1JK2: Zif268 D20A mutant

Zif268 D20A mutant bound to the GCT DNA site. Determined by X-ray diffraction at 1.65 Å resolution. Released 19 Oct 2001.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Mus musculus
Chains: 3
Atoms: 1,377
Mol. weight: 17.72 kDa
Ligands: ZN
Released: 19 Oct 2001

Explore 1JK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1JK2 contains 5 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	105-106	2	1
β-strand	115-116	2	1
α-helix	119-125	7
α-helix	127-130	4
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
5'-d(apgpcpgptpgpgpgpcptp*g)-3'	B	DNA	11
5'-d(tpcpapgpcpcpcpapcpgp*c)-3'	C	DNA	11
ZIF268	A	protein	90	Mus musculus	P08046 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1JK2_1 5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*TP*G)-3' (chains B)
AGCGTGGGCTG

Sequence of entity 2 (C), FASTA

>1JK2_2 5'-D(*TP*CP*AP*GP*CP*CP*CP*AP*CP*GP*C)-3' (chains C)
TCAGCCCACGC

Sequence of entity 3 (A), FASTA

>1JK2_3 ZIF268 (chains A)
MERPYACPVESCDRRFSRSAELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGE
KPFACDICGRKFARSDERKRHTKIHLRQKD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. Miller, J.C., Pabo, C.O. J Mol Biol (2001) 313:309-315. DOI 10.1006/jmbi.2001.4975 · 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)
1AAY 1.6 Å, ZIF268 zinc finger-DNA complex
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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