MolNFT v1 · #3818 · DNA
Stabilization of Z-DNA by demethylation of thymine bases: 1.3 ångströms single-crystal structure of D(M5CGUAM5CG)
1D41 · DNA (5'-D(*(5CM)P*GP*UP*AP*(5CM)P*G)-3'): “Stabilization of Z-DNA by demethylation of thymine bases: 1.3 ångströms single-crystal structure of…”. X-ray diffraction, 1 ligand (MG). MolNFT v1 #3818 on GenesisL1: 3D structure, binding…
- PDB
- 1D41
- Type
- DNA
- Length
- 12 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*(5CM)P*GP*UP*AP*(5CM)P*G)-3')
- Ligands
- MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*(5CM)P*GP*UP*AP*(5CM)P*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 337 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1D41 · Stabilization of Z-DNA by demethylation of thymine bases: 1.3 ångströms single-crystal… · 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 1D41 · PDBe 1D41
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