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Crystal structure of D(GCGGGAGC): the base-intercalated duplex

Analyse Crystal structure of D(GCGGGAGC): the base-intercalated duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FZA
Type: DNA
Length: 16 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3'
Ligands: NA, CA

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GP(CBR)PGPGPGPAPGPC)-3'	dna	8	—	—

Ligands and binding sites

NA · Sodium ion · metal · 5 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Interfaces

1 interface between chains.

A–B · 655 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2FZA · Crystal structure of d(GCGGGAGC): the base-intercalated duplex · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2FZA · PDBe 2FZA

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