SMTL ID : 5vmz.1

Kaiso (ZBTB33) E535Q mutant zinc finger DNA binding domain in complex with a double CpG-methylated DNA resembling the specific Kaiso binding sequence (KBS)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.26, C.29, H.42, H.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.29, A:H.42, A:H.46 ZN.2: 4 residues within 4Å: Chain A: C.54, C.57, H.70, H.74 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.54, A:C.57, A:H.70, A:H.74 ZN.3: 4 residues within 4Å: Chain A: C.82, C.85, H.98, H.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.82, A:C.85, A:H.98, A:H.103

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.78, R.120 Ligand excluded by PLIP

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.5: 10 residues within 4Å: Chain A: Q.65, K.69, Y.80, N.91, Y.92, Q.93 Chain B: T.5, C.6, C.7 Chain C: G.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.65, A:Y.80, A:N.91, A:Y.92, A:Q.93 Water bridges: A:K.69, A:K.69 Salt bridges: A:K.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikolova, E.N. et al., CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso. Biochemistry (2018)

Release Date

2018-04-04

Peptides

Transcriptional regulator Kaiso: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcriptional regulator Kaiso

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