Silver in PDB 7xlw: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant), PDB code: 7xlw was solved by J.Kondo, C.Cerretani, T.Vosch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.76 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.232, 49.663, 55.885, 74.03, 90.37, 83.73
R / Rfree (%)	15 / 18.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 108;

Binding sites:

The binding sites of Silver atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) (pdb code 7xlw). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 108 binding sites of Silver where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant), PDB code: 7xlw:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:22.4 occ:1.00 N3 A:DC3 2.3 22.4 1.0 O2 A:DC1 2.5 25.7 1.0 AG A:AG105 2.7 20.6 1.0 AG B:AG102 2.8 19.3 1.0 AG B:AG101 2.8 20.1 1.0 AG A:AG102 2.8 19.6 1.0 O2 A:DC3 2.8 21.4 1.0 N1 A:DA2 2.9 22.2 1.0 C2 A:DC3 2.9 24.3 1.0 C2 A:DA2 3.2 20.2 1.0 C6 A:DA2 3.4 22.7 1.0 C4 A:DC3 3.4 25.7 1.0 C2 A:DC1 3.5 27.1 1.0 N4 A:DC3 3.6 25.5 1.0 O6 A:DI9 3.6 20.3 1.0 N3 A:DC4 3.7 22.8 1.0 N3 A:DA2 3.8 20.7 1.0 N3 A:DC1 3.9 26.3 1.0 N6 A:DA2 3.9 18.9 1.0 C5 A:DA2 3.9 22.4 1.0 AG B:AG105 4.0 21.7 1.0 C4 A:DA2 4.1 22.4 1.0 C6 A:DI9 4.1 26.5 1.0 N4 A:DC4 4.3 24.2 1.0 N1 A:DC3 4.3 24.7 1.0 C4 A:DC4 4.4 23.4 1.0 O2 A:DC4 4.4 24.9 1.0 C2 A:DC4 4.5 27.3 1.0 N3 B:DC1 4.6 20.2 1.0 N1 A:DI9 4.6 31.3 1.0 O2 B:DC3 4.6 24.0 1.0 C5 A:DC3 4.7 25.7 1.0 O2 B:DC1 4.7 18.4 1.0 N1 A:DC1 4.7 28.4 1.0 C5 A:DI9 4.8 28.7 1.0 AG A:AG106 4.9 22.1 1.0 N3 B:DC3 5.0 25.6 1.0 N7 A:DA2 5.0 20.6 1.0 O2 B:DC4 5.0 23.6 1.0 C6 A:DC3 5.0 25.8 1.0

Silver binding site 2 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:19.6 occ:1.00 O6 A:DI9 2.4 20.3 1.0 N3 A:DC4 2.4 22.8 1.0 AG B:AG102 2.8 19.3 1.0 AG A:AG101 2.8 22.4 1.0 AG A:AG106 2.8 22.1 1.0 AG B:AG105 2.8 21.7 1.0 AG A:AG103 2.9 22.6 1.0 AG B:AG103 2.9 21.7 1.0 AG A:AG105 3.0 20.6 1.0 O2 A:DC4 3.1 24.9 1.0 C2 A:DC4 3.1 27.3 1.0 C6 A:DI9 3.2 26.5 1.0 C4 A:DC4 3.4 23.4 1.0 N1 A:DI9 3.5 31.3 1.0 N4 A:DC4 3.6 24.2 1.0 N3 A:DC3 3.9 22.4 1.0 O2 A:DC3 4.0 21.4 1.0 AG B:AG106 4.0 23.0 1.0 AG B:AG101 4.1 20.1 1.0 N3 A:DC8 4.1 27.6 1.0 C2 A:DC3 4.3 24.3 1.0 O2 B:DC4 4.3 23.6 1.0 O2 A:DC1 4.4 25.7 1.0 N1 B:DI9 4.5 22.7 1.0 AG A:AG109 4.5 28.7 0.3 N1 A:DC4 4.5 26.3 1.0 C2 A:DC8 4.6 26.8 1.0 C5 A:DI9 4.6 28.7 1.0 C4 A:DC8 4.6 25.0 1.0 O2 A:DC8 4.7 25.1 1.0 N4 A:DC8 4.7 24.6 1.0 C5 A:DC4 4.7 24.6 1.0 C4 A:DC3 4.8 25.7 1.0 C2 A:DI9 4.8 29.1 1.0 N3 B:DC4 4.9 25.3 1.0 N3 A:DC1 4.9 26.3 1.0 O6 B:DI9 4.9 22.0 1.0 N4 A:DC3 5.0 25.5 1.0

Silver binding site 3 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:22.6 occ:1.00 N3 A:DC8 2.3 27.6 1.0 AG B:AG103 2.7 21.7 1.0 AG B:AG106 2.8 23.0 1.0 AG A:AG106 2.8 22.1 1.0 AG B:AG108 2.8 26.6 1.0 AG A:AG107 2.9 25.1 1.0 AG A:AG102 2.9 19.6 1.0 AG A:AG109 3.0 28.7 0.3 C2 A:DC8 3.0 26.8 1.0 O2 A:DC8 3.1 25.1 1.0 AG A:AG104 3.2 28.8 1.0 C4 A:DC8 3.2 25.0 1.0 N4 A:DC8 3.4 24.6 1.0 O6 A:DI9 3.7 20.3 1.0 N3 A:DC4 3.8 22.8 1.0 O2 A:DC4 4.0 24.9 1.0 C2 A:DC4 4.1 27.3 1.0 AG B:AG105 4.1 21.7 1.0 N1 A:DI9 4.2 31.3 1.0 N1 A:DC8 4.3 32.2 1.0 AG B:AG109 4.3 26.7 0.3 C6 A:DI9 4.4 26.5 1.0 AG B:AG107 4.5 27.0 1.0 C4 A:DC4 4.5 23.4 1.0 OP1 A:DA6 4.5 32.4 1.0 C5 A:DC8 4.5 27.0 1.0 O2 B:DC8 4.7 27.3 1.0 N4 A:DC4 4.8 24.2 1.0 O6 A:DI7 4.8 27.3 1.0 N7 A:DI7 4.9 32.5 1.0 C6 A:DC8 4.9 29.3 1.0 N3 B:DC8 4.9 29.6 1.0 N1 B:DI9 4.9 22.7 1.0 AG B:AG102 5.0 19.3 1.0 N1 A:DC4 5.0 26.3 1.0

Silver binding site 4 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:28.8 occ:1.00 OP1 A:DA6 2.4 32.4 1.0 N7 A:DI7 2.5 32.5 1.0 AG A:AG108 2.7 32.1 1.0 AG B:AG104 2.7 31.2 1.0 AG A:AG107 2.8 25.1 1.0 AG B:AG108 2.8 26.6 1.0 N3 A:DC8 3.0 27.6 1.0 O6 A:DI7 3.2 27.3 1.0 AG A:AG103 3.2 22.6 1.0 P A:DA6 3.3 31.3 1.0 C5 A:DI7 3.3 32.5 1.0 OP2 A:DA6 3.3 30.3 1.0 C2 A:DC8 3.6 26.8 1.0 C8 A:DI7 3.6 32.2 1.0 C6 A:DI7 3.6 35.0 1.0 O2 A:DC8 3.6 25.1 1.0 AG B:AG107 3.7 27.0 1.0 C4 A:DC8 3.7 25.0 1.0 N4 A:DC8 3.9 24.6 1.0 N7 A:DA6 4.1 35.7 1.0 AG A:AG109 4.1 28.7 0.3 C8 A:DA6 4.2 34.8 1.0 O6 B:DI7 4.2 26.4 1.0 O5' A:DA6 4.2 39.0 1.0 C4 A:DI7 4.5 34.2 1.0 O3' A:DT5 4.6 39.3 1.0 AG B:AG106 4.6 23.0 1.0 N1 A:DC8 4.6 32.2 1.0 N9 A:DI7 4.6 33.8 1.0 OP2 B:DA6 4.8 31.8 1.0 C5 A:DC8 4.8 27.0 1.0 N7 B:DA6 4.9 34.8 1.0 C5 A:DA6 5.0 35.4 1.0

Silver binding site 5 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:20.6 occ:1.00 O2 B:DC4 2.4 23.6 1.0 N3 A:DC1 2.5 26.3 1.0 AG A:AG101 2.7 22.4 1.0 AG B:AG101 2.7 20.1 1.0 AG B:AG105 2.8 21.7 1.0 AG A:AG102 3.0 19.6 1.0 N1 A:DI9 3.0 31.3 1.0 O2 A:DC1 3.1 25.7 1.0 AG A:AG106 3.2 22.1 1.0 C2 A:DC1 3.2 27.1 1.0 O2 B:DC3 3.2 24.0 1.0 C2 B:DC4 3.3 27.2 1.0 C6 A:DI9 3.4 26.5 1.0 C4 A:DC1 3.5 31.5 1.0 N3 B:DC4 3.5 25.3 1.0 O6 A:DI9 3.5 20.3 1.0 N4 A:DC1 3.7 27.7 1.0 C2 A:DI9 3.7 29.1 1.0 C2 B:DC3 3.8 25.1 1.0 AG B:AG102 3.9 19.3 1.0 N3 B:DC3 3.9 25.6 1.0 N6 A:DA2 4.0 18.9 1.0 N1 A:DA2 4.1 22.2 1.0 C5 A:DI9 4.3 28.7 1.0 C6 A:DA2 4.4 22.7 1.0 N3 A:DI9 4.5 29.6 1.0 N1 B:DC4 4.5 27.9 1.0 N1 A:DC1 4.5 28.4 1.0 C4 A:DI9 4.7 26.6 1.0 C4 B:DC4 4.8 25.7 1.0 N3 A:DC3 4.8 22.4 1.0 C5 A:DC1 4.8 28.4 1.0 N1 B:DC3 4.9 25.7 1.0 C4 B:DC3 5.0 26.7 1.0 C1' B:DC4 5.0 31.1 1.0 AG B:AG103 5.0 21.7 1.0

Silver binding site 6 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


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 A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:22.1 occ:1.00 N1 A:DI9 2.1 31.3 1.0 O2 B:DC4 2.6 23.6 1.0 AG B:AG109 2.7 26.7 0.3 AG B:AG106 2.8 23.0 1.0 AG A:AG103 2.8 22.6 1.0 AG A:AG102 2.8 19.6 1.0 AG B:AG105 3.0 21.7 1.0 C6 A:DI9 3.1 26.5 1.0 C2 A:DI9 3.1 29.1 1.0 O6 A:DI9 3.1 20.3 1.0 AG A:AG105 3.2 20.6 1.0 AG A:AG107 3.3 25.1 1.0 C2 B:DC4 3.3 27.2 1.0 O2 A:DC8 3.3 25.1 1.0 N3 B:DC4 3.7 25.3 1.0 AG B:AG103 3.9 21.7 1.0 C2 A:DC8 4.0 26.8 1.0 N6 A:DA10 4.1 30.5 1.0 N3 A:DC8 4.2 27.6 1.0 N1 B:DC4 4.3 27.9 1.0 N3 A:DI9 4.5 29.6 1.0 C5 A:DI9 4.5 28.7 1.0 C1' B:DC4 4.6 31.1 1.0 N3 A:DC1 4.8 26.3 1.0 N3 B:DC8 4.8 29.6 1.0 AG B:AG108 4.8 26.6 1.0 AG A:AG101 4.9 22.4 1.0 C4 B:DC4 4.9 25.7 1.0 N4 B:DC8 4.9 30.3 1.0 AG B:AG102 5.0 19.3 1.0

Silver binding site 7 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:25.1 occ:1.00 O6 A:DI7 2.4 27.3 1.0 AG B:AG109 2.6 26.7 0.3 AG B:AG107 2.7 27.0 1.0 AG A:AG104 2.8 28.8 1.0 O2 A:DC8 2.8 25.1 1.0 AG A:AG108 2.9 32.1 1.0 AG A:AG103 2.9 22.6 1.0 AG B:AG106 2.9 23.0 1.0 AG B:AG108 3.2 26.6 1.0 AG A:AG106 3.3 22.1 1.0 C6 A:DI7 3.3 35.0 1.0 C2 A:DC8 3.6 26.8 1.0 OP1 B:DA6 3.6 34.3 1.0 N3 A:DC8 3.7 27.6 1.0 N6 A:DA10 3.9 30.5 1.0 OP2 B:DA6 4.0 31.8 1.0 C5 A:DI7 4.1 32.5 1.0 AG B:AG104 4.1 31.2 1.0 N7 A:DI7 4.2 32.5 1.0 P B:DA6 4.2 36.4 1.0 N3 B:DC8 4.3 29.6 1.0 N1 A:DI7 4.4 35.0 1.0 N1 A:DI9 4.7 31.3 1.0 C2' B:DT5 4.7 37.1 1.0 O3' B:DT5 4.8 33.0 1.0 N4 B:DC8 4.8 30.3 1.0 AG B:AG103 4.8 21.7 1.0 N1 A:DC8 4.9 32.2 1.0 C4 A:DC8 5.0 25.0 1.0 C3' B:DT5 5.0 36.0 1.0

Silver binding site 8 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag108 b:32.1 occ:1.00 O6 A:DI7 2.0 27.3 1.0 OP2 B:DA6 2.1 31.8 1.0 N7 A:DA6 2.4 35.7 1.0 AG B:AG104 2.6 31.2 1.0 AG A:AG104 2.7 28.8 1.0 AG B:AG107 2.8 27.0 1.0 AG A:AG107 2.9 25.1 1.0 C6 A:DI7 3.0 35.0 1.0 P B:DA6 3.2 36.4 1.0 C8 A:DA6 3.3 34.8 1.0 C5 A:DA6 3.4 35.4 1.0 OP1 B:DA6 3.6 34.3 1.0 C5 A:DI7 3.6 32.5 1.0 N6 A:DA6 3.7 39.5 1.0 N7 A:DI7 3.7 32.5 1.0 C8 B:DA6 3.7 32.9 1.0 N7 B:DA6 3.7 34.8 1.0 C6 A:DA6 3.9 34.1 1.0 OP2 A:DA6 4.0 30.3 1.0 AG B:AG108 4.0 26.6 1.0 O3' B:DT5 4.1 33.0 1.0 N1 A:DI7 4.2 35.0 1.0 O5' B:DA6 4.4 34.0 1.0 N9 A:DA6 4.5 38.5 1.0 C4 A:DA6 4.5 35.2 1.0 O6 B:DI7 4.6 26.4 1.0 OP1 A:DA6 4.7 32.4 1.0 N7 B:DI7 4.7 31.4 1.0 O2 A:DC8 4.8 25.1 1.0 P A:DA6 4.8 31.3 1.0 C4 A:DI7 4.9 34.2 1.0 AG B:AG109 4.9 26.7 0.3 C8 A:DI7 5.0 32.2 1.0 N9 B:DA6 5.0 37.0 1.0

Silver binding site 9 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag109 b:28.7 occ:0.34 AG B:AG103 2.6 21.7 1.0 AG B:AG108 2.7 26.6 1.0 AG A:AG103 3.0 22.6 1.0 O2 A:DC4 3.1 24.9 1.0 N6 B:DA10 3.3 30.6 1.0 N4 A:DC8 3.4 24.6 1.0 C2 A:DC4 3.4 27.3 1.0 N1 A:DC4 3.6 26.3 1.0 C2' A:DT5 3.7 33.9 1.0 C1' A:DC4 3.7 22.0 1.0 C2' A:DC4 3.8 30.0 1.0 OP1 A:DA6 3.9 32.4 1.0 N1 B:DI9 3.9 22.7 1.0 C2 B:DI9 4.0 24.7 1.0 O2 B:DC8 4.1 27.3 1.0 N3 A:DC4 4.1 22.8 1.0 AG A:AG104 4.1 28.8 1.0 O6 B:DI7 4.2 26.4 1.0 N3 A:DC8 4.2 27.6 1.0 C3' A:DT5 4.2 33.4 1.0 C4 A:DC8 4.3 25.0 1.0 AG B:AG106 4.3 23.0 1.0 N7 B:DA10 4.4 33.2 1.0 C6 B:DA10 4.4 32.2 1.0 AG A:AG102 4.5 19.6 1.0 C6 A:DC4 4.5 25.2 1.0 C5 B:DA10 4.8 37.1 1.0 O3' A:DT5 4.8 39.3 1.0 P A:DA6 4.8 31.3 1.0 AG B:AG104 4.8 31.2 1.0 C4 A:DC4 4.9 23.4 1.0

Silver binding site 10 out of 108 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (G7I/G9I Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:20.1 occ:1.00 N3 B:DC3 2.3 25.6 1.0 N1 A:DA2 2.4 22.2 1.0 O2 B:DC1 2.5 18.4 1.0 AG B:AG102 2.7 19.3 1.0 AG A:AG105 2.7 20.6 1.0 AG A:AG101 2.8 22.4 1.0 AG B:AG105 3.0 21.7 1.0 O2 B:DC3 3.1 24.0 1.0 C2 B:DC3 3.1 25.1 1.0 C2 A:DA2 3.1 20.2 1.0 C4 B:DC3 3.3 26.7 1.0 C6 A:DA2 3.4 22.7 1.0 C2 B:DC1 3.5 22.7 1.0 N4 B:DC3 3.5 21.7 1.0 N6 A:DA2 3.6 18.9 1.0 N3 B:DC1 3.7 20.2 1.0 N3 B:DC4 4.0 25.3 1.0 AG A:AG102 4.1 19.6 1.0 N6 I:DA2 4.1 25.2 1.0 O6 B:DI9 4.2 22.0 1.0 O2 A:DC3 4.3 21.4 1.0 O2 A:DC1 4.4 25.7 1.0 O2 B:DC4 4.4 23.6 1.0 N3 A:DA2 4.4 20.7 1.0 N1 B:DC3 4.4 25.7 1.0 C6 I:DA2 4.4 22.8 1.0 N3 A:DC1 4.5 26.3 1.0 C2 B:DC4 4.6 27.2 1.0 N1 I:DA2 4.6 23.6 1.0 C5 A:DA2 4.6 22.4 1.0 C5 B:DC3 4.6 24.9 1.0 C6 B:DI9 4.7 26.7 1.0 N1 B:DC1 4.7 22.9 1.0 C2 A:DC1 4.8 27.1 1.0 N4 B:DC4 4.9 21.5 1.0 C4 B:DC4 4.9 25.7 1.0 N3 A:DC3 4.9 22.4 1.0 C4 A:DA2 4.9 22.4 1.0 N1 B:DI9 5.0 22.7 1.0

C.Cerretani, M.B.Liisberg, V.Ruck, J.Kondo, T.Vosch. The Effect of Inosine on the Spectroscopic Properties and Crystal Structure of A Nir-Emitting Dna-Stabilized Silver Nanocluster. Nanoscale Adv V. 4 3212 2022.
ISSN: ESSN 2516-0230
PubMed: 36132821
DOI: 10.1039/D2NA00325B