SMTL ID : 8tlg.1

CDCA7 (Mouse) Binds Non-B-form 34-mer DNA oligo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 4 residues within 4Å: Chain A: C.57, C.62, 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: 4 residues within 4Å: Chain C: C.57, C.62, 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

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

EDO.4: 4 residues within 4Å: Chain B: G.11, T.12 Chain C: N.76 Chain D: G.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.76 EDO.5: 3 residues within 4Å: Chain B: G.17, A.18, G.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.10 EDO.10: 4 residues within 4Å: Chain A: N.76 Chain B: G.28 Chain D: G.11, T.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.76 EDO.11: 3 residues within 4Å: Chain D: G.17, A.18, G.19 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.10

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: M.6 Chain B: G.19 Chain C: M.6 Chain D: G.19 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: M.6 Chain B: G.19 Chain C: M.6 Chain D: G.19 Ligands: MG.6 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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