SMTL ID : 8tlj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.63, R.66, F.104, C.105 Chain B: A.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.66, A:R.108 Water bridges: A:W.63 GOL.10: 2 residues within 4Å: Chain B: G.21, C.22 No protein-ligand interaction detected (PLIP) GOL.15: 2 residues within 4Å: Chain D: G.21, C.22 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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.4: 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.12: 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.13: 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.14: 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.5: 3 residues within 4Å: Chain A: N.36, R.37, S.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.36, A:R.37, A:S.38, A:S.38 EDO.6: 4 residues within 4Å: Chain A: R.77, Y.78, I.99, N.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.99, A:N.101 EDO.9: 4 residues within 4Å: Chain A: D.61 Chain B: G.16, A.17, G.18 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Chain B: C.8 No protein-ligand interaction detected (PLIP)

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

MG.7: 3 residues within 4Å: Chain A: S.5, M.6 Chain B: G.18 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) 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
B

Cell division cycle-associated protein 7

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