MolNFT v1 · #105415 · DNA

Racemic crystal structure of a magnesium-bound B-DNA duplex

4R4D · 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3': “Racemic crystal structure of a magnesium-bound B-DNA duplex”. X-ray diffraction, 2 ligands (MG, NA). MolNFT v1 #105415 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4R4D
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
Ligands: MG, NA

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	5'-D(CPCPGPGPTPAPCPCPGPG)-3'	dna	10	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
NA · Sodium ion · metal · chains C, D

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

Interfaces

3 interfaces between chains.

C–D · 472 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–B · 466 Å² buried · 38 hydrogen bonds · nucleic-nucleic
A–D · 14 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

4R4D · Racemic crystal structure of a magnesium-bound B-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 4R4D · PDBe 4R4D

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