Calcium in PDB 6m2p: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion Mutant)

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion Mutant), PDB code: 6m2p 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)	29.14 / 1.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	24.211, 33.713, 58.551, 90.00, 98.11, 90.00
R / Rfree (%)	8.5 / 9.6

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion 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 (A10-Deletion Mutant) (pdb code 6m2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion Mutant), PDB code: 6m2p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion 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 (A10-Deletion Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca110 b:8.5 occ:1.00 OP1 A:DC3 2.3 9.0 1.0 O A:HOH223 2.4 14.5 1.0 P A:DC3 3.6 8.0 1.0 H5'' A:DC3 3.7 11.5 1.0 O5' A:DC3 4.2 8.2 1.0 OP2 A:DC3 4.2 9.6 1.0 O A:HOH219 4.3 21.8 1.0 C5' A:DC3 4.3 9.6 1.0 O A:HOH205 4.4 14.4 1.0 O A:HOH202 4.6 16.1 1.0 H5' A:DC3 4.6 11.5 1.0 O3' A:DA2 4.8 8.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion 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 (A10-Deletion Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca110 b:10.9 occ:0.59 CA D:CA110 0.0 10.9 0.6 CA D:CA110 1.5 12.4 0.4 OP1 D:DC3 2.0 16.0 0.6 OP1 D:DC3 2.0 15.9 0.4 P D:DC3 3.4 15.6 0.6 P D:DC3 3.4 15.5 0.4 OP2 D:DC3 4.0 16.3 0.6 OP2 D:DC3 4.1 15.8 0.4 H5'' D:DC3 4.2 16.0 0.4 H5'' D:DC3 4.2 15.8 0.6 O3' D:DA2 4.3 15.0 1.0 O5' D:DC3 4.3 13.9 0.6 O5' D:DC3 4.5 14.3 0.4 C5' D:DC3 4.7 13.3 0.4 H5' D:DC3 4.7 16.0 0.4 C5' D:DC3 4.8 13.2 0.6

Calcium binding site 3 out of 3 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (A10-Deletion 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 (A10-Deletion Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca110 b:12.4 occ:0.41 CA D:CA110 0.0 12.4 0.4 CA D:CA110 1.5 10.9 0.6 OP1 D:DC3 2.6 15.9 0.4 OP1 D:DC3 2.6 16.0 0.6 H5'' D:DC3 3.7 16.0 0.4 H5'' D:DC3 4.0 15.8 0.6 P D:DC3 4.0 15.6 0.6 P D:DC3 4.0 15.5 0.4 O5' D:DC3 4.4 13.9 0.6 C5' D:DC3 4.5 13.3 0.4 O5' D:DC3 4.6 14.3 0.4 H5' D:DC3 4.7 16.0 0.4 C5' D:DC3 4.7 13.2 0.6 O D:HOH206 4.7 27.5 1.0 OP2 D:DC3 4.8 16.3 0.6 OP2 D:DC3 4.8 15.8 0.4

C.Cerretani, J.Kondo, T.Vosch. Removal of the A10 Adenosine in A Dna-Stabilized AG16 Nanocluster. Rsc Adv V. 10 23854 2020.
ISSN: ESSN 2046-2069
DOI: 10.1039/D0RA02672G