Silver in PDB 7bsg: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G Mutant)

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G Mutant), PDB code: 7bsg 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)	22.35 / 2.19
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	29.882, 33.677, 76.750, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Silver atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G Mutant) (pdb code 7bsg). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 18 binding sites of Silver where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G Mutant), PDB code: 7bsg:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:35.1 occ:1.00 N3 A:DC3 2.2 37.4 1.0 O2 A:DC1 2.5 41.0 1.0 AG A:AG111 2.6 38.0 1.0 AG A:AG105 2.6 34.7 1.0 AG A:AG110 2.7 39.3 1.0 O2 A:DC3 2.8 39.1 1.0 C2 A:DC3 2.9 38.5 1.0 AG A:AG102 2.9 33.1 1.0 C2 A:DA2 3.0 38.1 1.0 N1 A:DA2 3.0 41.1 1.0 C4 A:DC3 3.3 38.9 1.0 N3 A:DA2 3.4 46.3 1.0 C6 A:DA2 3.4 39.0 1.0 O6 A:DG9 3.4 35.2 1.0 N4 A:DC3 3.5 38.5 1.0 C2 A:DC1 3.6 39.1 1.0 C4 A:DA2 3.7 40.2 1.0 N3 A:DC4 3.7 34.4 1.0 C5 A:DA2 3.8 37.3 1.0 AG B:AG101 3.8 35.9 1.0 N3 A:DC1 3.9 41.5 1.0 O2 B:DC3 4.1 35.2 1.0 C6 A:DG9 4.1 38.7 1.0 N6 A:DA2 4.2 36.7 1.0 O2 A:DC4 4.2 31.3 1.0 N1 A:DC3 4.3 39.8 1.0 C2 A:DC4 4.3 35.9 1.0 O2 B:DC1 4.4 37.2 1.0 N3 B:DC1 4.5 41.4 1.0 C4 A:DC4 4.6 33.0 1.0 N4 A:DC4 4.6 36.5 1.0 C5 A:DC3 4.6 37.3 1.0 N1 A:DG9 4.7 35.6 1.0 N9 A:DA2 4.7 42.5 1.0 N1 A:DC1 4.8 40.7 1.0 N7 A:DA2 4.8 41.5 1.0 N3 B:DC3 4.8 38.2 1.0 C2 B:DC1 4.8 38.2 1.0 AG A:AG106 4.9 31.0 1.0 C2 B:DC3 4.9 33.9 1.0 C6 A:DC3 4.9 37.4 1.0

Silver binding site 2 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:33.1 occ:1.00 N3 A:DC4 2.2 34.4 1.0 O6 A:DG9 2.3 35.2 1.0 AG B:AG101 2.7 35.9 1.0 AG A:AG106 2.7 31.0 1.0 AG A:AG111 2.8 38.0 1.0 AG A:AG112 2.8 38.7 1.0 O2 A:DC4 2.9 31.3 1.0 AG A:AG101 2.9 35.1 1.0 AG A:AG105 2.9 34.7 1.0 C2 A:DC4 2.9 35.9 1.0 AG A:AG103 2.9 30.5 1.0 C4 A:DC4 3.2 33.0 1.0 C6 A:DG9 3.3 38.7 1.0 N4 A:DC4 3.5 36.5 1.0 N1 A:DG9 3.5 35.6 1.0 N3 A:DC3 3.7 37.4 1.0 AG B:AG102 4.0 34.5 1.0 AG A:AG110 4.0 39.3 1.0 O2 A:DC3 4.1 39.1 1.0 O2 B:DC4 4.2 35.9 1.0 C2 A:DC3 4.2 38.5 1.0 N1 A:DC4 4.3 39.6 1.0 N3 A:DC8 4.4 35.2 1.0 O6 B:DG9 4.4 36.4 1.0 O2 A:DC1 4.4 41.0 1.0 C4 A:DC3 4.5 38.9 1.0 C5 A:DC4 4.5 33.9 1.0 AG A:AG109 4.6 42.2 0.4 N4 A:DC3 4.6 38.5 1.0 C5 A:DG9 4.7 40.5 1.0 N1 B:DG9 4.7 38.5 1.0 C2 A:DC8 4.8 37.5 1.0 O2 A:DC8 4.8 34.7 1.0 N3 B:DC4 4.8 35.7 1.0 C2 A:DG9 4.9 34.8 1.0 C6 A:DC4 4.9 40.5 1.0 C4 A:DC8 4.9 37.1 1.0 C2 B:DC4 4.9 36.7 1.0 C6 B:DG9 5.0 38.6 1.0

Silver binding site 3 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag103 b:30.5 occ:1.00 N3 A:DC8 2.4 35.2 1.0 AG A:AG107 2.7 36.4 1.0 AG A:AG112 2.7 38.7 1.0 AG B:AG104 2.8 35.4 1.0 AG B:AG102 2.8 34.5 1.0 AG A:AG106 2.9 31.0 1.0 AG A:AG102 2.9 33.1 1.0 O2 A:DC8 2.9 34.7 1.0 C2 A:DC8 3.0 37.5 1.0 AG A:AG109 3.0 42.2 0.4 AG A:AG104 3.1 31.1 1.0 C4 A:DC8 3.4 37.1 1.0 N3 A:DC4 3.6 34.4 1.0 N4 A:DC8 3.7 32.3 1.0 C2 A:DC4 3.9 35.9 1.0 O6 A:DG9 4.0 35.2 1.0 O2 A:DC4 4.0 31.3 1.0 AG B:AG101 4.2 35.9 1.0 C4 A:DC4 4.2 33.0 1.0 OP1 A:DA6 4.3 39.0 1.0 N1 A:DC8 4.3 40.3 1.0 N1 A:DG9 4.5 35.6 1.0 N4 A:DC4 4.5 36.5 1.0 AG B:AG103 4.5 36.9 1.0 AG B:AG105 4.5 41.9 0.3 O2 B:DC8 4.6 33.2 1.0 C6 A:DG9 4.6 38.7 1.0 C5 A:DC8 4.7 39.5 1.0 N7 A:DG7 4.7 37.2 1.0 N1 A:DC4 4.8 39.6 1.0 O6 A:DG7 4.8 33.6 1.0 N3 B:DC8 4.9 40.5 1.0 AG A:AG108 5.0 37.9 1.0

Silver binding site 4 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag104 b:31.1 occ:1.00 AG A:AG107 2.5 36.4 1.0 N7 A:DG7 2.5 37.2 1.0 OP1 A:DA6 2.6 39.0 1.0 AG A:AG108 2.8 37.9 1.0 AG B:AG104 2.8 35.4 1.0 AG A:AG113 2.8 39.9 1.0 N3 A:DC8 2.9 35.2 1.0 AG A:AG103 3.1 30.5 1.0 OP2 A:DA6 3.3 39.8 1.0 P A:DA6 3.3 33.1 1.0 O2 A:DC8 3.3 34.7 1.0 C2 A:DC8 3.4 37.5 1.0 C8 A:DG7 3.5 37.6 1.0 C5 A:DG7 3.5 36.2 1.0 O6 A:DG7 3.6 33.6 1.0 AG B:AG103 3.6 36.9 1.0 C4 A:DC8 3.8 37.1 1.0 C6 A:DG7 3.9 38.5 1.0 O5' A:DA6 3.9 35.0 1.0 AG A:AG109 4.0 42.2 0.4 N4 A:DC8 4.1 32.3 1.0 C8 A:DA6 4.1 39.0 1.0 N7 A:DA6 4.2 34.0 1.0 AG B:AG102 4.4 34.5 1.0 N1 A:DC8 4.6 40.3 1.0 N9 A:DG7 4.7 39.1 1.0 O6 B:DG7 4.7 46.0 1.0 C4 A:DG7 4.7 37.4 1.0 O3' A:DG5 4.8 45.0 1.0 OP2 B:DA6 4.9 38.3 1.0 C5 A:DC8 4.9 39.5 1.0 C5 A:DA6 4.9 36.2 1.0 N9 A:DA6 5.0 40.3 1.0

Silver binding site 5 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag105 b:34.7 occ:1.00 O2 B:DC4 2.5 35.9 1.0 N3 A:DC1 2.5 41.5 1.0 O2 B:DC3 2.5 35.2 1.0 AG B:AG101 2.6 35.9 1.0 AG A:AG101 2.6 35.1 1.0 AG A:AG110 2.7 39.3 1.0 AG A:AG102 2.9 33.1 1.0 O2 A:DC1 3.0 41.0 1.0 N1 A:DG9 3.0 35.6 1.0 AG A:AG106 3.1 31.0 1.0 C2 A:DC1 3.2 39.1 1.0 C2 B:DC4 3.3 36.7 1.0 O6 A:DG9 3.3 35.2 1.0 C6 A:DG9 3.4 38.7 1.0 N3 B:DC4 3.5 35.7 1.0 C2 B:DC3 3.6 33.9 1.0 C4 A:DC1 3.6 38.4 1.0 AG A:AG111 3.7 38.0 1.0 N4 A:DC1 3.8 39.4 1.0 C2 A:DG9 3.9 34.8 1.0 N3 B:DC3 4.0 38.2 1.0 N1 A:DA2 4.1 41.1 1.0 N2 A:DG9 4.2 37.0 1.0 N6 A:DA2 4.2 36.7 1.0 C6 A:DA2 4.3 39.0 1.0 C5 A:DG9 4.5 40.5 1.0 N1 B:DC4 4.5 37.0 1.0 N1 A:DC1 4.5 40.7 1.0 N3 A:DC3 4.6 37.4 1.0 N1 B:DC3 4.6 33.4 1.0 C4 B:DC4 4.7 32.4 1.0 AG A:AG112 4.8 38.7 1.0 O6 B:DG9 4.8 36.4 1.0 C2 A:DA2 4.8 38.1 1.0 AG B:AG102 4.9 34.5 1.0 N3 A:DG9 4.9 33.8 1.0 N3 A:DC4 4.9 34.4 1.0 C5 A:DC1 4.9 36.9 1.0 C1' B:DC3 5.0 41.9 1.0

Silver binding site 6 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag106 b:31.0 occ:1.00 N1 A:DG9 2.3 35.6 1.0 O2 B:DC4 2.4 35.9 1.0 AG B:AG102 2.7 34.5 1.0 AG A:AG102 2.7 33.1 1.0 AG A:AG103 2.9 30.5 1.0 AG B:AG101 3.0 35.9 1.0 AG A:AG105 3.1 34.7 1.0 AG B:AG105 3.2 41.9 0.3 N2 A:DG9 3.2 37.0 1.0 C2 A:DG9 3.2 34.8 1.0 C6 A:DG9 3.2 38.7 1.0 O6 A:DG9 3.2 35.2 1.0 C2 B:DC4 3.3 36.7 1.0 AG A:AG107 3.4 36.4 1.0 O2 A:DC8 3.5 34.7 1.0 AG A:AG112 3.7 38.7 1.0 N3 B:DC4 3.8 35.7 1.0 C2 A:DC8 4.2 37.5 1.0 N1 B:DC4 4.3 37.0 1.0 N3 A:DC8 4.4 35.2 1.0 N3 A:DG9 4.5 33.8 1.0 C5 A:DG9 4.5 40.5 1.0 C1' B:DC4 4.6 42.4 1.0 N3 A:DC4 4.7 34.4 1.0 AG B:AG104 4.7 35.4 1.0 N3 A:DC1 4.8 41.5 1.0 N3 B:DC8 4.9 40.5 1.0 AG A:AG101 4.9 35.1 1.0 C4 A:DG9 4.9 41.5 1.0 AG A:AG111 5.0 38.0 1.0

Silver binding site 7 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag107 b:36.4 occ:1.00 O6 A:DG7 2.4 33.6 1.0 AG A:AG104 2.5 31.1 1.0 O2 A:DC8 2.6 34.7 1.0 AG A:AG108 2.6 37.9 1.0 AG A:AG103 2.7 30.5 1.0 AG B:AG105 2.8 41.9 0.3 AG B:AG103 2.8 36.9 1.0 AG B:AG102 2.8 34.5 1.0 AG B:AG104 3.0 35.4 1.0 C6 A:DG7 3.3 38.5 1.0 AG A:AG106 3.4 31.0 1.0 C2 A:DC8 3.5 37.5 1.0 OP2 B:DA6 3.6 38.3 1.0 N3 A:DC8 3.7 35.2 1.0 N7 A:DG7 3.7 37.2 1.0 C5 A:DG7 3.8 36.2 1.0 AG A:AG113 3.9 39.9 1.0 OP1 B:DA6 4.2 43.3 1.0 N1 A:DG7 4.4 39.0 1.0 P B:DA6 4.5 42.4 1.0 N3 B:DC8 4.5 40.5 1.0 AG A:AG112 4.6 38.7 1.0 N1 A:DC8 4.8 40.3 1.0 N7 A:DA6 4.8 34.0 1.0 C8 A:DG7 4.9 37.6 1.0 OP1 A:DA6 4.9 39.0 1.0 C4 A:DC8 5.0 37.1 1.0 O2 B:DC8 5.0 33.2 1.0 AG A:AG109 5.0 42.2 0.4

Silver binding site 8 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag108 b:37.9 occ:1.00 N7 A:DA6 2.3 34.0 1.0 O6 A:DG7 2.3 33.6 1.0 OP2 B:DA6 2.4 38.3 1.0 AG A:AG107 2.6 36.4 1.0 AG B:AG103 2.6 36.9 1.0 AG A:AG113 2.7 39.9 1.0 AG A:AG104 2.8 31.1 1.0 C8 A:DA6 3.0 39.0 1.0 C6 A:DG7 3.1 38.5 1.0 C5 A:DA6 3.1 36.2 1.0 N7 A:DG7 3.3 37.2 1.0 C5 A:DG7 3.5 36.2 1.0 P B:DA6 3.5 42.4 1.0 N6 A:DA6 3.6 40.6 1.0 C6 A:DA6 3.7 40.1 1.0 O5' B:DA6 3.9 38.5 1.0 OP1 B:DA6 4.0 43.3 1.0 AG B:AG104 4.0 35.4 1.0 N9 A:DA6 4.1 40.3 1.0 C8 B:DA6 4.2 42.5 1.0 C4 A:DA6 4.2 36.4 1.0 OP2 A:DA6 4.2 39.8 1.0 N7 B:DA6 4.3 45.4 1.0 N1 A:DG7 4.4 39.0 1.0 AG B:AG105 4.4 41.9 0.3 O2 A:DC8 4.4 34.7 1.0 C8 A:DG7 4.5 37.6 1.0 N7 B:DG7 4.7 36.6 1.0 C4 A:DG7 4.8 37.4 1.0 O3' B:DG5 4.9 44.3 1.0 AG B:AG102 4.9 34.5 1.0 AG A:AG103 5.0 30.5 1.0 N1 A:DA6 5.0 40.4 1.0 OP1 A:DA6 5.0 39.0 1.0 C5' B:DA6 5.0 34.9 1.0 P A:DA6 5.0 33.1 1.0

Silver binding site 9 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag109 b:42.2 occ:0.41 AG B:AG104 2.8 35.4 1.0 AG A:AG112 2.9 38.7 1.0 AG A:AG103 3.0 30.5 1.0 OP1 A:DA6 3.3 39.0 1.0 O2 A:DC4 3.3 31.3 1.0 C2 A:DC4 3.4 35.9 1.0 N2 B:DG9 3.4 40.7 1.0 C2' A:DC4 3.5 46.2 1.0 N1 A:DC4 3.5 39.6 1.0 N4 A:DC8 3.6 32.3 1.0 C1' A:DC4 3.6 42.8 1.0 C2' A:DG5 3.7 47.0 1.0 O2 B:DC8 3.9 33.2 1.0 N1 B:DG9 3.9 38.5 1.0 AG A:AG104 4.0 31.1 1.0 N3 A:DC4 4.1 34.4 1.0 N3 A:DC8 4.1 35.2 1.0 C2 B:DG9 4.2 40.3 1.0 C6 A:DC4 4.3 40.5 1.0 C4 A:DC8 4.4 37.1 1.0 C3' A:DG5 4.4 43.3 1.0 AG B:AG102 4.5 34.5 1.0 O6 B:DG7 4.5 46.0 1.0 P A:DA6 4.5 33.1 1.0 AG A:AG102 4.6 33.1 1.0 C4 A:DC4 4.8 33.0 1.0 O3' A:DG5 4.8 45.0 1.0 OP2 A:DA6 4.9 39.8 1.0 AG A:AG113 4.9 39.9 1.0 C5 A:DC4 4.9 33.9 1.0 C3' A:DC4 5.0 43.7 1.0 AG A:AG107 5.0 36.4 1.0 O4' A:DC4 5.0 41.6 1.0 C1' A:DG5 5.0 43.7 1.0

Silver binding site 10 out of 18 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5G 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 (T5G Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag110 b:39.3 occ:1.00 N3 B:DC3 2.2 38.2 1.0 O2 B:DC1 2.5 37.2 1.0 N1 A:DA2 2.5 41.1 1.0 AG A:AG111 2.6 38.0 1.0 O2 B:DC3 2.6 35.2 1.0 AG A:AG101 2.7 35.1 1.0 AG A:AG105 2.7 34.7 1.0 C2 B:DC3 2.8 33.9 1.0 AG B:AG101 2.8 35.9 1.0 C2 A:DA2 3.0 38.1 1.0 C4 B:DC3 3.4 40.3 1.0 C2 B:DC1 3.5 38.2 1.0 C6 A:DA2 3.5 39.0 1.0 O6 B:DG9 3.6 36.4 1.0 N4 B:DC3 3.7 40.3 1.0 N3 B:DC1 3.8 41.4 1.0 N3 B:DC4 3.8 35.7 1.0 N6 A:DA2 3.9 36.7 1.0 AG A:AG102 4.0 33.1 1.0 N1 B:DC3 4.2 33.4 1.0 O2 A:DC3 4.2 39.1 1.0 N3 A:DA2 4.2 46.3 1.0 O2 A:DC1 4.3 41.0 1.0 C6 B:DG9 4.4 38.6 1.0 O2 B:DC4 4.4 35.9 1.0 N3 A:DC1 4.5 41.5 1.0 C2 B:DC4 4.5 36.7 1.0 N4 B:DC4 4.5 33.1 1.0 C4 B:DC4 4.6 32.4 1.0 C5 B:DC3 4.6 36.0 1.0 C5 A:DA2 4.6 37.3 1.0 N3 A:DC3 4.7 37.4 1.0 N1 B:DC1 4.7 40.8 1.0 C2 A:DC1 4.8 39.1 1.0 C4 A:DA2 4.8 40.2 1.0 AG A:AG112 4.8 38.7 1.0 C6 B:DC3 4.9 34.4 1.0 O2 A:DC4 4.9 31.3 1.0 C2 A:DC3 4.9 38.5 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