MolNFT v1 · #122176 · DNA

CALCIUM(II) and COPPER(II) bound to the Z-DNA form of D(CGCGCG), complexed by L-lactate and succinate

5IHD · DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'): “CALCIUM(II) and COPPER(II) bound to the Z-DNA form of D(CGCGCG), complexed by L-lactate and succinate”. X-ray diffraction, 3 ligands (2OP, CU, CA). MolNFT v1 #122176 on GenesisL1: 3D structure…

PDB: 5IHD
Type: DNA
Length: 24 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
Ligands: 2OP, CU, CA

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(CPGPCPGPCPG)-3')	dna	6	—	—

Ligands and binding sites

2OP · (2S)-2-hydroxypropanoic acid · ligand · 2 copies · chains A, D, B, C
CU · Copper (II) ion · metal · 4 copies · chains A, D, B, C
CA · Calcium ion · metal · 2 copies · chains A, C
SIN · Succinic acid · additive · chains A, B, C, D

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

Interfaces

5 interfaces between chains.

A–B · 322 Å² buried · 21 hydrogen bonds · nucleic-nucleic
C–D · 322 Å² buried · 19 hydrogen bonds · nucleic-nucleic
B–D · 139 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–C · 79 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–D · 72 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

5IHD · Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by L-lactate… · 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 5IHD · PDBe 5IHD

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