SMTL ID : 6ml7.1

ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpG 5mC Modification)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.10, C.13, H.26, H.30 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:C.13, A:H.26, A:H.30 ZN.2: 4 residues within 4Å: Chain A: C.38, C.41, H.54, H.58 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.38, A:C.41, A:H.54, A:H.58 ZN.3: 4 residues within 4Å: Chain A: C.66, C.69, H.82, H.86 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.82, A:H.86 ZN.4: 4 residues within 4Å: Chain A: C.94, C.97, H.110, H.114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.94, A:C.97, A:H.110, A:H.114 ZN.5: 4 residues within 4Å: Chain A: C.122, C.125, H.138, H.142 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.122, A:C.125, A:H.138, A:H.142

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 2 residues within 4Å: Chain A: P.123, E.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.124, A:E.124 EDO.7: 6 residues within 4Å: Chain A: K.71, H.82, I.85, H.86 Chain B: T.8, C.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82 EDO.8: 3 residues within 4Å: Chain B: T.19, T.20 Chain C: T.1 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain B: G.7, T.8, C.9, C.10 Chain C: A.14 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain B: T.11, G.12, G.13 Chain C: A.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, R. et al., Structural basis of specific DNA binding by the transcription factor ZBTB24. Nucleic Acids Res. (2019)

Release Date

2019-07-03

Peptides

Zinc finger and BTB domain-containing protein 24: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Zinc finger and BTB domain-containing protein 24

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