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Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (A10-deletion mutant)

Analyse Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M2P
Type: DNA
Length: 36 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.13
Molecule: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
Ligands: AG, CA, CL

Structure

x-ray diffraction · resolution 1.13 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(CPAPCPCPTPAPGPCP*G)-3')	dna	9	—	—

Ligands and binding sites

AG · Silver ion · metal · 32 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

6 interfaces between chains.

A–B · 363 Å² buried · 23 hydrogen bonds · nucleic-nucleic
C–D · 357 Å² buried · 23 hydrogen bonds · nucleic-nucleic
A–C · 118 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 41 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 41 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

6M2P · Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster (A10-deletion mutant) · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6M2P · PDBe 6M2P

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