Calcium 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:

Silver

(Ag)

36 atoms

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant), PDB code: 7bse:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca110 b:15.1 occ:1.00 OP2 B:DC3 2.5 15.7 1.0 O C:HOH210 2.5 17.4 1.0 OP2 C:DC3 2.6 17.0 1.0 P B:DC3 3.7 15.1 1.0 O B:HOH210 3.7 17.5 1.0 P C:DC3 3.9 16.0 1.0 OP1 B:DC3 4.1 16.1 1.0 O B:HOH206 4.2 18.4 1.0 O C:HOH212 4.3 19.3 1.0 OP1 C:DC3 4.4 16.2 1.0 C4' B:DA2 4.5 11.8 1.0 C4' C:DA2 4.6 12.8 1.0 O3' B:DA2 4.6 13.9 1.0 O3' C:DA2 4.7 13.8 1.0 O C:HOH209 4.8 21.7 1.0 O5' B:DC3 4.8 11.9 1.0 C5' C:DA2 4.9 12.6 1.0 C3' C:DA2 4.9 13.6 1.0 C3' B:DA2 5.0 12.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca111 b:21.0 occ:1.00 OP2 B:DC8 2.3 16.5 1.0 OP2 C:DA5 2.4 16.2 1.0 O C:HOH223 2.5 22.2 1.0 O B:HOH215 2.5 26.4 1.0 O B:HOH205 2.5 25.0 1.0 O C:HOH225 3.1 24.9 1.0 P B:DC8 3.4 13.8 1.0 P C:DA5 3.7 14.8 1.0 O5' B:DC8 3.9 11.6 1.0 OP1 B:DC8 4.0 18.4 1.0 O C:HOH221 4.0 14.6 1.0 OP1 C:DA5 4.3 17.8 1.0 O3' C:DC4 4.5 13.5 1.0 OP2 C:DC4 4.6 22.1 1.0 O5' C:DC4 4.6 20.7 1.0 OP2 B:DG9 4.6 16.4 1.0 C3' C:DC4 4.7 14.9 1.0 O C:HOH231 4.7 25.3 1.0 O3' B:DG7 4.7 15.9 1.0 CA B:CA112 4.7 18.4 1.0 O5' C:DA5 4.9 14.6 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca112 b:18.4 occ:1.00 OP1 B:DC8 2.3 18.4 1.0 OP1 C:DA5 2.3 17.8 1.0 O C:HOH226 2.5 24.1 1.0 O C:HOH225 2.6 24.9 1.0 O C:HOH230 2.8 25.5 1.0 P B:DC8 3.6 13.8 1.0 P C:DA5 3.7 14.8 1.0 OP2 C:DA5 4.1 16.2 1.0 OP2 B:DC8 4.2 16.5 1.0 O B:HOH229 4.2 23.4 1.0 O C:HOH216 4.3 20.1 1.0 O5' B:DC8 4.4 11.6 1.0 C5' B:DC8 4.6 11.8 1.0 O5' C:DA5 4.6 14.6 1.0 O3' C:DC4 4.6 13.5 1.0 OP1 B:DG9 4.6 18.8 1.0 O3' B:DG7 4.6 15.9 1.0 CA B:CA111 4.7 21.0 1.0 C5' C:DA5 4.9 13.0 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca113 b:21.8 occ:1.00 OP1 B:DA5 2.3 17.5 1.0 OP1 C:DC8 2.3 18.8 1.0 O B:HOH224 2.6 26.2 1.0 O B:HOH225 3.1 21.2 1.0 P B:DA5 3.6 13.2 1.0 P C:DC8 3.7 13.3 1.0 OP2 B:DA5 4.0 15.9 1.0 O5' C:DC8 4.4 14.1 1.0 C5' C:DC8 4.4 14.8 1.0 OP2 C:DC8 4.5 13.5 1.0 O5' B:DA5 4.6 14.8 1.0 O3' B:DC4 4.7 14.5 1.0 O3' C:DG7 4.7 14.2 1.0 C5' B:DA5 4.7 12.4 1.0 OP1 C:DG9 4.8 18.8 1.0 CA C:CA110 4.9 18.0 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca114 b:15.9 occ:1.00 OP1 B:DA2 2.3 17.9 1.0 O B:HOH226 2.4 27.0 1.0 P B:DA2 3.6 17.3 1.0 O5' B:DA2 3.9 16.2 1.0 O C:HOH220 4.4 22.0 1.0 O3' B:DC1 4.5 18.0 1.0 O C:HOH210 4.7 17.4 1.0 OP2 B:DA2 4.7 19.1 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 C:Ca110 b:18.0 occ:1.00 OP2 C:DC8 2.3 13.5 1.0 O C:HOH219 2.4 19.8 1.0 OP2 B:DA5 2.4 15.9 1.0 O B:HOH220 2.5 16.0 1.0 O B:HOH225 2.6 21.2 1.0 O C:HOH229 2.7 26.1 1.0 P C:DC8 3.4 13.3 1.0 O B:HOH222 3.7 18.8 1.0 P B:DA5 3.8 13.2 1.0 O5' C:DC8 3.8 14.1 1.0 OP1 C:DC8 3.9 18.8 1.0 O C:HOH217 4.0 23.1 1.0 O C:HOH231 4.3 25.3 1.0 OP1 B:DA5 4.4 17.5 1.0 OP2 B:DC4 4.5 16.6 1.0 O3' B:DC4 4.6 14.5 1.0 O5' B:DC4 4.6 14.5 1.0 C3' B:DC4 4.6 13.4 1.0 O C:HOH228 4.6 20.3 1.0 OP2 C:DG9 4.6 14.3 1.0 O3' C:DG7 4.8 14.2 1.0 O5' B:DA5 4.8 14.8 1.0 CA B:CA113 4.9 21.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 C:Ca111 b:19.4 occ:1.00 OP1 C:DA2 2.3 15.8 1.0 O C:HOH222 2.3 20.3 1.0 P C:DA2 3.6 14.0 1.0 O5' C:DA2 3.8 14.5 1.0 OP2 C:DA2 4.6 16.6 1.0 O3' C:DC1 4.6 14.4 1.0 O B:HOH214 4.8 19.9 1.0 O B:HOH210 4.8 17.5 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (T5A Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 C:Ca112 b:38.2 occ:1.00 OP1 C:DG9 2.6 18.8 1.0 O B:HOH201 2.6 27.8 1.0 OP1 C:DA10 3.5 34.5 1.0 O5' C:DG9 3.6 16.9 1.0 P C:DG9 3.6 15.2 1.0 C5' C:DG9 3.9 18.2 1.0 OP2 C:DG9 4.3 14.3 1.0 O5' C:DA10 4.6 30.8 1.0 C3' C:DG9 4.6 20.6 1.0 OP1 B:DC4 4.6 22.9 1.0 P C:DA10 4.7 43.8 1.0 C4' C:DG9 4.8 18.3 1.0 O B:HOH225 4.9 21.2 1.0 O3' C:DC8 4.9 16.7 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