Silver in PDB 7bse: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant), PDB code: 7bse 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)	32.07 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.353, 45.353, 82.722, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 13.7

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant) also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Silver atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant) (pdb code 7bse). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 36 binding sites of Silver where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant), PDB code: 7bse:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:10.4 occ:1.00 N3 A:DC3 2.3 10.8 1.0 O2 A:DC1 2.4 12.5 1.0 AG A:AG105 2.7 9.5 1.0 AG A:AG102 2.8 8.9 1.0 AG B:AG101 2.8 10.5 1.0 AG B:AG102 2.8 9.9 1.0 N1 A:DA2 3.0 12.4 1.0 O2 A:DC3 3.0 9.0 1.0 C2 A:DC3 3.0 12.5 1.0 C2 A:DA2 3.1 11.2 1.0 C4 A:DC3 3.3 12.0 1.0 C6 A:DA2 3.4 12.5 1.0 C2 A:DC1 3.4 11.7 1.0 N4 A:DC3 3.4 10.7 1.0 O6 A:DG9 3.4 10.0 1.0 N3 A:DA2 3.7 13.7 1.0 N3 A:DC1 3.7 11.2 1.0 N3 A:DC4 3.8 9.7 1.0 AG B:AG105 3.9 9.0 1.0 C5 A:DA2 3.9 11.2 1.0 N6 A:DA2 4.0 14.1 1.0 C4 A:DA2 4.0 12.2 1.0 C6 A:DG9 4.1 9.7 1.0 N4 A:DC4 4.3 13.4 1.0 N1 A:DC3 4.4 13.3 1.0 O2 B:DC3 4.4 11.1 1.0 C4 A:DC4 4.4 9.3 1.0 O2 B:DC1 4.5 9.1 1.0 O2 A:DC4 4.5 8.8 1.0 C2 A:DC4 4.5 9.6 1.0 N3 B:DC1 4.6 12.3 1.0 C5 A:DC3 4.6 12.3 1.0 N1 A:DC1 4.6 10.9 1.0 N1 A:DG9 4.8 8.5 1.0 C5 A:DG9 4.8 9.8 1.0 AG A:AG106 4.8 8.9 1.0 C2 B:DC1 4.9 11.2 1.0 N3 B:DC3 4.9 8.9 1.0 N7 A:DA2 4.9 13.6 1.0

Silver binding site 2 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:8.9 occ:1.00 O6 A:DG9 2.4 10.0 1.0 N3 A:DC4 2.4 9.7 1.0 AG B:AG102 2.8 9.9 1.0 AG B:AG105 2.8 9.0 1.0 AG A:AG106 2.8 8.9 1.0 AG A:AG101 2.8 10.4 1.0 AG A:AG103 2.9 8.4 1.0 AG B:AG103 3.0 8.6 1.0 AG A:AG105 3.0 9.5 1.0 O2 A:DC4 3.2 8.8 1.0 C2 A:DC4 3.2 9.6 1.0 C6 A:DG9 3.3 9.7 1.0 C4 A:DC4 3.4 9.3 1.0 N4 A:DC4 3.5 13.4 1.0 N1 A:DG9 3.6 8.5 1.0 N3 A:DC3 3.9 10.8 1.0 AG B:AG106 3.9 8.5 1.0 AG B:AG101 4.0 10.5 1.0 N3 A:DC8 4.1 7.5 1.0 O2 A:DC3 4.2 9.0 1.0 C2 A:DC3 4.3 12.5 1.0 O2 A:DC1 4.4 12.5 1.0 O2 B:DC4 4.4 10.7 1.0 N1 A:DC4 4.5 9.0 1.0 C2 A:DC8 4.6 7.2 1.0 O6 B:DG9 4.6 10.9 1.0 C4 A:DC8 4.6 8.0 1.0 C5 A:DG9 4.6 9.8 1.0 N1 B:DG9 4.6 9.4 1.0 C4 A:DC3 4.7 12.0 1.0 O2 A:DC8 4.7 9.3 1.0 AG A:AG109 4.7 9.2 0.3 C5 A:DC4 4.7 7.6 1.0 N4 A:DC8 4.7 7.7 1.0 N3 A:DC1 4.7 11.2 1.0 N4 A:DC3 4.8 10.7 1.0 N3 B:DC4 4.9 8.3 1.0 C2 A:DG9 5.0 11.0 1.0 C2 A:DC1 5.0 11.7 1.0

Silver binding site 3 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:8.4 occ:1.00 N3 A:DC8 2.2 7.5 1.0 AG B:AG103 2.7 8.6 1.0 AG A:AG106 2.8 8.9 1.0 AG B:AG106 2.8 8.5 1.0 AG B:AG108 2.8 8.2 1.0 AG A:AG107 2.8 8.4 1.0 AG A:AG102 2.9 8.9 1.0 AG A:AG109 3.0 9.2 0.3 C2 A:DC8 3.0 7.2 1.0 O2 A:DC8 3.1 9.3 1.0 AG A:AG104 3.1 8.0 1.0 C4 A:DC8 3.1 8.0 1.0 N4 A:DC8 3.3 7.7 1.0 N3 A:DC4 3.6 9.7 1.0 O6 A:DG9 3.9 10.0 1.0 C2 A:DC4 3.9 9.6 1.0 O2 A:DC4 4.0 8.8 1.0 AG B:AG105 4.1 9.0 1.0 N1 A:DC8 4.3 9.9 1.0 C4 A:DC4 4.3 9.3 1.0 AG B:AG109 4.4 9.8 0.3 N1 A:DG9 4.4 8.5 1.0 C5 A:DC8 4.5 10.2 1.0 O2 B:DC8 4.5 7.7 1.0 OP1 A:DA6 4.5 8.3 1.0 C6 A:DG9 4.6 9.7 1.0 AG B:AG107 4.6 7.8 1.0 N7 A:DG7 4.6 9.3 1.0 N4 A:DC4 4.7 13.4 1.0 N3 B:DC8 4.8 8.6 1.0 N1 A:DC4 4.9 9.0 1.0 C6 A:DC8 4.9 9.1 1.0 AG B:AG102 4.9 9.9 1.0 N1 B:DG9 4.9 9.4 1.0 AG B:AG104 5.0 8.1 1.0

Silver binding site 4 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:8.0 occ:1.00 OP1 A:DA6 2.4 8.3 1.0 N7 A:DG7 2.4 9.3 1.0 AG A:AG107 2.7 8.4 1.0 AG B:AG104 2.8 8.1 1.0 AG B:AG108 2.8 8.2 1.0 AG A:AG108 2.8 8.1 1.0 N3 A:DC8 2.9 7.5 1.0 AG A:AG103 3.1 8.4 1.0 P A:DA6 3.3 8.4 1.0 C8 A:DG7 3.3 8.4 1.0 C5 A:DG7 3.4 10.1 1.0 OP2 A:DA6 3.4 9.2 1.0 C2 A:DC8 3.4 7.2 1.0 O2 A:DC8 3.5 9.3 1.0 O6 A:DG7 3.6 9.8 1.0 C4 A:DC8 3.6 8.0 1.0 AG A:AG109 3.8 9.2 0.3 AG B:AG107 3.9 7.8 1.0 N4 A:DC8 3.9 7.7 1.0 C6 A:DG7 3.9 10.1 1.0 C8 A:DA6 3.9 9.9 1.0 N7 A:DA6 4.0 7.4 1.0 O5' A:DA6 4.4 10.1 1.0 O6 B:DG7 4.4 7.7 1.0 O3' A:DA5 4.5 11.2 1.0 N1 A:DC8 4.5 9.9 1.0 N9 A:DG7 4.6 10.6 1.0 AG B:AG106 4.6 8.5 1.0 O A:HOH210 4.6 13.0 1.0 C4 A:DG7 4.6 8.8 1.0 C5 A:DC8 4.7 10.2 1.0 N7 B:DA6 4.8 8.4 1.0 N9 A:DA6 4.9 10.1 1.0

Silver binding site 5 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:9.5 occ:1.00 N3 A:DC1 2.3 11.2 1.0 O2 B:DC4 2.5 10.7 1.0 AG A:AG101 2.7 10.4 1.0 O2 B:DC3 2.7 11.1 1.0 AG B:AG105 2.7 9.0 1.0 AG B:AG101 2.8 10.5 1.0 AG A:AG102 3.0 8.9 1.0 O2 A:DC1 3.1 12.5 1.0 C2 A:DC1 3.1 11.7 1.0 AG A:AG106 3.2 8.9 1.0 N1 A:DG9 3.2 8.5 1.0 C4 A:DC1 3.3 11.2 1.0 C2 B:DC4 3.3 9.2 1.0 O6 A:DG9 3.4 10.0 1.0 C6 A:DG9 3.4 9.7 1.0 N4 A:DC1 3.5 12.3 1.0 N3 B:DC4 3.5 8.3 1.0 C2 B:DC3 3.6 10.3 1.0 N3 B:DC3 3.9 8.9 1.0 AG B:AG102 4.0 9.9 1.0 C2 A:DG9 4.0 11.0 1.0 N6 A:DA2 4.1 14.1 1.0 N1 A:DA2 4.1 12.4 1.0 C5 A:DG9 4.3 9.8 1.0 C6 A:DA2 4.3 12.5 1.0 N1 A:DC1 4.4 10.9 1.0 N2 A:DG9 4.4 13.2 1.0 N1 B:DC4 4.6 9.4 1.0 C5 A:DC1 4.6 14.2 1.0 C4 B:DC4 4.7 9.0 1.0 N1 B:DC3 4.8 11.6 1.0 N3 A:DG9 4.8 11.3 1.0 N3 A:DC3 4.8 10.8 1.0 C4 A:DG9 4.8 14.0 1.0 AG B:AG106 4.9 8.5 1.0 O6 B:DG9 4.9 10.9 1.0 C2 A:DA2 5.0 11.2 1.0

Silver binding site 6 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:8.9 occ:1.00 N1 A:DG9 2.3 8.5 1.0 O2 B:DC4 2.6 10.7 1.0 AG B:AG106 2.7 8.5 1.0 AG B:AG109 2.8 9.8 0.3 AG A:AG102 2.8 8.9 1.0 AG A:AG103 2.8 8.4 1.0 AG B:AG105 3.0 9.0 1.0 C6 A:DG9 3.1 9.7 1.0 O6 A:DG9 3.1 10.0 1.0 AG A:AG105 3.2 9.5 1.0 AG A:AG107 3.2 8.4 1.0 C2 A:DG9 3.2 11.0 1.0 O2 A:DC8 3.2 9.3 1.0 N2 A:DG9 3.3 13.2 1.0 C2 B:DC4 3.5 9.2 1.0 N3 B:DC4 3.9 8.3 1.0 C2 A:DC8 3.9 7.2 1.0 AG B:AG103 4.0 8.6 1.0 N3 A:DC8 4.0 7.5 1.0 C5 A:DG9 4.4 9.8 1.0 N3 A:DG9 4.5 11.3 1.0 N1 B:DC4 4.6 9.4 1.0 N3 A:DC1 4.6 11.2 1.0 N3 B:DC8 4.8 8.6 1.0 O A:HOH208 4.8 15.9 1.0 AG B:AG108 4.8 8.2 1.0 N4 A:DC1 4.8 12.3 1.0 AG A:AG101 4.8 10.4 1.0 N3 A:DC4 4.9 9.7 1.0 C4 A:DG9 4.9 14.0 1.0 C1' B:DC4 4.9 11.7 1.0 N4 B:DC8 5.0 9.1 1.0 N1 A:DC8 5.0 9.9 1.0

Silver binding site 7 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:8.4 occ:1.00 AG B:AG109 2.6 9.8 0.3 O2 A:DC8 2.7 9.3 1.0 AG A:AG104 2.7 8.0 1.0 AG A:AG108 2.8 8.1 1.0 AG B:AG107 2.8 7.8 1.0 AG A:AG103 2.8 8.4 1.0 O6 A:DG7 2.9 9.8 1.0 AG B:AG106 2.9 8.5 1.0 AG B:AG108 3.2 8.2 1.0 AG A:AG106 3.2 8.9 1.0 C2 A:DC8 3.5 7.2 1.0 N3 A:DC8 3.6 7.5 1.0 C6 A:DG7 3.8 10.1 1.0 O A:HOH208 3.9 15.9 1.0 N7 A:DG7 3.9 9.3 1.0 OP1 B:DA6 3.9 8.1 1.0 AG B:AG104 4.0 8.1 1.0 C5 A:DG7 4.2 10.1 1.0 OP2 B:DA6 4.3 7.5 1.0 N3 B:DC8 4.3 8.6 1.0 P B:DA6 4.5 8.8 1.0 N1 A:DG9 4.8 8.5 1.0 N1 A:DC8 4.8 9.9 1.0 AG B:AG103 4.8 8.6 1.0 N7 A:DA6 4.9 7.4 1.0 C4 A:DC8 4.9 8.0 1.0 N4 B:DC8 4.9 9.1 1.0 N2 A:DG9 4.9 13.2 1.0 O3' B:DA5 4.9 11.5 1.0 N1 A:DG7 5.0 11.2 1.0 O2 B:DC8 5.0 7.7 1.0 AG A:AG109 5.0 9.2 0.3

Silver binding site 8 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag108 b:8.1 occ:1.00 N7 A:DA6 2.3 7.4 1.0 O6 A:DG7 2.3 9.8 1.0 OP2 B:DA6 2.4 7.5 1.0 AG B:AG104 2.7 8.1 1.0 AG A:AG107 2.8 8.4 1.0 AG B:AG107 2.8 7.8 1.0 AG A:AG104 2.8 8.0 1.0 C8 A:DA6 3.1 9.9 1.0 C6 A:DG7 3.2 10.1 1.0 C5 A:DA6 3.3 9.7 1.0 P B:DA6 3.4 8.8 1.0 C8 B:DA6 3.6 8.7 1.0 N7 A:DG7 3.6 9.3 1.0 N6 A:DA6 3.6 9.4 1.0 N7 B:DA6 3.6 8.4 1.0 OP1 B:DA6 3.6 8.1 1.0 C5 A:DG7 3.7 10.1 1.0 C6 A:DA6 3.9 9.4 1.0 AG B:AG108 4.0 8.2 1.0 OP2 A:DA6 4.2 9.2 1.0 O3' B:DA5 4.2 11.5 1.0 N9 A:DA6 4.3 10.1 1.0 N1 A:DG7 4.3 11.2 1.0 C4 A:DA6 4.4 10.7 1.0 O2 A:DC8 4.6 9.3 1.0 AG B:AG109 4.6 9.8 0.3 N7 B:DG7 4.7 8.1 1.0 O5' B:DA6 4.7 10.1 1.0 OP1 A:DA6 4.7 8.3 1.0 O A:HOH208 4.9 15.9 1.0 C8 A:DG7 4.9 8.4 1.0 O6 B:DG7 4.9 7.7 1.0 N9 B:DA6 4.9 7.6 1.0 P A:DA6 5.0 8.4 1.0 C4 A:DG7 5.0 8.8 1.0

Silver binding site 9 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag109 b:9.2 occ:0.33 AG B:AG108 2.6 8.2 1.0 AG B:AG103 2.8 8.6 1.0 AG A:AG103 3.0 8.4 1.0 N4 A:DC8 3.3 7.7 1.0 O2 A:DC4 3.3 8.8 1.0 N2 B:DG9 3.4 9.4 1.0 C2 A:DC4 3.6 9.6 1.0 OP1 A:DA6 3.7 8.3 1.0 AG A:AG104 3.8 8.0 1.0 O2 B:DC8 3.9 7.7 1.0 C1' A:DC4 3.9 10.8 1.0 C2' A:DC4 3.9 9.0 1.0 N1 A:DC4 3.9 9.0 1.0 O6 B:DG7 4.0 7.7 1.0 N3 A:DC8 4.0 7.5 1.0 N1 B:DG9 4.1 9.4 1.0 C3' A:DA5 4.1 10.0 1.0 C4 A:DC8 4.1 8.0 1.0 C2' A:DA5 4.2 9.8 1.0 C2 B:DG9 4.3 11.0 1.0 N3 A:DC4 4.3 9.7 1.0 AG B:AG106 4.4 8.5 1.0 O3' A:DA5 4.4 11.2 1.0 P A:DA6 4.6 8.4 1.0 AG B:AG104 4.6 8.1 1.0 AG A:AG102 4.7 8.9 1.0 C6 A:DC4 4.8 9.6 1.0 AG A:AG107 5.0 8.4 1.0

Silver binding site 10 out of 36 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A 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 (T5A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:10.5 occ:1.00 N3 B:DC3 2.3 8.9 1.0 O2 B:DC1 2.5 9.1 1.0 N1 A:DA2 2.5 12.4 1.0 AG B:AG102 2.8 9.9 1.0 AG A:AG105 2.8 9.5 1.0 AG A:AG101 2.8 10.4 1.0 AG B:AG105 2.8 9.0 1.0 O2 B:DC3 2.9 11.1 1.0 C2 B:DC3 3.0 10.3 1.0 C2 A:DA2 3.1 11.2 1.0 C4 B:DC3 3.4 9.1 1.0 C6 A:DA2 3.4 12.5 1.0 C2 B:DC1 3.4 11.2 1.0 N4 B:DC3 3.6 10.2 1.0 N6 A:DA2 3.7 14.1 1.0 O6 B:DG9 3.8 10.9 1.0 N3 B:DC1 3.8 12.3 1.0 N3 B:DC4 3.9 8.3 1.0 AG A:AG102 4.0 8.9 1.0 O2 A:DC1 4.3 12.5 1.0 N1 B:DC3 4.3 11.6 1.0 C6 B:DG9 4.4 11.1 1.0 O2 A:DC3 4.4 9.0 1.0 N3 A:DA2 4.4 13.7 1.0 N3 A:DC1 4.5 11.2 1.0 O2 B:DC4 4.5 10.7 1.0 N4 B:DC4 4.6 9.7 1.0 C2 B:DC4 4.6 9.2 1.0 C4 B:DC4 4.6 9.0 1.0 N1 B:DC1 4.7 10.6 1.0 C5 A:DA2 4.7 11.2 1.0 C5 B:DC3 4.7 10.5 1.0 C2 A:DC1 4.8 11.7 1.0 N3 A:DC3 4.8 10.8 1.0 N1 B:DG9 4.9 9.4 1.0 C4 A:DA2 5.0 12.2 1.0 AG B:AG103 5.0 8.6 1.0

C.Cerretani, J.Kondo, T.Vosch. Mutation of Position 5 As A Crystal Engineering Tool For A Nir-Emitting Dna-Stabilized AG16 Nanocluster. Crystengcomm V. 22 8136 2020.
ISSN: ISSN 1466-8033
DOI: 10.1039/D0CE01225D