MolNFT v1 · #89741 · DNA
Interactions of MN2+ with a non-self-complementary Z-type DNA duplex
4DY8 · DNA (5'-D(*CP*AP*CP*GP*CP*G)-3'): “Interactions of MN2+ with a non-self-complementary Z-type DNA duplex”. X-ray diffraction, 1 ligand (MN). MolNFT v1 #89741 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DY8
- Type
- DNA
- Length
- 16 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*CP*GP*CP*G)-3'); DNA (5'-D(*CP*GP*CP*GP*TP*G)-3'); DNA (5'-D(P*TP*G)-3')
- Ligands
- MN
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*AP*CP*GP*CP*G)-3') | dna | 6 | — | — |
| B | DNA (5'-D(*CP*GP*CP*GP*TP*G)-3') | dna | 6 | — | — |
| C, D | DNA (5'-D(P*TP*G)-3') | dna | 2 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 325 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–D · 116 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- A–D · 14 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DY8 · Interactions of Mn2+ with a non-self-complementary Z-type DNA 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 4DY8 · PDBe 4DY8
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