SMTL ID : 8tlk.1 (1 other biounit)

CDCA7 (Human) Binds Non-B-form 32-mer DNA oligo Containing a 5mC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.33, C.43, C.46, C.70, C.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.43, A:C.46, A:C.70, A:C.73 ZN.2: 4 residues within 4Å: Chain A: H.44, C.100, C.102, C.105 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.44, A:C.100, A:C.102, A:C.105 ZN.3: 5 residues within 4Å: Chain A: C.57, C.62, R.66, C.93, C.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.57, A:C.62, A:C.93, A:C.96 ZN.7: 5 residues within 4Å: Chain C: K.33, C.43, C.46, C.70, C.73 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.43, C:C.46, C:C.70, C:C.73 ZN.8: 4 residues within 4Å: Chain C: H.44, C.100, C.102, C.105 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.44, C:C.100, C:C.102, C:C.105 ZN.9: 5 residues within 4Å: Chain C: C.57, C.62, R.66, C.93, C.96 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.57, C:C.62, C:C.93, C:C.96

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

EDO.4: 4 residues within 4Å: Chain A: D.61 Chain B: G.16, A.17, G.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.61 EDO.10: 4 residues within 4Å: Chain C: D.61 Chain D: G.16, A.17, G.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.61

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: A.19, A.20, G.21, C.22 Chain D: T.15 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain B: T.15 Chain D: A.19, A.20, G.21, C.22 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 2 residues within 4Å: Chain B: A.17, G.18 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: A.17, G.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hardikar, S. et al., The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA. Biorxiv (2023)

Release Date

2024-08-21

Peptides

Cell division cycle-associated protein 7: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Cell division cycle-associated protein 7

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