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At-rich DNA dodecamer with extra helical guanine-nickel coordination

Analyse At-rich DNA dodecamer with extra helical guanine-nickel coordination in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M68
Type: DNA
Length: 66 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*TP*TP*CP*G)-3')
Ligands: NI

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA (5'-D(CPGPAPAPTPTPAPAPTPTPCPG)-3')	dna	11	—	—

Ligands and binding sites

NI · Nickel (II) ion · metal · 11 copies · chains A, B, C, D, E, F

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

Interfaces

4 interfaces between chains.

E–F · 461 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–B · 444 Å² buried · 40 hydrogen bonds · nucleic-nucleic
C–D · 435 Å² buried · 40 hydrogen bonds · nucleic-nucleic
B–D · 38 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

5M68 · AT-rich DNA dodecamer with extra helical guanine-nickel coordination · 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 5M68 · PDBe 5M68

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