1AAY: ZIF268 zinc finger-DNA complex

ZIF268 zinc finger-DNA complex. Determined by X-ray diffraction at 1.6 Å resolution. Released 21 Apr 1997.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 3
Atoms: 1,330
Mol. weight: 17.76 kDa
Ligands: ZN
Released: 21 Apr 1997

Explore 1AAY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1AAY contains 4 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	1
β-strand	115-116	2	1
α-helix	119-130	12
β-strand	135-136	2	2
β-strand	143-144	2	2
α-helix	147-158	12
β-strand	163-164	2	3
β-strand	171-172	2	3
α-helix	175-182	8
α-helix	183-185	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(apgpcpgptpgpgpgpcpgp*t)-3')	B	DNA	11
DNA (5'-d(tpapcpgpcpcpcpapcpgp*c)-3')	C	DNA	11
Protein (ZIF268 zinc finger peptide)	A	protein	90	Mus musculus	P08046 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1AAY_1 DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3') (chains B)
AGCGTGGGCGT

Sequence of entity 2 (C), FASTA

>1AAY_2 DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3') (chains C)
TACGCCCACGC

Sequence of entity 3 (A), FASTA

>1AAY_3 PROTEIN (ZIF268 ZINC FINGER PEPTIDE) (chains A)
MERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGE
KPFACDICGRKFARSDERKRHTKIHLRQKD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Elrod-Erickson, M., Rould, M.A., Nekludova, L. et al. Structure (1996) 4:1171-1180. DOI 10.1016/S0969-2126(96)00125-6 · PubMed

Other PDB entries of the same protein (UniProt P08046 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LLM 1.5 Å, Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA
1A1H 1.6 Å, Qgsr (ZIF268 variant) zinc finger-DNA complex (gcac site)
1A1I 1.6 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gcac site)
1JK2 1.65 Å, Zif268 D20A mutant bound to the GCT DNA site
1A1G 1.9 Å, Dsnr (ZIF268 variant) zinc finger-DNA complex (gcgt site)
1A1K 1.9 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gacc site)
1JK1 1.9 Å, Zif268 D20A Mutant Bound to WT DNA Site
1A1J 2.0 Å, Radr (ZIF268 variant) zinc finger-DNA complex (gcgt site)
1G2F 2.0 Å, Structure of a CYS2HIS2 zinc finger/tata box complex (tatazf;clone #6)
1A1F 2.1 Å, Dsnr (ZIF268 variant) zinc finger-DNA complex (gacc site)
1ZAA 2.1 Å, Zinc finger-DNA recognition: crystal structure of a ZIF268-DNA complex at 2.1 Å
1G2D 2.2 Å, Structure of a CYS2HIS2 zinc finger/tata box complex (clone #2)

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