Calcium in PDB 6jr4: Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster

The structure of Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster, PDB code: 6jr4 was solved by J.Kondo, C.Cerretani, H.Kanazawa, T.Vosch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.02 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	24.241, 33.849, 58.863, 90.00, 97.81, 90.00
R / Rfree (%)	12.6 / 14.6

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

Silver

(Ag)

38 atoms

The binding sites of Calcium atom in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster (pdb code 6jr4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster, PDB code: 6jr4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca107 b:15.6 occ:1.00 OP1 B:DC3 2.3 16.2 1.0 O B:HOH205 2.4 20.4 1.0 P B:DC3 3.6 18.0 1.0 O5' B:DC3 4.2 15.8 1.0 OP2 B:DC3 4.4 20.0 1.0 C5' B:DC3 4.5 17.0 1.0 O3' B:DA2 4.7 17.9 1.0 OP2 B:DC4 5.0 23.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Nir-Emitting Dna-Stabilized AG16 Nanocluster


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca107 b:25.9 occ:1.00 OP1 D:DG7 2.4 21.3 1.0 P D:DG7 3.7 20.1 1.0 O3' D:DA6 4.0 20.3 1.0 C5' D:DG7 4.2 17.8 1.0 O5' D:DG7 4.4 20.9 1.0 OP2 D:DG7 4.9 21.4 1.0

C.Cerretani, H.Kanazawa, T.Vosch, J.Kondo. Crystal Structure of A Nir-Emitting Dna-Stabilized AG16NANOCLUSTER. Angew.Chem.Int.Ed.Engl. V. 58 17153 2019.
ISSN: ESSN 1521-3773
PubMed: 31411360
DOI: 10.1002/ANIE.201906766