.0 N1 A:DG7 4.9 10.2 1.0

Silver binding site 10 out of 28 in the A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of A Dna-Stabilized Atomically Precise Silver Nanorod with Emission at 960 Nm within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag110 b:9.2 occ:0.90 N3 A:DC1 2.4 8.4 1.0 O6 A:DG5 2.5 8.9 1.0 AG A:AG109 2.8 9.0 0.9 AG A:AG108 2.8 8.8 0.9 AG A:AG107 2.9 8.8 0.9 C2 A:DC1 3.1 8.9 1.0 AG A:AG112 3.2 9.1 0.9 O2 A:DC1 3.2 10.2 1.0 AG A:AG105 3.2 8.7 1.0 C4 A:DC1 3.3 9.1 1.0 AG A:AG113 3.3 9.4 0.9 AG A:AG111 3.4 8.9 1.0 N4 A:DC1 3.4 9.2 1.0 C6 A:DG5 3.6 9.5 1.0 N4 A:DC4 3.8 10.9 1.0 N7 A:DG5 4.1 8.4 1.0 C2 A:DA16 4.2 8.8 1.0 N3 A:DC4 4.2 9.0 1.0 AG A:AG106 4.2 8.5 1.0 C5 A:DG5 4.3 8.8 1.0 N1 A:DA16 4.3 8.7 1.0 O2 A:DC2 4.3 13.3 1.0 N1 A:DA15 4.4 9.6 1.0 C4 A:DC4 4.4 7.6 1.0 CL B:CL115 4.4 9.6 1.0 N1 A:DC1 4.4 8.9 1.0 C2 A:DA15 4.4 8.5 1.0 C5 A:DC1 4.6 9.6 1.0 N3 A:DC6 4.6 9.5 1.0 O6 A:DG9 4.7 9.3 1.0 N1 A:DG5 4.8 7.8 1.0

G.Romolini, H.Kanazawa, C.Mollerup, M.Lisberg, S.Lind, Z.Huang, C.Cerretani, J.Kondo, T.Vosch. Shining Bright at 960 Nm: A 28-Silver-Atom Nanorod Stabilized By Dna Small Struct 2025.
ISSN: ESSN 2688-4062
DOI: 10.1002/SSTR.202500022