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

CDCA7 (Mouse) Binds Non-B-form DNA oligo 36-mer (sg C2-Form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.77, I.99, N.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.77, A:I.99, A:N.101 GOL.7: 2 residues within 4Å: Chain B: G.7, C.8 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain C: R.77, I.99, N.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.77, C:I.99, C:N.101 GOL.17: 2 residues within 4Å: Chain D: G.7, C.8 No protein-ligand interaction detected (PLIP)

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

EDO.2: 5 residues within 4Å: Chain A: E.80, D.84, A.85, D.88, W.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.88, A:D.88 Water bridges: A:E.81 EDO.6: 3 residues within 4Å: Chain A: R.37 Chain B: C.24, G.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.37 EDO.12: 5 residues within 4Å: Chain C: E.80, D.84, A.85, D.88, W.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.88 Water bridges: C:E.81 EDO.16: 3 residues within 4Å: Chain C: R.37 Chain D: C.24, G.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.37

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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.5: 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.13: 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.14: 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.15: 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

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

MG.8: 1 residues within 4Å: Chain B: G.25 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: G.31 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain D: G.25 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain D: G.31 No protein-ligand interaction detected (PLIP) MG.20: 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
A

Cell division cycle-associated protein 7

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